diff --git a/studies/Cultivation/resources/lpa2_mappingfile.txt b/studies/Cultivation/resources/lpa2_mappingfile.txt
new file mode 100644
index 0000000000000000000000000000000000000000..438cc4db42d154e4f4e61393846bdaaa6037a5ff
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+++ b/studies/Cultivation/resources/lpa2_mappingfile.txt
@@ -0,0 +1,1783 @@
+Name Synonym MapMan MapManTerm GO SubLoc
+Cre17.g726350 integral component of membrane Chloroplast
+Cre03.g181200 amino acid metabolism.degradation.branched chain group.leucine 13.2.4.4 Mitochondrion
+Cre16.g685250 SUB11 protein.degradation.subtilases 29.5.1 proteolysis;serine-type endopeptidase activity
+Cre13.g571251
+Cre12.g537100 TSV2 protein.aa activation.valine-tRNA ligase;protein.aa activation 29.1.9;29.1 valyl-tRNA aminoacylation;tRNA aminoacylation for protein translation;ATP binding;valine-tRNA ligase activity;aminoacyl-tRNA ligase activity;nucleotide binding
+Cre02.g095117 protein phosphorylation;ATP binding;protein kinase activity
+Cre10.g439350 Chloroplast
+Cre-1.g2717027 ccsA Chloroplast
+Cre08.g378300
+Cre06.g251500 SPS1 polyamine metabolism.synthesis.spermine synthase;polyamine metabolism.synthesis.spermidine synthase 22.1.7;22.1.6 methyltransferase activity;metabolic process
+Cre04.g213251 protein.degradation.alanine protease;protein.degradation 29.5.31;29.5 proteolysis Mitochondrion
+Cre17.g714900 CGL11 secondary metabolism.flavonoids.flavonols.flavonol synthase (FLS) 16.8.4.1
+Cre12.g503300 nucleotide metabolism.synthesis.purine.AIR carboxylase 23.1.2.6 'de novo' IMP biosynthetic process Chloroplast
+Cre06.g249850
+Cre03.g160850 Mitochondrion
+Cre02.g143400 PDE27 signalling.in sugar and nutrient physiology.misc 30.1.1 signal transduction;3',5'-cyclic-nucleotide phosphodiesterase activity Secretory pathway
+Cre02.g077800 FAP310 cell.motility.eukaryotes.flagellar associated proteins 31.6.1.10 Secretory pathway
+Cre09.g402800 Mitochondrion
+Cre12.g520600 PRPS6 protein.synthesis.ribosomal protein.unknown.small subunit.S6 29.2.1.99.1.6 rRNA binding;translation;ribosome;structural constituent of ribosome Chloroplast
+Cre08.g365400 PRPL31 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit.L31 29.2.1.1.1.2.31 translation;ribosome;intracellular;structural constituent of ribosome Chloroplast
+Cre06.g303200 MAW7 cell.motility.eukaryotes.flagellar associated proteins 31.6.1.10 Secretory pathway
+Cre13.g579950
+Cre02.g073500 FAP241 Chloroplast
+Cre06.g257050 GBS2 major CHO metabolism.synthesis.starch.starch synthase 2.1.2.2
+Cre02.g095650 FAD binding Chloroplast
+Cre17.g708300 RPN12 protein.degradation.ubiquitin.proteasom 29.5.11.20 proteolysis;proteasome regulatory particle
+Cre05.g242550 RSP6 cell.organisation 31.1
+Cre02.g104500 CDJ4 signalling.unspecified;protein.co-chaperones;stress.abiotic.heat 30.99;29.9;20.2.1 Chloroplast
+Cre03.g202000 KIN4-2 cell.organisation 31.1 microtubule binding;microtubule-based movement;kinesin complex;ATP binding;microtubule motor activity
+Cre07.g324100 oxidation-reduction process
+Cre06.g256400 Secretory pathway
+Cre03.g168950 Chloroplast
+Cre14.g612750 FAP197 Mitochondrion
+Cre01.g013801 secondary metabolism.isoprenoids.tocopherol biosynthesis.tocopherol cyclase 16.1.3.4 tocopherol cyclase activity Chloroplast
+Cre02.g079850 POLK1 DNA.repair 28.2 DNA repair;damaged DNA binding
+Cre02.g095109 integral component of membrane;carbohydrate transport;sugar:proton symporter activity;Golgi membrane Secretory pathway
+Cre01.g026300
+Cre01.g015600 protein.synthesis 29.2
+Cre13.g577400 ELG16 misc.UDP glucosyl and glucoronyl transferases 26.2 Secretory pathway
+Cre12.g546000 MRPL54 Mitochondrion
+Cre03.g207713 ISA3 major CHO metabolism.degradation.starch.ISA3;major CHO metabolism.synthesis.starch.debranching 2.2.2.8;2.1.2.4 cation binding;carbohydrate metabolic process;hydrolase activity, hydrolyzing O-glycosyl compounds;catalytic activity Chloroplast
+Cre06.g309500 OPR28 Chloroplast
+Cre14.g625400 RPT1 protein.degradation.ubiquitin.proteasom 29.5.11.20 ATPase activity;ATP binding
+Cre12.g547500 Chloroplast
+Cre07.g341350
+Cre07.g337800 MRPS17 protein.synthesis.ribosomal protein 29.2.1 translation;ribosome;intracellular;structural constituent of ribosome Chloroplast
+Cre05.g247550 misc.glutathione S transferases 26.9 protein binding Mitochondrion
+Cre09.g412000 Chloroplast
+Cre02.g118350 MFT14
+Cre06.g267700 SPP1B protein.degradation.serine protease;protein.degradation 29.5.5;29.5 peptidase activity;proteolysis Mitochondrion
+Cre08.g384390 POLQ2 DNA.synthesis/chromatin structure 28.1 ATP binding;nucleic acid binding Chloroplast
+Cre03.g203450 RPS21 protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S21 29.2.1.2.1.21 translation;ribosome;intracellular;structural constituent of ribosome
+Cre08.g369600 MFT2 transport.misc 34.99 transmembrane transport;membrane;antiporter activity;drug transmembrane transporter activity;drug transmembrane transport Mitochondrion
+Cre07.g326600 PDI6 redox.thioredoxin.PDIL;redox.thioredoxin 21.1.1;21.1 cell redox homeostasis
+Cre10.g459250 RPL35A protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L35A;protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L35A 29.2.1.2.2.535;29.2.1.2.2.0535 translation;ribosome;intracellular;structural constituent of ribosome
+Cre10.g430501 RNA.processing 27.1 protein binding
+Cre16.g685450 DHC8 cell.motility.eukaryotes.axonemal dyneins.inner arm.monomeric species 31.6.1.4.2.1 dynein complex;ATPase activity;microtubule-based movement;ATP binding;microtubule motor activity
+Cre08.g382350 EZY14 transport.metabolite transporters at the envelope membrane 34.8
+Cre08.g381483
+Cre14.g616900 SULP2 integral component of membrane;membrane;sulfate transmembrane transporter activity;sulfate transport;transport Secretory pathway
+Cre12.g528050 Chloroplast
+Cre10.g450550 PAO3 cell.cell death.plants;misc.other Ferredoxins and Rieske domain;misc.gluco-, galacto- and mannosidases 31.5.1;26.30;26.3 oxidation-reduction process;2 iron, 2 sulfur cluster binding;oxidoreductase activity;chlorophyllide a oxygenase [overall] activity
+Cre16.g678851 PSBP2 PS.lightreaction.photosystem II.PSII polypeptide subunits 1.1.1.2 extrinsic component of membrane;photosynthesis;photosystem II oxygen evolving complex;photosystem II;calcium ion binding Chloroplast
+Cre17.g728300 FAP226 protein.degradation.cysteine protease 29.5.3 proteolysis;intracellular;calcium-dependent cysteine-type endopeptidase activity
+Cre13.g607900 CPLD68 Mitochondrion
+Cre09.g387393 RNA.regulation of transcription.HDA 27.3.55
+Cre06.g278183 redox.glutaredoxins 21.4 cell redox homeostasis;protein disulfide oxidoreductase activity;electron carrier activity
+Cre11.g477500 Chloroplast
+Cre16.g671950 DNA 28 Chloroplast.Stroma
+Cre09.g393654 RNA.regulation of transcription.chromatin remodeling factors 27.3.44
+Cre03.g193950 redox.thioredoxin 21.1 oxidation-reduction process;oxidoreductase activity, acting on iron-sulfur proteins as donors Chloroplast
+Cre06.g305650 cell.cell death.plants;protein.targeting.chloroplast;misc.other Ferredoxins and Rieske domain 31.5.1;29.3.3;26.30 oxidation-reduction process;2 iron, 2 sulfur cluster binding;oxidoreductase activity;chlorophyllide a oxygenase [overall] activity Mitochondrion
+Cre01.g065822 IFT122 cell.motility.eukaryotes.intraflagellar transport.IFT particle protein.complex A 31.6.1.3.2.1 protein binding
+Cre02.g090650 SEC20
+Cre11.g467603 Chloroplast
+Cre12.g524600 Secretory pathway
+Cre02.g095045 hlm15 development.unspecified;RNA.regulation of transcription.PHD finger transcription factor 33.99;27.3.63 regulation of transcription, DNA-templated;protein binding Mitochondrion
+Cre06.g278097 RAE1 cell.division;RNA.processing 31.2;27.1 protein binding
+Cre06.g268600 NAB1 PS.lightreaction.photosystem II.LHC biogenesis 1.1.1.4 regulation of transcription, DNA-templated;DNA binding;nucleic acid binding
+Cre06.g290950 RPS5 protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S5 29.2.1.2.1.5 translation
+Cre12.g509350 FAP238 Chloroplast
+Cre05.g241650 protein.degradation 29.5 Chloroplast
+Cre02.g096450
+Cre06.g306601 ANS1 amino acid metabolism.synthesis.aromatic aa.tryptophan.anthranilate synthase 13.1.6.5.1 oxo-acid-lyase activity;biosynthetic process Chloroplast
+Cre06.g273050 CGLD10 RNA.regulation of transcription.SET-domain transcriptional regulator family 27.3.69 Chloroplast
+Cre06.g251650 PTC1 transport.unspecified cations 34.14 transmembrane transport;membrane;sodium ion transport;transporter activity
+Cre02.g099601 DNA binding Mitochondrion
+Cre12.g489750 FAP52 development.unspecified;cell.motility.eukaryotes.flagellar associated proteins 33.99;31.6.1.10 protein binding
+Cre03.g149650 CCD1 hormone metabolism.abscisic acid.synthesis-degradation.synthesis.9-cis-epoxycarotenoid dioxygenase;secondary metabolism.isoprenoids.carotenoids.carotenoid cleavage dioxygenase 17.1.1.1.10;16.1.4.10 Secretory pathway
+Cre07.g325741 PTB2 transport.phosphate 34.7 membrane;phosphate ion transport;inorganic phosphate transmembrane transporter activity
+Cre10.g462816 Chloroplast
+Cre09.g386753 RNA.regulation of transcription.S1FA 27.3.81 regulation of transcription, DNA-templated;nucleus;DNA binding
+Cre09.g394954 Chloroplast
+Cre03.g152550 development.unspecified 33.99 protein binding Secretory pathway
+Cre-1.g2717054 rpl23 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit.L23 29.2.1.1.1.2.23 Chloroplast
+Cre03.g191250 LCI34 Chloroplast
+Cre10.g418100 POA3 protein.degradation.ubiquitin.proteasom 29.5.11.20 proteolysis involved in cellular protein catabolic process;proteasome core complex, alpha-subunit complex;ubiquitin-dependent protein catabolic process;proteasome core complex;threonine-type endopeptidase activity;endopeptidase activity
+Cre10.g423650 PRPL11 protein.synthesis.ribosomal protein.prokaryotic.non-organellar.50S subunit;protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit.L11 29.2.1.1.4.2;29.2.1.1.1.2.11 translation;ribosome;structural constituent of ribosome Chloroplast
+Cre03.g144747 RNA.regulation of transcription.MYB domain transcription factor family 27.3.25
+Cre06.g278245 cell.cell death.plants;protein.targeting.chloroplast 31.5.1;29.3.3 oxidation-reduction process;2 iron, 2 sulfur cluster binding;oxidoreductase activity;chlorophyllide a oxygenase [overall] activity Chloroplast
+Cre06.g280050 XRN1 DNA.unspecified;RNA.processing.ribonucleases 28.99;27.1.19 exonuclease activity;nucleic acid binding
+Cre10.g436500 misc.acid and other phosphatases 26.13 hydrolase activity
+Cre03.g182900 membrane Secretory pathway
+Cre10.g448650 KDG5 lipid metabolism.phospholipid synthesis.diacylglycerol kinase 11.3.5 kinase activity
+Cre10.g452800 LCIB PS.carbon concentrating mechanism.algal 1.5.3 Chloroplast
+Cre05.g230900 misc.acid and other phosphatases;lipid metabolism.phospholipid synthesis 26.13;11.3 Secretory pathway
+Cre03.g172950 PUS21 protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications.snoRNPs;DNA.synthesis/chromatin structure 29.2.2.3.1;28.1 RNA processing;RNA binding
+Cre07.g349700 signalling.light 30.11 Chloroplast
+Cre03.g145747 amino acid metabolism.synthesis.aromatic aa.chorismate.chorismate synthase 13.1.6.1.7 aromatic amino acid family biosynthetic process;chorismate synthase activity Chloroplast
+Cre06.g307200
+Cre02.g143550 ELI4 PS.lightreaction.unspecified 1.1.99 Chloroplast
+Cre03.g144584 Mitochondrion
+Cre10.g464100 protein.postranslational modification 29.4 protein phosphorylation;ATP binding;protein kinase activity
+Cre07.g332450 thiamine biosynthetic process
+Cre01.g036950 CBA1 adenosylcobinamide-GDP ribazoletransferase activity;cobalamin biosynthetic process;cobalamin 5'-phosphate synthase activity Chloroplast
+Cre13.g578750 TBA1 nucleotide metabolism.degradation.pyrimidine.dihydrouracil dehydrogenase;PS.lightreaction.photosystem II.biogenesis 23.2.1.3;1.1.1.3 oxidation-reduction process;oxidoreductase activity, acting on the CH-CH group of donors;cytoplasm Chloroplast
+Cre03.g172700 Chloroplast
+Cre05.g234200 nucleic acid binding Chloroplast
+Cre04.g217949 AXL6
+Cre03.g192350 protein binding Secretory pathway
+Cre03.g170600 POC4
+Cre03.g180151 Chloroplast
+Cre02.g095123 Mitochondrion
+Cre03.g171500 Chloroplast
+Cre01.g031600 Secretory pathway
+Cre01.g023250
+Cre03.g186150
+Cre01.g010450 protein binding Secretory pathway
+Cre17.g744247 DNA replication;nuclear origin of replication recognition complex;DNA binding
+Cre17.g708750 NSG1 cell.motility.eukaryotes.flagellar associated proteins 31.6.1.10 Secretory pathway
+Cre17.g697334 protein.degradation.cysteine protease 29.5.3 Mitochondrion
+Cre16.g681200 Mitochondrion
+Cre16.g665364 glycolysis.cytosolic branch.phosphoenolpyruvate carboxykinase (PEPCK);signalling.calcium;protein.postranslational modification 4.1.16;30.3;29.4 protein phosphorylation;ATP binding;protein kinase activity Chloroplast
+Cre06.g252550 DLA3 TCA / organic transformation.TCA.pyruvate DH.E2 8.1.1.2 transferase activity, transferring acyl groups;metabolic process Mitochondrion
+Cre16.g649650 response to stress
+Cre06.g285150 APX2 misc.peroxidases;redox.ascorbate and glutathione.ascorbate 26.12;21.2.1 oxidation-reduction process;heme binding;response to oxidative stress;peroxidase activity Chloroplast
+Cre03.g178700
+Cre16.g670754 transport.potassium 34.15 Chloroplast
+Cre15.g639050
+Cre15.g637249 Mitochondrion
+Cre03.g173900 protein.degradation.ubiquitin.E3.RING 29.5.11.4.2 Chloroplast
+Cre14.g618400 transport.ABC transporters and multidrug resistance systems 34.16 ATPase activity;integral component of membrane;transport;ATP binding;transporter activity Chloroplast
+Cre14.g609950 Mitochondrion
+Cre13.g587600 Mitochondrion
+Cre03.g174900 lipid metabolism.lipid degradation.lipases 11.9.2 protein binding
+Cre11.g475750 Secretory pathway
+Cre11.g467619 Chloroplast
+Cre03.g176700 CPL4 Mitochondrion
+Cre10.g454900 PDE29 signalling.in sugar and nutrient physiology.misc 30.1.1 signal transduction;3',5'-cyclic-nucleotide phosphodiesterase activity
+Cre10.g440600
+Cre10.g421250 EXO70 cell.vesicle transport 31.4 exocytosis;exocyst Mitochondrion
+Cre-1.g2716993 rpoB-1 Chloroplast
+Cre09.g389356 transport.nucleotides;transport.p- and v-ATPases 34.10;34.1 transmembrane transport;membrane;transporter activity Chloroplast
+Cre08.g380250 CP12 PS.calvin cycle.GAP 1.3.4 Chloroplast
+Cre07.g321600 Secretory pathway
+Cre05.g246800 GUN4 tetrapyrrole synthesis.regulation;tetrapyrrole synthesis.ALA dehydratase 19.40;19.4 Chloroplast
+Cre14.g614000 CGL17 Chloroplast
+Cre13.g574000 CLV1 transport.unspecified anions 34.18 transmembrane transport;membrane;chloride transport;voltage-gated chloride channel activity
+Cre01.g048850 RNA.regulation of transcription.chromatin remodeling factors 27.3.44 DNA binding
+Cre02.g142266 misc.misc2;secondary metabolism.isoprenoids.carotenoids.carotenoid epsilon ring hydroxylase 26.1;16.1.4.7 oxidation-reduction process;heme binding;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen;iron ion binding Chloroplast
+Cre02.g095148 Chloroplast
+Cre01.g014350 PRX5 redox.peroxiredoxin 21.5 oxidation-reduction process;oxidoreductase activity;antioxidant activity Chloroplast
+Cre-2.g801491 nad2 Mitochondrion
+Cre17.g705500 PHC23 Secretory pathway
+Cre16.g687294 4 iron, 4 sulfur cluster binding;lipoate synthase activity;photosynthesis;lipoate biosynthetic process Chloroplast
+Cre16.g685573 FAP214 cell.motility.eukaryotes.flagellar associated proteins 31.6.1.10 protein binding
+Cre16.g683700 integral component of membrane
+Cre16.g683150 Mitochondrion
+Cre16.g676981
+Cre16.g673729 CPN11 protein.co-chaperones;protein.folding.chaperones and co-chaperones.co-chaperones 29.9;29.6.2.6 protein folding;cytoplasm Chloroplast
+Cre16.g662250 Secretory pathway
+Cre03.g156350 OPR15 Mitochondrion
+Cre16.g650050 misc.rhodanese 26.23 Chloroplast
+Cre05.g245950 DRP1 signalling.G-proteins;misc.dynamin 30.5;26.17 GTP binding;GTPase activity
+Cre13.g585100 intracellular protein transport
+Cre03.g148201 Chloroplast
+Cre14.g612633 PHC58
+Cre03.g162000 transport.metabolite transporters at the envelope membrane 34.8 Secretory pathway
+Cre06.g278141
+Cre12.g560900 AOF7 secondary metabolism.isoprenoids.carotenoids 16.1.4 Chloroplast
+Cre12.g531450 HPAT3
+Cre03.g167924 protein.postranslational modification 29.4
+Cre10.g465650 development.unspecified 33.99 protein binding
+Cre10.g463200
+Cre09.g399300 FKB17-1 cell.cycle.peptidylprolyl isomerase;protein.folding.immunophilins (IMM).FKBPs 31.3.1;29.6.3.1 protein folding Secretory pathway
+Cre09.g394750 PRPS1 protein.synthesis.ribosomal protein.prokaryotic.unknown organellar.30S subunit.S1;protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit.S1 29.2.1.1.3.1.1;29.2.1.1.1.1.1 nucleic acid binding Chloroplast
+Cre09.g386744
+Cre09.g386735 DLA1 TCA / organic transformation.TCA.pyruvate DH.E2 8.1.1.2 transferase activity, transferring acyl groups;metabolic process Mitochondrion
+Cre08.g374950 Chloroplast
+Cre07.g356150 protein.degradation 29.5 CAAX-box protein processing;peptidase activity;proteolysis;metalloendopeptidase activity Secretory pathway
+Cre07.g352850 PRPL32 protein.synthesis.ribosomal protein.prokaryotic.non-organellar.50S subunit 29.2.1.1.4.2 large ribosomal subunit;translation;structural constituent of ribosome Chloroplast
+Cre03.g195850 protein.postranslational modification;RNA.regulation of transcription.putative transcription regulator 29.4;27.3.67 oxidation-reduction process;peptide-methionine (R)-S-oxide reductase activity;protein repair;oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor;response to oxidative stress Chloroplast
+Cre07.g335650 Secretory pathway
+Cre07.g326200
+Cre03.g199800 HYDA1 fermentation;development.unspecified;PS.lightreaction.hydrogenase.FeFe-hydrogenase 5;33.99;1.1.7.1 Chloroplast
+Cre06.g278300 transport.misc;transport.p- and v-ATPases 34.99;34.1 membrane
+Cre06.g264300 PRPS15 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit.S15 29.2.1.1.1.1.15 translation;ribosome;intracellular;structural constituent of ribosome Chloroplast
+Cre01.g040300 O-methyltransferase activity Mitochondrion
+Cre08.g380201 SHKD1 amino acid metabolism.synthesis.aromatic aa.chorismate.3-dehydroquinate dehydratase/shikimate dehydrogenase 13.1.6.1.10 oxidation-reduction process;shikimate 3-dehydrogenase (NADP+) activity;3-dehydroquinate dehydratase activity Mitochondrion
+Cre01.g004350 HLM1 not assigned.no ontology.hydroxyproline rich proteins 35.1.41 protein binding
+Cre12.g560450
+Cre01.g012150 MSRA4 protein.postranslational modification 29.4 oxidation-reduction process;protein repair;oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor;peptide-methionine (S)-S-oxide reductase activity;response to oxidative stress;protein folding Mitochondrion
+Cre01.g005950 Chloroplast
+Cre13.g569900
+Cre01.g002400 TGL1 lipid metabolism.lipid degradation.lipases.triacylglycerol lipase;lipid metabolism.lipid degradation.lipases 11.9.2.1;11.9.2 lipid metabolic process
+Cre02.g074900 not assigned.no ontology.C2 domain-containing protein 35.1.19 protein binding Mitochondrion
+Cre13.g584950 Mitochondrion
+Cre02.g081500 transport.NDP-sugars at the ER 34.11 integral component of membrane;transport
+Cre17.g736350 Mitochondrion
+Cre17.g706600
+Cre14.g609600 Mitochondrion
+Cre15.g641700
+Cre15.g638400 USPA stress.abiotic.heat 20.2.1 Chloroplast
+Cre14.g615600
+Cre14.g611517 misc.glutathione S transferases 26.9
+Cre12.g556150 CGL100 protein.degradation 29.5 membrane
+Cre13.g586550 CYB4 redox.ascorbate and glutathione 21.2 Secretory pathway
+Cre12.g552550
+Cre12.g533351 CLPB5 stress.abiotic.heat 20.2.1 ATPase activity;ATP binding Chloroplast
+Cre12.g529400 RPS27E1 protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S27 29.2.1.2.1.27 translation;ribosome;intracellular;structural constituent of ribosome
+Cre03.g202113 nucleotide metabolism.synthesis.purine.SAICAR synthetase 23.1.2.7 Chloroplast
+Cre03.g199647 protein.synthesis.initiation;protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications.DExD-box helicases 29.2.3;29.2.2.3.5 ATP binding;nucleic acid binding
+Cre03.g177200 CRB3 RNA.RNA binding 27.4 nucleic acid binding
+Cre03.g170150 development.unspecified;signalling.calcium;protein.degradation.ubiquitin.E3.RING 33.99;30.3;29.5.11.4.2 protein binding
+Cre06.g307100 AKC2 not assigned.no ontology.ABC1 family protein 35.1.1
+Cre12.g511200 NUOS5 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).localisation not clear;mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.2;9.1.1
+Cre03.g144667 CLPT4 Chloroplast
+Cre12.g531700 nucleotide metabolism.degradation 23.2 IMP salvage;deaminase activity;AMP deaminase activity Mitochondrion
+Cre12.g511850 GSK3 protein.postranslational modification.kinase;protein.postranslational modification 29.4.1;29.4 protein phosphorylation;protein kinase activity
+Cre02.g102250 RPS3 protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S3 29.2.1.2.1.3 RNA binding
+Cre02.g095071 RNA.processing.ribonucleases 27.1.19 nucleus Chloroplast
+Cre12.g520300 Secretory pathway
+Cre12.g521050
+Cre02.g081450 CGL123 Mitochondrion
+Cre12.g521450 CLPP2 protein.degradation.serine protease 29.5.5
+Cre02.g074370 signalling.calcium;minor CHO metabolism.sugar alcohols;protein.postranslational modification 30.3;3.3;29.4 protein phosphorylation;protein kinase activity
+Cre12.g517150 MET16 S-assimilation.APR;PS.lightreaction.photosystem II.PSII polypeptide subunits 14.2;1.1.1.2 cell redox homeostasis;metabolic process;catalytic activity Chloroplast
+Cre03.g209057 Mitochondrion
+Cre12.g522050 protein.degradation.metalloprotease 29.5.7 Mitochondrion
+Cre14.g625625 FTSH11 protein.degradation.metalloprotease 29.5.7 ATPase activity;proteolysis;ATP binding;metalloendopeptidase activity Mitochondrion
+Cre16.g695850
+Cre17.g724150 DRP3 misc.dynamin 26.17 GTP binding;GTPase activity
+Cre06.g267400 protein.postranslational modification 29.4 protein phosphorylation;protein kinase activity Mitochondrion
+Cre06.g260950 signalling.calcium;minor CHO metabolism.sugar alcohols 30.3;3.3
+Cre03.g213537 RNA.regulation of transcription.putative transcription regulator;RNA.regulation of transcription.general transcription 27.3.67;27.3.50 Chloroplast
+Cre03.g194900 intracellular signal transduction;phosphorus-oxygen lyase activity;cyclic nucleotide biosynthetic process Secretory pathway
+Cre01.g039550 PLAP1 cell.organisation 31.1 Chloroplast
+Cre16.g682750
+Cre03.g173650
+Cre03.g150800 misc.calcineurin-like phosphoesterase family protein;misc.acid and other phosphatases 26.27;26.13
+Cre01.g037350 CGLD2 Mitochondrion
+Cre02.g141500 Secretory pathway
+Cre02.g119450 Chloroplast
+Cre01.g035650
+Cre02.g099750 protein.postranslational modification 29.4 protein phosphorylation;ATP binding;protein kinase activity
+Cre02.g083650 Secretory pathway
+Cre17.g736650 protein.degradation.alanine protease;protein.degradation 29.5.31;29.5 zinc ion binding;metallopeptidase activity;proteolysis
+Cre12.g510800 CHLI2 tetrapyrrole synthesis.magnesium chelatase;tetrapyrrole synthesis.glu-tRNA synthetase 19.10;19.1 magnesium chelatase activity;chlorophyll biosynthetic process;photosynthesis Chloroplast
+Cre01.g049000 CGL31 4-alpha-hydroxytetrahydrobiopterin dehydratase activity;tetrahydrobiopterin biosynthetic process Chloroplast
+Cre08.g379650 TIC20 Mitochondrion
+Cre12.g510100 ATG4 protein.degradation.autophagy 29.5.2 Mitochondrion
+Cre12.g509250 EYE2 redox.thioredoxin 21.1 cell redox homeostasis Mitochondrion
+Cre14.g627850 amino acid metabolism.synthesis.aspartate family.lysine.dihydrodipicolinate reductase 13.1.3.5.2 oxidation-reduction process;lysine biosynthetic process via diaminopimelate;4-hydroxy-tetrahydrodipicolinate reductase Chloroplast
+Cre14.g629650 NIK1 transport.metal 34.12 Chloroplast
+Cre16.g653350 lipid A biosynthetic process;UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity Mitochondrion
+Cre12.g495050 OPR51 Secretory pathway
+Cre16.g669123 Mitochondrion
+Cre16.g677250 TEH5 Mitochondrion
+Cre10.g445050 SLT3 transmembrane transport;membrane;cation transmembrane transporter activity;sodium ion transport;potassium ion transport;transporter activity Secretory pathway
+Cre16.g672750 RNA.RNA binding 27.4 RNA binding
+Cre-1.g2717055 rpl2 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit.L2 29.2.1.1.1.2.2 Chloroplast
+Cre09.g414050 development.unspecified;DNA.unspecified;DNA.synthesis/chromatin structure.histone 33.99;28.99;28.1.3 ATP-dependent 5'-3' DNA helicase activity;ATP binding;DNA helicase activity
+Cre09.g407850 Chloroplast
+Cre09.g400516 lipid metabolism.exotics (steroids, squalene etc).sphingolipids 11.8.1 integral component of membrane;endoplasmic reticulum
+Cre09.g395288 transport.metal 34.12 transmembrane transport;integral component of membrane
+Cre09.g390208 Chloroplast
+Cre10.g439050 MCP7 transport.metabolite transporters at the mitochondrial membrane 34.9 Chloroplast
+Cre01.g028350 DEG8 protein.degradation.serine protease 29.5.5 protein binding Chloroplast
+Cre03.g156050 cell.division;protein.synthesis.release 31.2;29.2.5 translation Chloroplast
+Cre04.g217050
+Cre12.g556450 mediator complex;regulation of transcription from RNA polymerase II promoter;RNA polymerase II transcription cofactor activity
+Cre12.g556350 minor CHO metabolism.others;cell wall.degradation.pectate lyases and polygalacturonases 3.5;10.6.3 carbohydrate metabolic process;polygalacturonase activity
+Cre12.g552150 protein.postranslational modification.kinase;protein.postranslational modification 29.4.1;29.4 protein phosphorylation;ATP binding;protein binding;protein kinase activity Chloroplast
+Cre12.g546500 TEF22 integral component of membrane Secretory pathway
+Cre01.g054400
+Cre08.g381516 misc.short chain dehydrogenase/reductase (SDR) 26.22 oxidoreductase activity;metabolic process
+Cre02.g141150 Chloroplast
+Cre12.g503450 protein binding Secretory pathway
+Cre01.g024950
+Cre09.g395362 Chloroplast
+Cre10.g448051 transport.misc 34.99
+Cre04.g216950 lipid metabolism.FA synthesis and FA elongation.ketoacyl ACP synthase 11.1.3 transferase activity, transferring acyl groups other than amino-acyl groups;lipid biosynthetic process;metabolic process Chloroplast
+Cre10.g441400 NOP58 protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications.snoRNPs;RNA.regulation of transcription.putative transcription regulator 29.2.2.3.1;27.3.67
+Cre09.g395950 AOX1 mitochondrial electron transport / ATP synthesis.alternative oxidase 9.4 oxidation-reduction process;alternative oxidase activity Mitochondrion
+Cre09.g396250 VTE5 Co-factor and vitamine metabolism;secondary metabolism.isoprenoids.tocopherol biosynthesis;lipid metabolism.phospholipid synthesis.phosphatidate cytidylyltransferase 18;16.1.3;11.3.3 Secretory pathway
+Cre13.g562150 signalling.G-proteins;minor CHO metabolism.others 30.5;3.5 GTP binding Chloroplast
+Cre13.g567800 protein.postranslational modification 29.4 protein phosphatase type 2A regulator activity;signal transduction;protein phosphatase type 2A complex Chloroplast
+Cre08.g378850 RPPK1 nucleotide metabolism.synthesis.PRS-PP 23.1.3 nucleotide biosynthetic process;ribose phosphate diphosphokinase activity;magnesium ion binding Chloroplast
+Cre15.g644051 ATPase activity;ATP binding Chloroplast
+Cre19.g750747 NCL38 Chloroplast
+Cre17.g742200 cell.division 31.2
+Cre06.g307950 translation;ribosome;intracellular;structural constituent of ribosome Mitochondrion
+Cre17.g723250 CPE1 protein.degradation 29.5 Chloroplast
+Cre06.g308150 DNJ23 protein.co-chaperones;stress.abiotic.heat 29.9;20.2.1
+Cre07.g313700 TSE2 protein.aa activation.glutamate-tRNA ligase 29.1.17 tRNA aminoacylation;ligase activity, forming aminoacyl-tRNA and related compounds;ATP binding Chloroplast
+Cre17.g696550 Chloroplast
+Cre10.g427250 PRO1 cell.organisation 31.1
+Cre07.g330100 GTR25 stress.abiotic.drought/salt 20.2.3 membrane;protein glycosylation;oligosaccharyl transferase activity Secretory pathway
+Cre16.g680700
+Cre16.g677450 minor CHO metabolism.others 3.5 isomerase activity;carbohydrate metabolic process Chloroplast
+Cre16.g672385 HIS5 amino acid metabolism.synthesis.histidine.imidazoleglycerol-phosphate synthase (cyclase);amino acid metabolism.synthesis.histidine 13.1.7.7;13.1.7 pyridoxal phosphate binding;biosynthetic process
+Cre02.g142352 protein.aa activation.histidine-tRNA ligase 29.1.21 cytoplasm
+Cre08.g362750 metal ion binding;hydrolase activity;nucleic acid binding
+Cre08.g368300 HEL43 hydrolase activity;ATP binding;DNA binding Secretory pathway
+Cre16.g650700 amino acid metabolism.synthesis.central amino acid metabolism.alanine.alanine-glyoxylate aminotransferase 13.1.1.3.11 Mitochondrion
+Cre07.g335600 NAR1.4 transport.nitrate;PS.carbon concentrating mechanism.algal 34.4;1.5.3 membrane;transport;transporter activity
+Cre09.g400997 Chloroplast
+Cre10.g446500 CPL24 Chloroplast
+Cre03.g173000 Chloroplast
+Cre10.g461650 Mitochondrion
+Cre07.g349250 Secretory pathway
+Cre11.g467544 IDI1 secondary metabolism.isoprenoids.mevalonate pathway.isopentenyl pyrophosphate:dimethyllallyl pyrophosphate isomerase 16.1.2.7 hydrolase activity;isoprenoid biosynthetic process;isopentenyl-diphosphate delta-isomerase activity
+Cre09.g403034 metabolic process;catalytic activity
+Cre08.g358522 CEP5 protein.degradation.cysteine protease 29.5.3 cysteine-type peptidase activity;proteolysis Secretory pathway
+Cre11.g467550 nucleotide metabolism.synthesis.pyrimidine.dihydroorotase 23.1.1.3 pyrimidine nucleobase biosynthetic process;hydrolase activity;dihydroorotase activity Chloroplast
+Cre10.g432200
+Cre10.g428350 Chloroplast
+Cre06.g291800 COQ2 protein.postranslational modification 29.4 integral component of membrane;prenyltransferase activity Chloroplast
+Cre10.g427900 nucleotide metabolism.synthesis.purine 23.1.2 intracellular signal transduction;phosphorus-oxygen lyase activity;cyclic nucleotide biosynthetic process
+Cre09.g386758 ALS1 amino acid metabolism.synthesis.branched chain group.common.acetolactate synthase;amino acid metabolism.synthesis.branched chain group.common 13.1.4.1.1;13.1.4.1 thiamine pyrophosphate binding;catalytic activity;magnesium ion binding Chloroplast
+Cre06.g283600 Chloroplast
+Cre11.g467702 Chloroplast
+Cre06.g279150 TSD2 protein.aa activation.aspartate-tRNA ligase 29.1.12 tRNA aminoacylation for protein translation;ATP binding;aminoacyl-tRNA ligase activity;nucleic acid binding;nucleotide binding
+Cre09.g388060 VDR1 secondary metabolism.isoprenoids.carotenoids.violaxanthin de-epoxidase 16.1.4.21 Chloroplast
+Cre11.g467722
+Cre09.g389450 protein.postranslational modification.kinase.receptor like cytoplasmatic kinase IX 29.4.1.59 protein ubiquitination;ubiquitin-protein transferase activity;nucleic acid binding Mitochondrion
+Cre06.g261500 CPLD58 protein binding Chloroplast
+Cre02.g108450 FAP280 hormone metabolism.ethylene.induced-regulated-responsive-activated 17.5.3 sequence-specific DNA binding
+Cre09.g395250 FAP36 cell.motility.eukaryotes.flagellar associated proteins 31.6.1.10
+Cre-1.g2717004 rpoA Chloroplast
+Cre09.g410600 protein.postranslational modification 29.4 protein dephosphorylation;protein serine/threonine phosphatase activity;catalytic activity
+Cre09.g411600
+Cre11.g467737 Chloroplast
+Cre09.g417350
+Cre09.g412300 TIM16 protein import into mitochondrial matrix;mitochondrial inner membrane presequence translocase complex Chloroplast
+Cre11.g476800 MRPL15 protein.synthesis.ribosomal protein.prokaryotic.unknown organellar.50S subunit.L15 29.2.1.1.3.2.15 large ribosomal subunit;translation;structural constituent of ribosome Mitochondrion
+Cre12.g488500 ARC6 stress.abiotic.heat 20.2.1 Chloroplast
+Cre07.g346418 RNA.regulation of transcription.NAC domain transcription factor family 27.3.27
+Cre07.g329650
+Cre16.g671000 NDA5 mitochondrial electron transport / ATP synthesis.NADH-DH (type II).mitochondrial;mitochondrial electron transport / ATP synthesis.NADH-DH.type II.mitochondrial 9.2.3;9.2.1.3 oxidation-reduction process;oxidoreductase activity Mitochondrion
+Cre08.g369150 not assigned.no ontology.ABC1 family protein;transport.ABC transporters and multidrug resistance systems 35.1.1;34.16 Chloroplast
+Cre16.g669525 transport.ABC transporters and multidrug resistance systems 34.16 ATPase activity;ATP binding Chloroplast
+Cre09.g387245 stress.abiotic.drought/salt 20.2.3 membrane;protein glycosylation;oligosaccharyl transferase activity Secretory pathway
+Cre03.g179901 Mitochondrion
+Cre02.g088500 CPLD29 protein.targeting.nucleus 29.3.1 Mitochondrion
+Cre13.g564050 extrinsic component of membrane;photosynthesis;photosystem II oxygen evolving complex;photosystem II;calcium ion binding Chloroplast
+Cre06.g253350 GCSH PS.photorespiration.glycine cleavage.H protein;PS.photorespiration.glycine cleavage 1.2.4.4;1.2.4 Mitochondrion
+Cre12.g502250 PLAP4 cell.organisation 31.1 Chloroplast
+Cre05.g235400 RNA.regulation of transcription.PHD finger transcription factor 27.3.63 DNA integration;protein binding
+Cre07.g331900 RPS13 protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S13 29.2.1.2.1.13 translation;ribosome;intracellular;structural constituent of ribosome
+Cre13.g587100 oxidation-reduction process;cobalt ion binding;oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor;phytochromobilin biosynthetic process Chloroplast
+Cre02.g095080 Secretory pathway
+Cre06.g291550 Secretory pathway
+Cre02.g119900 CEP6 protein.degradation.cysteine protease 29.5.3 cysteine-type peptidase activity;proteolysis Secretory pathway
+Cre02.g111700 EFH1 Co-factor and vitamine metabolism.ubiquinone 18.8 calcium ion binding Chloroplast
+Cre01.g017050 MCP1
+Cre-1.g2717005 rps2 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit.S2 29.2.1.1.1.1.2 Chloroplast
+Cre03.g192050 FTR1 high-affinity iron permease complex;membrane;high-affinity iron ion transmembrane transport;iron ion transmembrane transporter activity
+Cre02.g142800 TRXz redox.thioredoxin 21.1 cell redox homeostasis;protein disulfide oxidoreductase activity;glycerol ether metabolic process Chloroplast
+Cre17.g741450 CPN60B1 protein.folding.chaperones and co-chaperones.HSP60s;protein.folding;PS.calvin cycle.rubisco interacting 29.6.2.2;29.6;1.3.13 ATP binding Chloroplast
+Cre12.g520200 CPL8 Chloroplast
+Cre01.g029750 DAAK1 nucleotide metabolism.phosphotransfer and pyrophosphatases.uridylate kinase;nucleotide metabolism.phosphotransfer and pyrophosphatases.adenylate kinase 23.4.3;23.4.1 nucleobase-containing compound kinase activity;nucleobase-containing compound metabolic process;ATP binding
+Cre03.g189350
+Cre07.g321300 Chloroplast
+Cre02.g118950 PRPS17 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit.S17 29.2.1.1.1.1.17 translation;ribosome;intracellular;structural constituent of ribosome Chloroplast
+Cre06.g278255 Chloroplast
+Cre08.g382100
+Cre02.g084900
+Cre17.g696300 protein.degradation.ubiquitin.E3.RING 29.5.11.4.2 nucleic acid binding Chloroplast
+Cre01.g051400 ERD2A protein.targeting.secretory pathway.ER 29.3.4.1 ER retention sequence binding;integral component of membrane;protein retention in ER lumen Secretory pathway
+Cre02.g082877 protein.aa activation.serine-tRNA ligase 29.1.11 seryl-tRNA aminoacylation;tRNA aminoacylation for protein translation;cytoplasm;ATP binding;serine-tRNA ligase activity;aminoacyl-tRNA ligase activity;DNA binding;nucleotide binding
+Cre10.g431500
+Cre07.g333950 VPS45 protein.targeting.secretory pathway.vacuole 29.3.4.3 vesicle-mediated transport;vesicle docking involved in exocytosis
+Cre17.g727450 signalling.G-proteins;minor CHO metabolism.others 30.5;3.5
+Cre04.g215850 IPA1 protein.targeting.nucleus 29.3.1 protein transporter activity;protein import into nucleus;cytoplasm;nucleus;protein binding
+Cre04.g212500 CGL42 Chloroplast
+Cre07.g340450 PKHD1 protein binding Secretory pathway
+Cre08.g362450 AMA2 major CHO metabolism.degradation.starch.starch cleavage.alpha amylase;major CHO metabolism.degradation.starch.starch cleavage 2.2.2.1.1;2.2.2.1 cation binding;carbohydrate metabolic process;calcium ion binding;alpha-amylase activity;catalytic activity Chloroplast
+Cre16.g677350 Mitochondrion
+Cre11.g468359 GAS31 Secretory pathway
+Cre06.g278103 oxidation-reduction process;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen;copper ion binding;monooxygenase activity Secretory pathway
+Cre17.g701500 DNJ1 protein.co-chaperones;protein.folding.chaperones and co-chaperones.co-chaperones;stress.abiotic.heat 29.9;29.6.2.6;20.2.1 unfolded protein binding;heat shock protein binding
+Cre17.g744547 Chloroplast
+Cre16.g687350 lipid metabolism.lipid degradation.beta-oxidation.acyl CoA DH 11.9.4.2 oxidation-reduction process;oxidoreductase activity, acting on the CH-CH group of donors;fatty acid beta-oxidation;peroxisome;acyl-CoA oxidase activity;acyl-CoA dehydrogenase activity Mitochondrion
+Cre02.g083935
+Cre14.g624950 DHC10 cell.motility.eukaryotes.axonemal dyneins.inner arm.monomeric species;cell.motility.eukaryotes.axonemal dyneins.inner arm 31.6.1.4.2.1;31.6.1.4.2 dynein complex;ATPase activity;microtubule-based movement;ATP binding;microtubule motor activity Secretory pathway
+Cre13.g566250 Mitochondrion
+Cre03.g153450
+Cre02.g090050 FAP170 Secretory pathway
+Cre11.g476550 ADH11 lipid metabolism.exotics (steroids, squalene etc).trans-2-enoyl-CoA reductase (NADPH) 11.8.7 oxidation-reduction process;oxidoreductase activity;zinc ion binding
+Cre17.g738300 RPP1 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.unknown;protein.synthesis.ribosomal protein.eukaryotic.60S subunit.P1 29.2.1.2.2.99;29.2.1.2.2.81
+Cre16.g690509
+Cre02.g096150 MSD1 redox.dismutases and catalases 21.6 oxidation-reduction process;metal ion binding;superoxide metabolic process;superoxide dismutase activity
+Cre09.g402500 ATPVA2 transport.p- and v-ATPases 34.1 proton-transporting V-type ATPase, V0 domain;ATP hydrolysis coupled proton transport;hydrogen ion transmembrane transporter activity
+Cre10.g430850
+Cre10.g441650 Secretory pathway
+Cre02.g106750 MRPS9 translation;ribosome;structural constituent of ribosome Mitochondrion
+Cre12.g538350 FTX1 development.unspecified 33.99 iron-sulfur cluster assembly;ferric iron binding Secretory pathway
+Cre12.g510900 HSLU1 protein.folding.chaperones and co-chaperones.HSP100s;protein.degradation.serine protease 29.6.2.5;29.5.5 peptidase activity, acting on L-amino acid peptides;ATPase activity;HslUV protease complex;cytoplasm;ATP binding Mitochondrion
+Cre09.g407300 Chloroplast
+Cre12.g522100 transport.misc;protein.targeting.secretory pathway.unspecified 34.99;29.3.4.99
+Cre07.g332500 AXT2
+Cre09.g388850 FAP329 transport.calcium;signalling.calcium;minor CHO metabolism.sugar alcohols 34.21;30.3;3.3 metal ion binding;nucleotide binding
+Cre10.g432250 cell.cycle;signalling.MAP kinases;minor CHO metabolism.callose;protein.postranslational modification.kinase 31.3;30.6;3.6;29.4.1 protein phosphorylation;protein kinase activity
+Cre13.g588700
+Cre08.g363700 protein binding
+Cre02.g088850 RFS2 Co-factor and vitamine metabolism.riboflavin.riboflavin synthase;Co-factor and vitamine metabolism 18.3.2;18 riboflavin synthase complex;riboflavin biosynthetic process Chloroplast
+Cre13.g606750 DNA.synthesis/chromatin structure 28.1 metal ion binding;hydrolase activity;ATP binding
+Cre01.g047800 GRX6 transport.calcium;redox.glutaredoxins 34.21;21.4 cell redox homeostasis;protein disulfide oxidoreductase activity;electron carrier activity Chloroplast
+Cre01.g007700 protein.degradation 29.5 proteolysis;intracellular;aminopeptidase activity Chloroplast
+Cre01.g021650
+Cre12.g511900 RPE1 PS.calvin cycle.RPE 1.3.11 racemase and epimerase activity, acting on carbohydrates and derivatives;carbohydrate metabolic process Chloroplast
+Cre05.g238364 PS.lightreaction.unspecified.TEF 1.1.99.1
+Cre01.g026650 Co-factor and vitamine metabolism.molybdenum cofactor;Co-factor and vitamine metabolism 18.1;18 Secretory pathway
+Cre07.g356850 response to stress
+Cre02.g098800 redox.thioredoxin 21.1 protein secretion;endoplasmic reticulum lumen;endoplasmic reticulum Secretory pathway
+Cre03.g201300 SSA10 oxidation-reduction process;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen;copper ion binding;monooxygenase activity Secretory pathway
+Cre02.g086650 SMC2 cell.division;DNA.synthesis/chromatin structure 31.2;28.1 chromosome organization;mitotic chromosome condensation;chromosome;ATP binding;protein binding;condensin complex
+Cre07.g325400 LEU3 secondary metabolism.sulfur-containing.glucosinolates.synthesis.aliphatic.methylthioalkylmalate dehydrogenase (MAM-DH);amino acid metabolism.synthesis.branched chain group.leucine specific.3-isopropylmalate dehydrogenase 16.5.1.1.1.5;13.1.4.4.3 oxidation-reduction process;NAD binding;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;magnesium ion binding Chloroplast
+Cre05.g232751 Chloroplast
+Cre03.g189650 RNA.regulation of transcription.Transcriptional Adaptor Zinc Bundle (TAZ) domain family;RNA.regulation of transcription.histone acetyltransferases 27.3.72;27.3.54 histone acetylation;zinc ion binding;regulation of transcription, DNA-templated;nucleus;histone acetyltransferase activity;transcription cofactor activity
+Cre06.g250250 ATPVC transport.p- and v-ATPases 34.1 proton-transporting V-type ATPase, V1 domain;ATP hydrolysis coupled proton transport;hydrogen ion transmembrane transporter activity
+Cre03.g196150
+Cre13.g592050 DAL1 nucleotide metabolism.degradation 23.2 hydrolase activity Secretory pathway
+Cre04.g213100 CGLD7 Chloroplast
+Cre03.g201900 RSP1 cell.motility.eukaryotes.radial spoke.head 31.6.1.5.1
+Cre06.g308500 CMP2 nucleotide metabolism.synthesis.pyrimidine.carbamoyl phosphate synthetase;amino acid metabolism.synthesis.glutamate family.arginine.carbamoyl-phosphate synthase 23.1.1.1;13.1.2.3.11 hydrolase activity;glutamine metabolic process Chloroplast
+Cre05.g233050 FAP162 cell.motility.eukaryotes.flagellar associated proteins 31.6.1.10
+Cre16.g664350 DNA.repair 28.2 Chloroplast
+Cre17.g743597
+Cre03.g167550 CEP290 cell.motility.eukaryotes.basal bodies 31.6.1.1 cilium morphogenesis;centrosome;nucleus
+Cre03.g176833 NAP1 cell.organisation.cytoskeleton.actin.Actin;cell.organisation 31.1.1.1.1;31.1 Chloroplast
+Cre14.g624850 Chloroplast
+Cre04.g217800 development.unspecified 33.99 Mitochondrion
+Cre03.g177900 TOB38 Mitochondrion
+Cre16.g692300 transport.ABC transporters and multidrug resistance systems 34.16 transmembrane transport;ATPase activity, coupled to transmembrane movement of substances;ATPase activity;integral component of membrane;transport;ATP binding Secretory pathway
+Cre12.g512400 transcription factor binding;regulation of transcription, DNA-templated;ATP binding
+Cre12.g546550 FEA1 metal handling.binding, chelation and storage 15.2 Secretory pathway
+Cre09.g389250 AOF1 misc.oxidases - copper, flavone etc 26.7
+Cre11.g474950 lipid metabolism.lipid degradation.lipases 11.9.2 Secretory pathway
+Cre12.g503600 protein.degradation.ubiquitin.ubiquitin 29.5.11.1 protein binding
+Cre09.g388400 RAT1
+Cre09.g392579 OPR10 Mitochondrion
+Cre07.g327079 minor CHO metabolism.sugar alcohols 3.3 FMN binding
+Cre09.g389726
+Cre03.g200543 MCP15 transport.metabolite transporters at the mitochondrial membrane 34.9
+Cre09.g391282 XYT1 transferase activity, transferring glycosyl groups
+Cre16.g688526 protein.postranslational modification;PS.lightreaction.state transition 29.4;1.1.30 protein phosphorylation;ATP binding;protein kinase activity Chloroplast
+Cre06.g267850 PLS1 Mitochondrion
+Cre12.g529500 protein.synthesis.ribosomal RNA;protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications.methylotransferases;RNA.regulation of transcription.putative transcription regulator 29.2.6;29.2.2.3.3;27.3.67 methylation;rRNA methylation;rRNA methyltransferase activity;methyltransferase activity;rRNA processing;nucleus;RNA methylation
+Cre12.g512300 hormone metabolism.jasmonate.synthesis-degradation.lipoxygenase 17.7.1.2 oxidation-reduction process;metal ion binding;oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen Mitochondrion
+Cre03.g181250 CGLD13 signalling.light 30.11 Chloroplast
+Cre16.g676550
+Cre06.g271200 PNO1 redox.ascorbate and glutathione.ascorbate 21.2.1 oxidation-reduction process;cell redox homeostasis;oxidoreductase activity Chloroplast
+Cre09.g416700
+Cre03.g171050 GHL1 misc.gluco-, galacto- and mannosidases;stress.biotic;secondary metabolism.sulfur-containing.glucosinolates.degradation.myrosinase 26.3;20.1;16.5.1.3.1 carbohydrate metabolic process;hydrolase activity, hydrolyzing O-glycosyl compounds
+Cre04.g226850 ASP1 protein.degradation.aspartate protease 29.5.4 lipid metabolic process;proteolysis;aspartic-type endopeptidase activity Secretory pathway
+Cre12.g537641 Secretory pathway
+Cre13.g577450 lipid metabolism.glycerol metabolism.FAD-dependent glycerol-3-phosphate dehydrogenase 11.5.3 oxidation-reduction process;oxidoreductase activity Secretory pathway
+Cre14.g612800 Chloroplast
+Cre12.g510450 RPS28 translation;ribosome;intracellular;structural constituent of ribosome
+Cre01.g000100 transport.metal 34.12
+Cre13.g567100 ALO1 redox.ascorbate and glutathione.ascorbate.L-galactono-1,4-lactone dehydrogenase 21.2.1.5 oxidation-reduction process;flavin adenine dinucleotide binding;oxidoreductase activity;membrane;D-arabinono-1,4-lactone oxidase activity Mitochondrion
+Cre04.g217954 transport.calcium;signalling.calcium;minor CHO metabolism.sugar alcohols 34.21;30.3;3.3 metal ion binding;nucleotide binding Chloroplast
+Cre12.g503500 membrane Secretory pathway
+Cre10.g420800 FAP46 cell.motility.eukaryotes.flagellar associated proteins 31.6.1.10
+Cre01.g046150 protein.degradation.metalloprotease 29.5.7 manganese ion binding;aminopeptidase activity Chloroplast
+Cre06.g286300 COQ5B methyltransferase activity;metabolic process Chloroplast
+Cre16.g687950 ETF1 mitochondrial electron transport / ATP synthesis.electron transfer flavoprotein 9.3 Mitochondrion
+Cre06.g282250 N-acetyltransferase activity
+Cre06.g288500 RRA2 Secretory pathway
+Cre11.g476950 Secretory pathway
+Cre01.g025350 FAP235
+Cre14.g621450 RPL5 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L5 29.2.1.2.2.5 5S rRNA binding;translation;ribosome;intracellular;structural constituent of ribosome
+Cre01.g025500 Mitochondrion
+Cre03.g148050 POLI1 DNA.repair 28.2 DNA repair;damaged DNA binding Mitochondrion
+Cre08.g360600 ERM4 stress.abiotic.drought/salt 20.2.3 membrane Secretory pathway
+Cre13.g590300 URK2 nucleotide metabolism.salvage.nucleoside kinases.uridine kinase 23.3.2.2 kinase activity;metabolic process;ATP binding
+Cre03.g148000 Chloroplast
+Cre-1.g2717044 atpH Chloroplast
+Cre07.g329882 VGK1 transport.potassium;protein.postranslational modification 34.15;29.4 transmembrane transport;membrane;ion transport;ion channel activity
+Cre03.g193550 MRPL46 Mitochondrion
+Cre13.g581850 transport.ABC transporters and multidrug resistance systems 34.16 Mitochondrion
+Cre01.g029650 VPS35 protein.targeting.secretory pathway.vacuole 29.3.4.3 retrograde transport, endosome to Golgi;retromer complex;protein transport;protein transporter activity
+Cre06.g301850
+Cre-1.g2716962 ORF2971 Chloroplast
+Cre03.g201750 Chloroplast
+Cre11.g467682 Chloroplast
+Cre07.g331700 Secretory pathway
+Cre06.g261150 BIO2 Co-factor and vitamine metabolism.biotin.biotin synthase 18.6.1 iron-sulfur cluster binding;catalytic activity Mitochondrion
+Cre09.g388750 TEF21 signalling.phosphinositides;lipid metabolism.lipid degradation.lysophospholipases.phosphoinositide phospholipase C;PS.lightreaction.unspecified.TEF 30.4;11.9.3.5;1.1.99.1 phosphoric ester hydrolase activity
+Cre06.g278104 Chloroplast
+Cre13.g581400 AAA2 transport.misc;transport.metabolite transporters at the mitochondrial membrane;transport.metabolite transporters at the envelope membrane 34.99;34.9;34.8 integral component of membrane;transport;ATP binding;ATP:ADP antiporter activity Chloroplast
+Cre01.g036200 protein binding;catalytic activity Mitochondrion
+Cre06.g292550 FAP15 protein.postranslational modification 29.4 hydrolase activity
+Cre12.g551950 CGL38 Chloroplast
+Cre06.g299700 SOUL1 tetrapyrrole synthesis.unspecified 19.99
+Cre-1.g2717057 rpl16 Chloroplast
+Cre13.g575850 signalling.light 30.11
+Cre12.g500950 CLPP4 protein.degradation.serine protease 29.5.5 Chloroplast
+Cre01.g052250 TRXx redox.thioredoxin 21.1 cell redox homeostasis;protein disulfide oxidoreductase activity;glycerol ether metabolic process Chloroplast
+Cre10.g453000
+Cre11.g474900 Chloroplast
+Cre09.g412150 PPR11 Chloroplast
+Cre04.g221250 Chloroplast
+Cre16.g674800 Chloroplast
+Cre06.g281350 LON1 protein.degradation.serine protease 29.5.5 protein catabolic process;proteolysis;ATP binding;serine-type endopeptidase activity;ATP-dependent peptidase activity Mitochondrion
+Cre16.g695800 starch binding Chloroplast
+Cre01.g047400
+Cre16.g662150 CCB1 protein.assembly and cofactor ligation;PS.lightreaction.cytochrome b6/f.biogenesis 29.8;1.1.3.5 Chloroplast
+Cre03.g201100 FHL1 protein.degradation.AAA type;protein.degradation.metalloprotease 29.5.9;29.5.7 ATP binding Chloroplast
+Cre07.g330750 PHC43 Secretory pathway
+Cre02.g113200 GLN1 N-metabolism.ammonia metabolism.glutamine synthetase 12.2.2 nitrogen compound metabolic process;glutamine biosynthetic process;glutamate-ammonia ligase activity
+Cre16.g675400 Mitochondrion
+Cre17.g725650 transport.unspecified cations 34.14 membrane Mitochondrion
+Cre03.g148300 Mitochondrion
+Cre03.g168150 protein.postranslational modification 29.4 protein phosphorylation;ATP binding;protein kinase activity
+Cre13.g605650 ALD7 secondary metabolism.N misc.betaine.betaine-aldehyde dehydrogenase 16.4.2.1 oxidation-reduction process;oxidoreductase activity;metabolic process
+Cre17.g713800 Chloroplast
+Cre12.g541750 ZPD1 secondary metabolism.isoprenoids.carotenoids 16.1.4 oxidation-reduction process;oxidoreductase activity Mitochondrion
+Cre01.g039150 TIC21 protein.targeting.chloroplast 29.3.3
+Cre02.g143000 PLSB1 lipid metabolism.phospholipid synthesis.1-acylglycerol-3-phosphate O-acyltransferase;lipid metabolism.phospholipid synthesis 11.3.1;11.3 transferase activity, transferring acyl groups;metabolic process;glycerol-3-phosphate O-acyltransferase activity Chloroplast
+Cre16.g659100 Secretory pathway
+Cre02.g092550 TPR1 not assigned.no ontology.tetratricopeptide repeat (TPR);protein.folding 35.1.27;29.6
+Cre03.g190850 ECH1
+Cre17.g718800 mpa14 misc.calcineurin-like phosphoesterase family protein 26.27 hydrolase activity
+Cre13.g584850 protein binding Chloroplast
+Cre12.g510650 FBP2 PS.calvin cycle.FBPase 1.3.7 phosphoric ester hydrolase activity;fructose 1,6-bisphosphate 1-phosphatase activity;carbohydrate metabolic process Chloroplast
+Cre09.g398215 protein.synthesis.initiation 29.2.3 translational initiation;translation initiation factor activity Mitochondrion
+Cre10.g423750 COQ3 Co-factor and vitamine metabolism.ubiquinone.hexaprenyldihydroxybenzoate methyltransferase 18.8.1 Chloroplast
+Cre12.g511700 secondary metabolism.isoprenoids.mevalonate pathway.geranyl diphosphate synthase;secondary metabolism.isoprenoids.non-mevalonate pathway.geranylgeranyl pyrophosphate synthase 16.1.2.8;16.1.1.10 isoprenoid biosynthetic process Mitochondrion
+Cre10.g428550 C1-metabolism.dihydropteridine diphosphokinase 25.3 pteridine-containing compound metabolic process;folic acid-containing compound biosynthetic process;2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity Mitochondrion
+Cre17.g735500
+Cre08.g378750
+Cre11.g479450 Secretory pathway
+Cre01.g053450 intracellular signal transduction;phosphorus-oxygen lyase activity;cyclic nucleotide biosynthetic process
+Cre07.g355600 NTR3 redox.thioredoxin 21.1 oxidation-reduction process;oxidoreductase activity
+Cre10.g452650 TIM17 protein.targeting.mitochondria 29.3.2 P-P-bond-hydrolysis-driven protein transmembrane transporter activity;intracellular protein transport;mitochondrial inner membrane presequence translocase complex
+Cre05.g234100 CYP745A1 misc.misc2;secondary metabolism.isoprenoids.carotenoids.carotenoid epsilon ring hydroxylase 26.1;16.1.4.7 oxidation-reduction process;heme binding;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen;iron ion binding Secretory pathway
+Cre01.g028600 misc.nitrilases, nitrile lyases, berberine bridge enzymes, reticuline oxidases, troponine reductases;secondary metabolism.N misc.alkaloid-like 26.8;16.4.1 Mitochondrion
+Cre06.g275050 GGH2 protein.degradation 29.5 hydrolase activity;omega peptidase activity;glutamine metabolic process;catalytic activity Secretory pathway
+Cre17.g733250 FKB16-4 cell.cycle.peptidylprolyl isomerase;protein.folding.immunophilins (IMM).FKBPs 31.3.1;29.6.3.1 protein folding Chloroplast
+Cre01.g039350 NCR2 misc.cytochrome P450;misc.misc2;secondary metabolism.phenylpropanoids 26.10;26.1;16.2 oxidation-reduction process;oxidoreductase activity;FMN binding Secretory pathway
+Cre10.g437050 ATP11 protein complex assembly;mitochondrion Mitochondrion
+Cre13.g606250 CYG41 nucleotide metabolism.synthesis.purine 23.1.2 intracellular signal transduction;phosphorus-oxygen lyase activity;cyclic nucleotide biosynthetic process
+Cre14.g615800 Chloroplast
+Cre02.g146400 CSB2
+Cre01.g015000 NAGK1 nucleotide metabolism.phosphotransfer and pyrophosphatases.misc;amino acid metabolism.synthesis.glutamate family.arginine.acetylglutamate kinase 23.4.99;13.1.2.3.2 Chloroplast
+Cre07.g336750
+Cre08.g377050 Secretory pathway
+Cre10.g462250 REF1 RNA.RNA binding 27.4 nucleic acid binding
+Cre10.g422300 PRX6 redox.peroxiredoxin 21.5 oxidoreductase activity Chloroplast
+Cre11.g467778 nucleotide metabolism.salvage.phosphoribosyltransferases.uracil phosphoribosyltransferase (UPP) 23.3.1.3 Chloroplast
+Cre17.g707850 DNA binding
+Cre14.g622750 RNA.processing.ribonucleases 27.1.19 Mitochondrion
+Cre13.g580200
+Cre17.g706950
+Cre02.g087700 APX1 redox.ascorbate and glutathione.ascorbate 21.2.1 oxidation-reduction process;heme binding;response to oxidative stress;peroxidase activity Chloroplast
+Cre09.g408700 Mitochondrion
+Cre16.g660900 KIL10 cell.organisation 31.1 microtubule binding;microtubule-based movement;kinesin complex;ATP binding;microtubule motor activity
+Cre02.g112850 COQ6 misc.oxidases - copper, flavone etc 26.7 FAD binding Mitochondrion
+Cre01.g043450 Chloroplast
+Cre17.g741000 endoplasmic reticulum membrane Secretory pathway
+Cre36.g759747 Secretory pathway
+Cre14.g611450 PLAP7 cell.organisation 31.1 Chloroplast
+Cre09.g398289 development.unspecified 33.99 transferase activity, transferring acyl groups;metabolic process Chloroplast
+Cre03.g194350
+Cre07.g315700 FKB16-1 protein.folding.immunophilins (IMM).FKBPs;protein.folding 29.6.3.1;29.6 protein folding Chloroplast
+Cre07.g319100 TEF18 PS.lightreaction.unspecified.TEF 1.1.99.1 protein binding Mitochondrion
+Cre12.g498350 SRE1
+Cre05.g241750 PDK3 signalling.in sugar and nutrient physiology.pyruvate dehydrogenase kinase 30.1.2 Mitochondrion
+Cre06.g281200 protein binding
+Cre14.g624350 VTE6 secondary metabolism.isoprenoids.tocopherol biosynthesis.tocopherol methyltransferase 16.1.3.5 methyltransferase activity;metabolic process Chloroplast
+Cre03.g150300 CAM8 signalling.calcium;minor CHO metabolism.sugar alcohols 30.3;3.3
+Cre10.g443550 protein.postranslational modification 29.4 protein phosphorylation;protein kinase activity;catalytic activity
+Cre07.g318350 CGL64 transport.misc 34.99
+Cre05.g242350 transport.calcium 34.21 metal ion binding;nucleotide binding
+Cre03.g180000 Chloroplast
+Cre16.g668600 Chloroplast
+Cre-1.g2716973 rps7 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit.S7 29.2.1.1.1.1.7 Chloroplast
+Cre12.g501000 transport.metabolite transporters at the envelope membrane 34.8 transmembrane transport Secretory pathway
+Cre12.g534350 HCD2 biodegradation of xenobiotics.3-hydroxybutyryl-CoA dehydrogenase;lipid metabolism.lipid degradation.beta-oxidation.multifunctional 24.3;11.9.4.9 oxidation-reduction process;oxidoreductase activity;fatty acid metabolic process;phosphogluconate dehydrogenase (decarboxylating) activity;3-hydroxyacyl-CoA dehydrogenase activity
+Cre04.g225900 VAMP72 cell.vesicle transport 31.4 vesicle-mediated transport;integral component of membrane
+Cre13.g568850 ISU1 protein.assembly and cofactor ligation;Co-factor and vitamine metabolism.iron-sulphur clusters 29.8;18.7 iron-sulfur cluster binding;iron-sulfur cluster assembly;iron ion binding Secretory pathway
+Cre02.g116250 Chloroplast
+Cre02.g097900 AST3 amino acid metabolism.synthesis.central amino acid metabolism.aspartate.aspartate aminotransferase 13.1.1.2.1 pyridoxal phosphate binding;biosynthetic process;transaminase activity;cellular amino acid metabolic process Chloroplast
+Cre17.g743897 PRX7 redox.peroxiredoxin.BAS1;redox.peroxiredoxin 21.5.1;21.5 oxidation-reduction process;peroxiredoxin activity;cell redox homeostasis;oxidoreductase activity Secretory pathway
+Cre02.g090850 CLPB3 protein.folding.chaperones and co-chaperones.HSP100s;stress.abiotic.heat 29.6.2.5;20.2.1 protein metabolic process;ATPase activity;ATP binding Chloroplast
+Cre02.g147850 HSLU2 protein.folding.chaperones and co-chaperones.HSP100s 29.6.2.5 peptidase activity, acting on L-amino acid peptides;ATPase activity;HslUV protease complex;cytoplasm;ATP binding Mitochondrion
+Cre12.g484250 DHC1 cell.motility.eukaryotes.axonemal dyneins.inner arm.monomeric species;cell.motility.eukaryotes.axonemal dyneins.inner arm 31.6.1.4.2.1;31.6.1.4.2 dynein complex;ATPase activity;microtubule-based movement;ATP binding;microtubule motor activity
+Cre12.g513750 GRX1 redox.glutaredoxins 21.4 cell redox homeostasis;protein disulfide oxidoreductase activity;electron carrier activity
+Cre16.g659950 PRPS5 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit.S5 29.2.1.1.1.1.5 translation;ribosome;structural constituent of ribosome;RNA binding Chloroplast
+Cre17.g745697 signalling.lipids;stress.biotic;major CHO metabolism.synthesis 30.9;20.1;2.1
+Cre16.g680230 SEC61G protein.targeting.secretory pathway.unspecified 29.3.4.99 membrane;intracellular protein transport;protein targeting
+Cre12.g489153 RPL31 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L31 29.2.1.2.2.31 translation;ribosome;intracellular;structural constituent of ribosome
+Cre03.g193800 TSN1 protein.aa activation.asparagine-tRNA ligase 29.1.22 tRNA aminoacylation for protein translation;ATP binding;aminoacyl-tRNA ligase activity;nucleotide binding
+Cre13.g562550 ARH1 PS.lightreaction.other electron carrier (ox/red).ferredoxin reductase 1.1.5.3 oxidation-reduction process;oxidoreductase activity Mitochondrion
+Cre03.g181300 SHKG1 amino acid metabolism.synthesis.aromatic aa.chorismate.5-enolpyruvylshikimate-3-phosphate synthase 13.1.6.1.6 transferase activity, transferring alkyl or aryl (other than methyl) groups Chloroplast
+Cre12.g485200 minor CHO metabolism.sugar alcohols 3.3 protein binding
+Cre14.g618950 Secretory pathway
+Cre06.g284100 RHP1 transport.ammonium;PS.carbon concentrating mechanism.algal 34.5;1.5.3 ammonium transmembrane transport;membrane;ammonium transport;ammonium transmembrane transporter activity
+Cre02.g120100 RBCS1 PS.calvin cycle.rubisco small subunit 1.3.2 Chloroplast
+Cre02.g120150 RBCS2 PS.calvin cycle.rubisco small subunit 1.3.2 Chloroplast
+Cre01.g032600 HPAT1 Secretory pathway
+Cre02.g092050 MCP6 transport.metabolite transporters at the mitochondrial membrane 34.9
+Cre07.g326050 KIL8 cell.organisation 31.1 microtubule binding;microtubule-based movement;ATP binding;microtubule motor activity Mitochondrion
+Cre09.g396363 TIM14 protein.targeting.mitochondria;stress.abiotic.heat 29.3.2;20.2.1 Mitochondrion
+Cre06.g254600 Mitochondrion
+Cre01.g038550 SQD2 lipid metabolism.glycolipid synthesis.sulfolipid synthase 11.10.4 Chloroplast
+Cre09.g413750 amino acid metabolism.degradation.branched chain group.shared;amino acid metabolism.synthesis.glutamate family.arginine.acetylornithine aminotransferase;amino acid metabolism.synthesis.central amino acid metabolism.alanine.alanine-glyoxylate aminotransferase 13.2.4.1;13.1.2.3.4;13.1.1.3.11 pyridoxal phosphate binding;transaminase activity Mitochondrion
+Cre17.g738200
+Cre17.g728100 hormone metabolism.auxin.synthesis-degradation 17.2.1 hydrolase activity;metabolic process Secretory pathway
+Cre06.g310100 signalling.MAP kinases;protein.postranslational modification 30.6;29.4 protein phosphorylation;protein kinase activity
+Cre02.g077300 NOP1 protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications.methylotransferases;RNA.processing 29.2.2.3.3;27.1 methyltransferase activity;tRNA processing;rRNA processing;RNA binding
+Cre07.g356400 POC7 cell.motility.eukaryotes.basal bodies 31.6.1.1
+Cre06.g308950
+Cre12.g537000 receptor activity Secretory pathway
+Cre01.g005050 membrane Secretory pathway
+Cre17.g702250 Chloroplast
+Cre06.g295400 MCP11 transport.metabolite transporters at the mitochondrial membrane 34.9
+Cre07.g332150
+Cre14.g618050 PLAP3 cell.organisation 31.1 Chloroplast
+Cre16.g672300 RNA.regulation of transcription.high mobility group family (HMG) 27.3.53 Chloroplast
+Cre12.g492750 starch binding Chloroplast
+Cre02.g106600 RPS19 protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S19 29.2.1.2.1.19 translation;ribosome;structural constituent of ribosome
+Cre12.g546050 DXR1 secondary metabolism.isoprenoids.non-mevalonate pathway.DXR 16.1.1.2 NADPH binding;oxidation-reduction process;metal ion binding;1-deoxy-D-xylulose-5-phosphate reductoisomerase activity;isoprenoid biosynthetic process;protein binding Chloroplast
+Cre02.g073850 CGL54 PS.lightreaction.photosystem II.biogenesis 1.1.1.3 photosystem II assembly Chloroplast.Stroma.Thylakoid.Lumen
+Cre09.g387875 IPY3 nucleotide metabolism.phosphotransfer and pyrophosphatases.misc 23.4.99 phosphate-containing compound metabolic process;cytoplasm;inorganic diphosphatase activity;magnesium ion binding
+Cre02.g113450
+Cre11.g468350 Mitochondrion
+Cre01.g032300 GBP1 DNA.unspecified 28.99 nucleic acid binding
+Cre03.g211409 Mitochondrion
+Cre11.g467759 Chloroplast
+Cre12.g510850 CGL73 Chloroplast
+Cre03.g180700
+Cre02.g105650 LPA2 PS.lightreaction.photosystem II.biogenesis 1.1.1.3 Chloroplast.Stroma.Thylakoid.Membrane
+Cre02.g110750 LHCB7 PS.lightreaction.photosystem II.LHC-II 1.1.1.1 membrane;photosynthesis, light harvesting Chloroplast
+Cre17.g726750 SHKA1 amino acid metabolism.synthesis.aromatic aa.chorismate.3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 13.1.6.1.1 aromatic amino acid family biosynthetic process;3-deoxy-7-phosphoheptulonate synthase activity Chloroplast
+Cre05.g240850 THIC Co-factor and vitamine metabolism.thiamine 18.2 iron-sulfur cluster binding;thiamine biosynthetic process Chloroplast
+Cre16.g652750 FMO10 misc.oxidases - copper, flavone etc 26.7 oxidation-reduction process;NADP binding;flavin adenine dinucleotide binding;N,N-dimethylaniline monooxygenase activity
+Cre16.g675300 PHT8 transport.phosphate;transport.sugars 34.7;34.2 transmembrane transport;integral component of membrane Chloroplast
+Cre01.g024100 Mitochondrion
+Cre14.g614950 MRPS2 translation;ribosome;intracellular;structural constituent of ribosome Secretory pathway
+Cre02.g083950 PSRP3 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit.PSRP3 29.2.1.1.1.1.83 translation;ribosome;structural constituent of ribosome Chloroplast
+Cre12.g517100 secondary metabolism.flavonoids.chalcones 16.8.2 intramolecular lyase activity Chloroplast
+Cre14.g626200 PFH7 misc.oxidases - copper, flavone etc 26.7 oxidation-reduction process;oxidoreductase activity Secretory pathway
+Cre07.g329000 CPLD47 PS.lightreaction.photosystem II.biogenesis 1.1.1.3 Chloroplast.Stroma.Thylakoid.Membrane
+Cre05.g240300 Chloroplast
+Cre03.g146527 GSD1 amino acid metabolism.synthesis.glutamate family.proline.delta 1-pyrroline-5-carboxylate synthetase;amino acid metabolism.synthesis.glutamate family.proline 13.1.2.2.1;13.1.2.2 oxidation-reduction process;oxidoreductase activity;metabolic process Chloroplast
+Cre17.g715250 BCC1 Co-factor and vitamine metabolism.biotin;lipid metabolism.FA synthesis and FA elongation.acetyl CoA carboxylation.heteromeric complex.biotin carboxyl carrier protein;lipid metabolism.FA synthesis and FA elongation.acetyl CoA carboxylation 18.6;11.1.1.2.3;11.1.1 Chloroplast
+Cre07.g339700 SUFC transport.ABC transporters and multidrug resistance systems;protein.assembly and cofactor ligation 34.16;29.8 ATPase activity;ATP binding Chloroplast
+Cre07.g353230 minor CHO metabolism.others 3.5 Mitochondrion
+Cre12.g544600 Secretory pathway
+Cre06.g260200 MCP18 transport.metabolite transporters at the mitochondrial membrane 34.9
+Cre12.g510750 Mitochondrion
+Cre10.g446350 CGLD14 PS.lightreaction.photosystem II.PSII polypeptide subunits 1.1.1.2 extrinsic component of membrane;photosynthesis;photosystem II oxygen evolving complex;photosystem II;calcium ion binding Chloroplast
+Cre03.g151200 CGLD16 Chloroplast
+Cre16.g679250 ELIP1 PS.lightreaction.unspecified 1.1.99 Chloroplast
+Cre06.g296850 FAP81
+Cre06.g289550 RPL32 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L32 29.2.1.2.2.32 translation;ribosome;intracellular;structural constituent of ribosome
+Cre17.g731850 misc.nitrilases, nitrile lyases, berberine bridge enzymes, reticuline oxidases, troponine reductases;misc.short chain dehydrogenase/reductase (SDR) 26.8;26.22 Mitochondrion
+Cre14.g619950
+Cre11.g467700 UROD1 tetrapyrrole synthesis.uroporphyrinogen decarboxylase 19.7 porphyrin-containing compound biosynthetic process;uroporphyrinogen decarboxylase activity Chloroplast
+Cre02.g096400
+Cre12.g485850 CPLD64 Chloroplast
+Cre17.g705400 POA1 protein.degradation.ubiquitin.proteasom 29.5.11.20 proteolysis involved in cellular protein catabolic process;proteasome core complex, alpha-subunit complex;ubiquitin-dependent protein catabolic process;proteasome core complex;threonine-type endopeptidase activity;endopeptidase activity
+Cre11.g479050 FKB15-1 cell.cycle.peptidylprolyl isomerase;protein.folding.immunophilins (IMM).FKBPs 31.3.1;29.6.3.1 protein folding Secretory pathway
+Cre12.g537581 nucleotide metabolism.synthesis.purine.AICAR transformylase and IMP synthase 23.1.2.9 purine nucleotide biosynthetic process;phosphoribosylaminoimidazolecarboxamide formyltransferase activity;IMP cyclohydrolase activity Chloroplast
+Cre07.g325720 intracellular signal transduction;phosphorus-oxygen lyase activity;cyclic nucleotide biosynthetic process Chloroplast
+Cre02.g103100 misc.short chain dehydrogenase/reductase (SDR) 26.22 Secretory pathway
+Cre06.g303300 CYN37 cell.cycle.peptidylprolyl isomerase;protein.folding.immunophilins (IMM).cyclophilins 31.3.1;29.6.3.2 protein folding;peptidyl-prolyl cis-trans isomerase activity
+Cre02.g099800 Mitochondrion
+Cre04.g212300 protein.postranslational modification 29.4 protein dephosphorylation;protein binding;protein serine/threonine phosphatase activity;phosphoprotein phosphatase activity;catalytic activity Secretory pathway
+Cre17.g706850 transport.misc;protein.degradation.serine protease 34.99;29.5.5 integral component of membrane;retrograde vesicle-mediated transport, Golgi to ER Secretory pathway
+Cre13.g578150 RRA1 C1-metabolism 25
+Cre06.g261450 RNA.regulation of transcription.high mobility group family (HMG) 27.3.53
+Cre09.g389763 HPAT4
+Cre-1.g2716997 rps3 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit.S3 29.2.1.1.1.1.3 Chloroplast
+Cre16.g674400 Secretory pathway
+Cre17.g702850 CAV5 transport.calcium 34.21 transmembrane transport;membrane;ion transport;ion channel activity Mitochondrion
+Cre17.g702500 TAB2 PS.lightreaction.photosystem I.biogenesis 1.1.2.3 Chloroplast
+Cre02.g094100 NRX1 not assigned.no ontology.DC1 domain containing protein;redox.thioredoxin 35.1.26;21.1
+Cre03.g156600 Chloroplast
+Cre14.g629000 AXT1 Chloroplast
+Cre12.g523300 GTR22 protein.glycosylation 29.7 integral component of membrane;protein glycosylation;endoplasmic reticulum;dolichyl-diphosphooligosaccharide-protein glycotransferase activity Secretory pathway
+Cre01.g001750 TIG1 protein.folding.prefoldin and trigger factor;protein.folding 29.6.1;29.6 protein transport;protein folding Chloroplast.Stroma
+Cre01.g050100 DPD1 amino acid metabolism.synthesis.aspartate family.lysine.diaminopimelate decarboxylase 13.1.3.5.5 catalytic activity Chloroplast
+Cre10.g434250 protein.targeting.mitochondria 29.3.2
+Cre10.g454734 LHCP2 PS.lightreaction.photosystem I.LHC-I;PS.lightreaction.photosystem II.LHC-II 1.1.2.1;1.1.1.1 Chloroplast
+Cre01.g026450 SRS1 RNA.processing.splicing 27.1.1 nucleic acid binding
+Cre13.g604150 transport.ABC transporters and multidrug resistance systems 34.16 transmembrane transport;ATPase activity, coupled to transmembrane movement of substances;ATPase activity;integral component of membrane;transport;ATP binding Mitochondrion
+Cre10.g458450 GPX5 redox.ascorbate and glutathione.glutathione;redox.ascorbate and glutathione 21.2.2;21.2 oxidation-reduction process;response to oxidative stress;glutathione peroxidase activity
+Cre06.g289150 MTP5 transport.metal 34.12 transmembrane transport;integral component of membrane;cation transmembrane transporter activity;cation transport Mitochondrion
+Cre08.g359350 CARB1 amino acid metabolism.degradation.branched chain group.leucine;lipid metabolism.FA synthesis and FA elongation.acetyl CoA carboxylation.heteromeric complex.biotin carboxylase;lipid metabolism.FA synthesis and FA elongation.acetyl CoA carboxylation 13.2.4.4;11.1.1.2.4;11.1.1 Chloroplast
+Cre12.g553678 Chloroplast
+Cre09.g392616 Secretory pathway
+Cre09.g416850 Mitochondrion
+Cre16.g694850 NGS1 amino acid metabolism.synthesis.glutamate family.arginine.acetylglutamate kinase;amino acid metabolism.synthesis.glutamate family.arginine 13.1.2.3.2;13.1.2.3 arginine biosynthetic process;glutamate N-acetyltransferase activity Chloroplast
+Cre06.g273600 RPS27A protein.degradation.ubiquitin;protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S27 29.5.11;29.2.1.2.1.27 translation;ribosome;protein binding;structural constituent of ribosome
+Cre05.g244550 protein phosphorylation;ATP binding;protein kinase activity
+Cre01.g004500 LEU1 secondary metabolism.sulfur-containing.glucosinolates.synthesis.aliphatic.methylthioalkylmalate isomerase large subunit (MAM-IL);amino acid metabolism.synthesis.branched chain group.leucine specific.3-isopropylmalate dehydrogenase 16.5.1.1.1.3;13.1.4.4.3 metabolic process Chloroplast
+Cre13.g603700 DII4 cell.motility.eukaryotes.axonemal dyneins.inner arm.monomeric species;cell.organisation.cytoskeleton.actin.Actin;cell.organisation 31.6.1.4.2.1;31.1.1.1.1;31.1
+Cre-1.g2716986 chlN tetrapyrrole synthesis.protochlorophyllide reductase 19.14 Chloroplast
+Cre09.g389689 ASD1 amino acid metabolism.synthesis.aspartate family.misc.homoserine.aspartate semialdehyde dehydrogenase 13.1.3.6.1.2 oxidation-reduction process;NAD binding;protein dimerization activity;oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor;cellular amino acid biosynthetic process;cytoplasm;N-acetyl-gamma-glutamyl-phosphate reductase activity Chloroplast
+Cre16.g690130 Chloroplast
+Cre12.g527050 transport.misc;protein.targeting.secretory pathway.unspecified;DNA.unspecified 34.99;29.3.4.99;28.99
+Cre17.g712400 TERC development.unspecified;PS.lightreaction.photosystem II.biogenesis 33.99;1.1.1.3 integral component of membrane Chloroplast.Stroma.Thylakoid.Membrane
+Cre04.g225400 minor CHO metabolism.sugar alcohols 3.3 Chloroplast
+Cre01.g032750 Chloroplast
+Cre17.g715300 PKD2 cell.motility.eukaryotes.flagellar membrane proteins 31.6.1.8
+Cre06.g278800 RNA.regulation of transcription.basic helix-loop-helix family (bHLH) 27.3.6 integral component of membrane Mitochondrion
+Cre06.g286000 Mitochondrion
+Cre06.g262850 RAB23 signalling.G-proteins;minor CHO metabolism.others 30.5;3.5 GTP binding
+Cre11.g467590 protein.postranslational modification 29.4 Chloroplast
+Cre01.g013350 Chloroplast
+Cre01.g037700 FAD3 lipid metabolism.FA desaturation.desaturase 11.2.1 lipid metabolic process Chloroplast
+Cre10.g425850
+Cre04.g217915 NAR1.3 transport.nitrate;PS.carbon concentrating mechanism.algal 34.4;1.5.3 membrane;transport;transporter activity Mitochondrion
+Cre12.g554800 PRK1 PS.calvin cycle.PRK 1.3.12 kinase activity;metabolic process;ATP binding Chloroplast
+Cre10.g437500 TOM7 protein.targeting.mitochondria 29.3.2 protein import into mitochondrial matrix;mitochondrial outer membrane translocase complex
+Cre10.g440400 Mitochondrion
+Cre05.g232150 GDH2 N-metabolism.N-degradation.glutamate dehydrogenase 12.3.1 oxidation-reduction process;oxidoreductase activity;cellular amino acid metabolic process Mitochondrion
+Cre11.g478850 Chloroplast
+Cre10.g423300 protein.degradation 29.5
+Cre12.g503650 Mitochondrion
+Cre04.g223450
+Cre16.g679500 NUOB8 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).localisation not clear;mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.2;9.1.1 Mitochondrion
+Cre16.g649300 Secretory pathway
+Cre09.g388467 GDI1 signalling.G-proteins;minor CHO metabolism.others 30.5;3.5
+Cre12.g526800 GND1 OPP.oxidative PP.6-phosphogluconate dehydrogenase 7.1.3 oxidation-reduction process;NADP binding;pentose-phosphate shunt;phosphogluconate dehydrogenase (decarboxylating) activity Chloroplast
+Cre14.g612450 PRPL15 protein.synthesis.ribosomal protein.prokaryotic.non-organellar.50S subunit;protein.synthesis.ribosomal protein.prokaryotic.unknown organellar.50S subunit.L15;protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit.L15 29.2.1.1.4.2;29.2.1.1.3.2.15;29.2.1.1.1.2.15 large ribosomal subunit;translation;structural constituent of ribosome Chloroplast
+Cre11.g468450 DLE2 cell.motility.eukaryotes.axonemal dyneins.inner arm.monomeric species;cell.motility.eukaryotes.deflagellation;cell.motility.eukaryotes.basal bodies;cell.organisation;DNA.synthesis/chromatin structure 31.6.1.4.2.1;31.6.1.2;31.6.1.1;31.1;28.1
+Cre03.g202400 MCP10 transport.metabolite transporters at the mitochondrial membrane 34.9 Chloroplast
+Cre07.g332300 GWD2 major CHO metabolism.degradation.starch.glucan water dikinase 2.2.2.3 phosphorylation;kinase activity;ATP binding Chloroplast
+Cre06.g293700 MRPL7 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit.L12 29.2.1.1.1.2.12 translation;structural constituent of ribosome Mitochondrion
+Cre-2.g801484 cob Mitochondrion
+Cre10.g434600 FAP148 development.unspecified;cell.motility.eukaryotes.flagellar associated proteins;signalling.G-proteins 33.99;31.6.1.10;30.5 transmembrane transport;membrane;ion transport;protein binding;ion channel activity
+Cre02.g143450 Chloroplast
+Cre09.g387000 CGL34 Chloroplast
+Cre17.g704600 Chloroplast
+Cre09.g392500
+Cre07.g316000 protein.targeting.nucleus 29.3.1 transport;intracellular Mitochondrion
+Cre03.g213425 COX23 mitochondrial electron transport / ATP synthesis.cytochrome c oxidase 9.7
+Cre03.g154550 PCR1 amino acid metabolism.degradation.glutamate family.arginine;amino acid metabolism.synthesis.glutamate family.proline.pyrroline-5-carboxylate reductase 13.2.2.3;13.1.2.2.2 oxidation-reduction process;proline biosynthetic process;pyrroline-5-carboxylate reductase activity Chloroplast
+Cre16.g685700
+Cre15.g636050 CPLD31 Chloroplast
+Cre01.g054850 Chloroplast
+Cre01.g001100
+Cre08.g367600 OASTL1 amino acid metabolism.synthesis.serine-glycine-cysteine group.cysteine.OASTL 13.1.5.3.1
+Cre08.g358552 Mitochondrion
+Cre02.g143200 TSA1 protein.aa activation.alanine-tRNA ligase 29.1.7 tRNA aminoacylation;ligase activity, forming aminoacyl-tRNA and related compounds;alanyl-tRNA aminoacylation;ATP binding;alanine-tRNA ligase activity;nucleic acid binding;nucleotide binding Secretory pathway
+Cre16.g691552 NDA1 mitochondrial electron transport / ATP synthesis.NADH-DH (type II).external;mitochondrial electron transport / ATP synthesis.NADH-DH.type II.internal matrix;mitochondrial electron transport / ATP synthesis.NADH-DH (type II).internal matrix 9.2.2;9.2.1.4;9.2.1 oxidation-reduction process;oxidoreductase activity Mitochondrion
+Cre03.g195388 Chloroplast
+Cre04.g214150 THI4 Co-factor and vitamine metabolism.thiamine 18.2 Chloroplast
+Cre17.g702650 Mitochondrion
+Cre10.g420750 RPL30 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L30 29.2.1.2.2.30 translation;ribosome;intracellular;structural constituent of ribosome
+Cre10.g456200 RPS24 protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S24 29.2.1.2.1.24 translation;ribosome;intracellular;structural constituent of ribosome
+Cre14.g619350 ATP binding Mitochondrion
+Cre10.g433400 mitochondrial pyruvate transport;mitochondrial inner membrane
+Cre17.g697650 protein.degradation.serine protease;protein.degradation 29.5.5;29.5 serine-type exopeptidase activity;serine-type peptidase activity;proteolysis;serine-type endopeptidase activity
+Cre06.g310350
+Cre13.g565800 UPT1 minor CHO metabolism.others;cell wall.cell wall proteins.RGP 3.5;10.5.5 cellulose biosynthetic process;intramolecular transferase activity
+Cre11.g467553 protein.synthesis.elongation 29.2.4 GTP binding Mitochondrion
+Cre07.g334900 Chloroplast
+Cre10.g457331 cell.motility.eukaryotes.flagellar associated proteins 31.6.1.10
+Cre10.g439600 development.unspecified;minor CHO metabolism.others 33.99;3.5
+Cre01.g052400 CCB3 PS.lightreaction.cytochrome b6/f 1.1.3 membrane Chloroplast
+Cre06.g260250 CEM1 PS.carbon concentrating mechanism.algal 1.5.3 integral component of membrane Mitochondrion
+Cre13.g570851 Secretory pathway
+Cre06.g257601 PRX1 redox.peroxiredoxin.BAS1 21.5.1 oxidation-reduction process;peroxiredoxin activity;oxidoreductase activity Chloroplast
+Cre12.g550400 GRX2 redox.glutaredoxins 21.4 cell redox homeostasis;protein disulfide oxidoreductase activity;electron carrier activity
+Cre01.g020918 PREP1 protein.degradation.metalloprotease;protein.degradation 29.5.7;29.5 proteolysis Chloroplast
+Cre08.g375550 methyltransferase activity;metabolic process
+Cre01.g053600 MRPL27 protein.synthesis.ribosomal protein.unknown.large subunit.L27 29.2.1.99.2.27 translation;ribosome;intracellular;structural constituent of ribosome
+Cre-2.g801494 nad4 Mitochondrion
+Cre16.g673650 LHCB5 PS.lightreaction.photosystem II.LHC-II 1.1.1.1 membrane;photosynthesis, light harvesting Chloroplast
+Cre02.g078966 FTSH9 protein.degradation.metalloprotease 29.5.7 ATPase activity;proteolysis;ATP binding;metalloendopeptidase activity Chloroplast
+Cre01.g003550 misc.rhodanese 26.23 Chloroplast
+Cre03.g180300 SIR3 misc.cytochrome P450;S-assimilation.sulfite redox 26.10;14.3 oxidation-reduction process;oxidoreductase activity;FMN binding
+Cre03.g196900 cell.vesicle transport;protein.targeting.secretory pathway.ER;DNA.unspecified 31.4;29.3.4.1;28.99 endoplasmic reticulum membrane
+Cre03.g176500 Mitochondrion
+Cre16.g666550 SOUL3 redox.heme 21.3 Chloroplast
+Cre08.g358580 CMP1 nucleotide metabolism.synthesis.pyrimidine.carbamoyl phosphate synthetase 23.1.1.1 Chloroplast
+Cre06.g250450 transport.misc 34.99 membrane Secretory pathway
+Cre09.g415700 CAH3 TCA / organic transformation.carbonic anhydrases;PS.carbon concentrating mechanism 8.3;1.5 Chloroplast
+Cre07.g352350 FHL3 protein.degradation.metalloprotease 29.5.7 proteolysis;ATP binding;metalloendopeptidase activity Mitochondrion
+Cre01.g004450 CPLD42 Chloroplast
+Cre03.g178450 CPN10 protein.co-chaperones;protein.folding.chaperones and co-chaperones.co-chaperones;protein.folding;protein.postranslational modification 29.9;29.6.2.6;29.6;29.4 protein folding;cytoplasm Mitochondrion
+Cre01.g021500 transport.misc 34.99 Secretory pathway
+Cre03.g188250 STA6 major CHO metabolism.synthesis.starch.AGPase 2.1.2.1 nucleotidyltransferase activity;biosynthetic process Chloroplast
+Cre17.g722200 MRPL11 protein.synthesis.ribosomal protein.prokaryotic.non-organellar.50S subunit;protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit.L11 29.2.1.1.4.2;29.2.1.1.1.2.11 translation;ribosome;structural constituent of ribosome
+Cre08.g365450
+Cre-1.g2717056 rps19 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit.S19 29.2.1.1.1.1.19 Chloroplast
+Cre11.g468353 voltage-gated potassium channel complex;potassium ion transport;voltage-gated potassium channel activity Chloroplast
+Cre12.g492700 FAS1 Mitochondrion
+Cre05.g237050 CGLD27 Chloroplast
+Cre09.g392319 VSP6 Secretory pathway
+Cre08.g370500 glutathione biosynthetic process;gamma-glutamylcyclotransferase activity Chloroplast
+Cre08.g385800
+Cre05.g246900 Mitochondrion
+Cre03.g182551 PCY1 PS.lightreaction.other electron carrier (ox/red).plastocyanin 1.1.5.1 Chloroplast
+Cre02.g142351 hormone metabolism.abscisic acid.synthesis-degradation 17.1.1 cell redox homeostasis Chloroplast
+Cre02.g091850 amino acid metabolism.degradation.aromatic aa.tryptophan;lipid metabolism.lipid degradation.beta-oxidation.enoyl CoA hydratase 13.2.6.3;11.9.4.3 metabolic process;catalytic activity Mitochondrion
+Cre16.g652550 PRPL24 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit.L24 29.2.1.1.1.2.24 translation;ribosome;intracellular;structural constituent of ribosome Chloroplast
+Cre06.g261300 Chloroplast
+Cre06.g293950 SHMT2 C1-metabolism.glycine hydroxymethyltransferase;C1-metabolism;PS.photorespiration.serine hydroxymethyltransferase 25.1;25;1.2.5 transferase activity
+Cre-1.g2717058 rpl14 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit.L14 29.2.1.1.1.2.14 Chloroplast
+Cre10.g423500 HMO1 tetrapyrrole synthesis.heme oxygenase 19.21 oxidation-reduction process;heme oxidation;heme oxygenase (decyclizing) activity Chloroplast
+Cre04.g217910 misc.rhodanese 26.23 Chloroplast
+Cre06.g288650 lipid metabolism.FA desaturation.omega 6 desaturase 11.2.4 lipid metabolic process Chloroplast
+Cre05.g244900 Mitochondrion
+Cre11.g467755 signalling.light;misc.short chain dehydrogenase/reductase (SDR) 30.11;26.22
+Cre16.g689983
+Cre17.g722800 MPPA1 protein.degradation;protein.targeting.mitochondria 29.5;29.3.2 Mitochondrion
+Cre06.g279400 protein.degradation.serine protease;protein.degradation 29.5.5;29.5 proteolysis;serine-type carboxypeptidase activity Secretory pathway
+Cre06.g255100 Chloroplast
+Cre06.g254500 Chloroplast
+Cre12.g510950
+Cre06.g284600 RBD2 Chloroplast
+Cre12.g501200 SKP1 protein.degradation.ubiquitin.E3.SCF.SKP 29.5.11.4.3.1 ubiquitin-dependent protein catabolic process
+Cre01.g027800 ATPVH transport.p- and v-ATPases.H+-transporting two-sector ATPase.subunit H;transport.p- and v-ATPases.H+-transporting two-sector ATPase 34.1.1.6;34.1.1 proton-transporting ATPase activity, rotational mechanism;hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances;ATP hydrolysis coupled proton transport;vacuolar proton-transporting V-type ATPase, V1 domain
+Cre17.g703200 transport.misc;protein.targeting.secretory pathway.unspecified;DNA.unspecified 34.99;29.3.4.99;28.99
+Cre01.g033400 TIM9 protein.targeting.mitochondria 29.3.2
+Cre06.g269950 CDC48 cell.division;protein.degradation.ubiquitin.proteasom 31.2;29.5.11.20 four-way junction helicase activity;DNA recombination;DNA repair;ATP binding
+Cre06.g296500
+Cre13.g589167 Chloroplast
+Cre06.g275100 signalling.G-proteins;protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications.snoRNPs;RNA.RNA binding 30.5;29.2.2.3.1;27.4 nucleic acid binding
+Cre08.g382300 CCB4 protein.assembly and cofactor ligation 29.8 Chloroplast
+Cre05.g245102 CGL3
+Cre04.g221550 Chloroplast
+Cre01.g066552 redox.thioredoxin 21.1 cell redox homeostasis;protein disulfide oxidoreductase activity;glycerol ether metabolic process Chloroplast
+Cre01.g042550 ER membrane protein complex Secretory pathway
+Cre10.g464650 CGL36 Chloroplast
+Cre07.g324200 BTA1 lipid metabolism.exotics (steroids, squalene etc) 11.8
+Cre06.g259850 PRPL29 protein.synthesis.ribosomal protein.prokaryotic.non-organellar.50S subunit 29.2.1.1.4.2 Chloroplast
+Cre09.g387800 FER1 metal handling.binding, chelation and storage 15.2 ferric iron binding;cellular iron ion homeostasis;iron ion transport Chloroplast
+Cre06.g278222 development.unspecified;signalling.G-proteins;signalling.receptor kinases.misc;protein.postranslational modification 33.99;30.5;30.2.99;29.4 protein binding
+Cre03.g174750 CYN26-2 cell.cycle.peptidylprolyl isomerase;protein.folding.immunophilins (IMM).cyclophilins 31.3.1;29.6.3.2 protein folding;peptidyl-prolyl cis-trans isomerase activity;protein peptidyl-prolyl isomerization Chloroplast
+Cre04.g224750 VAM1 cell.vesicle transport 31.4 vesicle-mediated transport;integral component of membrane Mitochondrion
+Cre03.g172850 OASTL3 amino acid metabolism.synthesis.serine-glycine-cysteine group.cysteine.OASTL 13.1.5.3.1 Chloroplast
+Cre08.g373346 Secretory pathway
+Cre12.g485900
+Cre09.g388800 GDH1 N-metabolism.N-degradation.glutamate dehydrogenase 12.3.1 oxidation-reduction process;oxidoreductase activity;cellular amino acid metabolic process Mitochondrion
+Cre03.g145547 CBR1 redox.misc;N-metabolism.nitrate metabolism.NR 21.99;12.1.1 oxidation-reduction process;oxidoreductase activity Secretory pathway
+Cre03.g145647
+Cre12.g545177 cell.division 31.2 translation Mitochondrion
+Cre13.g604300
+Cre14.g616600 FZL signalling.G-proteins;minor CHO metabolism.others 30.5;3.5 thiamine biosynthetic process;thiamine-phosphate diphosphorylase activity Mitochondrion
+Cre16.g684300 YGG3 membrane Chloroplast
+Cre02.g105800 Secretory pathway
+Cre13.g571500 CST2
+Cre17.g696600 FMR1 Mitochondrion
+Cre12.g530100 CGL83
+Cre09.g407650 Mitochondrion
+Cre14.g617300 PSL3 protein.degradation.aspartate protease 29.5.4 integral component of membrane;aspartic-type endopeptidase activity Chloroplast
+Cre12.g558050
+Cre11.g477300 FAP8 protein.postranslational modification 29.4 Mitochondrion
+Cre13.g585301 CPLD55 lipid metabolism.glycolipid synthesis.MGDG synthase 11.10.1 transferase activity, transferring hexosyl groups Secretory pathway
+Cre-1.g2717059 rpl5 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit.L5 29.2.1.1.1.2.5 Chloroplast
+Cre07.g315150 RBD1 protein.assembly and cofactor ligation;PS.lightreaction.photosystem II.biogenesis 29.8;1.1.1.3 iron ion binding Chloroplast.Stroma.Thylakoid.Membrane
+Cre17.g702200 ANK29 cell.organisation;RNA.regulation of transcription.AtSR transcription factor family 31.1;27.3.39 Chloroplast
+Cre06.g278210 GPM1 glycolysis.plastid branch.phosphoglucomutase (PGM);glycolysis.cytosolic branch.phosphoglucomutase (PGM) 4.2.2;4.1.2 organic substance metabolic process;intramolecular transferase activity, phosphotransferases;carbohydrate metabolic process Chloroplast
+Cre01.g042200 Chloroplast
+Cre03.g197650 Chloroplast
+Cre02.g106200 transport.metabolite transporters at the envelope membrane 34.8 transmembrane transport Secretory pathway
+Cre12.g504200 RPS23 protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S23 29.2.1.2.1.23 translation;ribosome;intracellular;structural constituent of ribosome
+Cre12.g503950 transport.misc;protein.targeting.secretory pathway.unspecified 34.99;29.3.4.99
+Cre16.g658900 TRP10 transport.misc 34.99
+Cre10.g438550 TATA protein.targeting.chloroplast 29.3.3 protein transport;protein transporter activity Chloroplast
+Cre14.g633000 ERV1 oxidation-reduction process;thiol oxidase activity
+Cre11.g477850 TXC1 RNA.regulation of transcription.Zn-finger(CCHC);RNA.regulation of transcription.silencing group 27.3.73;27.3.70 posttranscriptional gene silencing by RNA;transcription cofactor activity
+Cre02.g118850 fatty-acyl-CoA binding
+Cre12.g519300 TEF9 PS.lightreaction.unspecified.TEF 1.1.99.1 Chloroplast
+Cre09.g396252 GSR2 redox.ascorbate and glutathione.glutathione 21.2.2 oxidation-reduction process;cell redox homeostasis;oxidoreductase activity Mitochondrion
+Cre01.g030200 FAP6 protein.postranslational modification 29.4 protein dephosphorylation;protein serine/threonine phosphatase activity;catalytic activity
+Cre16.g679300 CGL139 Chloroplast
+Cre11.g468400 Chloroplast
+Cre08.g372950 IDS1 secondary metabolism.isoprenoids.non-mevalonate pathway.HDR 16.1.1.7 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase activity;dimethylallyl diphosphate biosynthetic process;metal ion binding;isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway Chloroplast
+Cre01.g021251 ARG7 amino acid metabolism.synthesis.glutamate family.arginine.argininosuccinate lyase;amino acid metabolism.synthesis.glutamate family.arginine 13.1.2.3.23;13.1.2.3 arginine biosynthetic process via ornithine;argininosuccinate lyase activity Chloroplast
+Cre01.g019600 Chloroplast
+Cre02.g112650
+Cre10.g459200 PMA2 transport.p- and v-ATPases.H+-exporting ATPase;transport.p- and v-ATPases 34.1.2;34.1 metal ion binding;nucleotide binding
+Cre01.g029300 TPIC1 glycolysis.cytosolic branch.triosephosphate isomerase (TPI);PS.calvin cycle.TPI 4.1.7;1.3.5 metabolic process;triose-phosphate isomerase activity Chloroplast
+Cre10.g439900 HSP70G protein.folding.chaperones and co-chaperones.HSP70s;stress.abiotic.heat 29.6.2.3;20.2.1 Secretory pathway
+Cre01.g039300 RB47 RNA.processing;PS.lightreaction.photosystem II.biogenesis 27.1;1.1.1.3 RNA binding;nucleic acid binding
+Cre09.g386550 minor CHO metabolism.others;protein.postranslational modification;RNA.regulation of transcription.unclassified 3.5;29.4;27.3.99 GTPase activator activity
+Cre06.g278264 Chloroplast
+Cre12.g525150 Mitochondrion
+Cre07.g318750 PURM nucleotide metabolism.synthesis.purine.AIR synthase 23.1.2.5 Chloroplast
+Cre07.g321400 MAW6 cell.motility.eukaryotes.flagellar associated proteins 31.6.1.10 integral component of membrane Secretory pathway
+Cre06.g259401 methyltransferase activity;metabolic process Chloroplast
+Cre17.g719000 UAP56 protein.synthesis.initiation;DNA.synthesis/chromatin structure;RNA.processing.RNA helicase 29.2.3;28.1;27.1.2 hydrolase activity;ATP binding;DNA binding
+Cre14.g630859 HID1 amino acid metabolism.degradation.branched chain group.valine 13.2.4.3 oxidation-reduction process;NAD binding;phosphogluconate dehydrogenase (decarboxylating) activity Chloroplast
+Cre09.g386400 FAP124 protein.degradation.ubiquitin.E1 29.5.11.2 small protein activating enzyme activity
+Cre17.g738050 AGG4
+Cre02.g095077 Chloroplast
+Cre06.g258800 GP2 cell wall.cell wall proteins.proline rich proteins 10.5.2 Secretory pathway
+Cre13.g568800 NUOB13 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.1 respiratory electron transport chain;oxidoreductase activity, acting on NAD(P)H;mitochondrial inner membrane Mitochondrion
+Cre02.g142146 CGL102 Chloroplast
+Cre12.g512600 RPL18 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L18 29.2.1.2.2.18 translation;ribosome;intracellular;structural constituent of ribosome Chloroplast
+Cre16.g685400 misc.short chain dehydrogenase/reductase (SDR) 26.22 Mitochondrion
+Cre11.g467578 RPL28 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L28 29.2.1.2.2.28 translation;ribosome;intracellular;structural constituent of ribosome
+Cre13.g568650 RPS3A protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S3A 29.2.1.2.1.53 translation;ribosome;intracellular;structural constituent of ribosome
+Cre02.g086100 CGL40 Chloroplast
+Cre01.g004300 ASN1 amino acid metabolism.synthesis.aspartate family.asparagine.asparagine synthetase;amino acid metabolism.synthesis.aspartate family.asparagine 13.1.3.1.1;13.1.3.1 asparagine biosynthetic process;asparagine synthase (glutamine-hydrolyzing) activity Chloroplast
+Cre08.g378550 NUOP4 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.1
+Cre08.g372200 Secretory pathway
+Cre05.g237450 PSRP1 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit.S30A;protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit.S30A 29.2.1.1.1.1.530;29.2.1.1.1.1.0530 primary metabolic process Chloroplast
+Cre16.g650625 MST1 cell.motility.eukaryotes.flagellar membrane proteins 31.6.1.8 serine-type exopeptidase activity;serine-type peptidase activity;proteolysis;serine-type endopeptidase activity Chloroplast
+Cre13.g562501 Mitochondrion
+Cre02.g080250 YGG1 membrane Chloroplast
+Cre09.g402100
+Cre09.g391023 protein.postranslational modification 29.4 hydrolase activity
+Cre09.g416050 AGS1 amino acid metabolism.synthesis.glutamate family.arginine.argininosuccinate synthase;amino acid metabolism.synthesis.glutamate family.arginine 13.1.2.3.22;13.1.2.3 arginine biosynthetic process;ATP binding;argininosuccinate synthase activity Chloroplast
+Cre17.g705900
+Cre06.g251000 Secretory pathway
+Cre09.g386743
+Cre02.g141606 DHC9 cell.motility.eukaryotes.axonemal dyneins.inner arm.monomeric species 31.6.1.4.2.1 dynein complex;microtubule-based movement;microtubule motor activity
+Cre-1.g2716959 atpI PS.lightreaction.ATP synthase 1.1.4 Chloroplast
+Cre02.g108900 CAM6
+Cre17.g698450 C1-metabolism.methylenetetrahydrofolate dehydrogenase and methenyltetrahydrofolate cyclohydrolase 25.5 oxidation-reduction process;folic acid-containing compound biosynthetic process;methylenetetrahydrofolate dehydrogenase (NADP+) activity;catalytic activity
+Cre01.g000900 CPLD20 Chloroplast
+Cre03.g183400 Chloroplast
+Cre16.g677000 HSP70E protein.folding.chaperones and co-chaperones.HSP70s;stress.abiotic.heat 29.6.2.3;20.2.1
+Cre02.g111000 RRA1 Secretory pathway
+Cre03.g190500 GLC2A misc.gluco-, galacto- and mannosidases.alpha-galactosidase;misc.gluco-, galacto- and mannosidases;major CHO metabolism.degradation.starch.starch cleavage 26.3.1;26.3;2.2.2.1 carbohydrate metabolic process;hydrolase activity, hydrolyzing O-glycosyl compounds Secretory pathway
+Cre13.g573351 protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S16 29.2.1.2.1.16 translation;ribosome;structural constituent of ribosome
+Cre10.g443850 protein.degradation.metalloprotease 29.5.7 Chloroplast
+Cre14.g621650 MCT1 lipid metabolism.FA synthesis and FA elongation.acetyl CoA transacylase 11.1.2 Chloroplast
+Cre11.g467527 misc.cytochrome P450;misc.misc2 26.10;26.1 oxidation-reduction process;heme binding;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen;iron ion binding
+Cre06.g271700 protein.degradation.metalloprotease 29.5.7
+Cre12.g498250 RPS17 protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S17 29.2.1.2.1.17 translation;ribosome;intracellular;structural constituent of ribosome
+Cre03.g206800 HXT1 transport.sugars;major CHO metabolism.degradation.starch.transporter 34.2;2.2.2.6 transmembrane transport;integral component of membrane Mitochondrion
+Cre16.g660800 TIM44 protein.targeting.mitochondria 29.3.2 Mitochondrion
+Cre16.g683350 TEH6
+Cre17.g730000 Chloroplast
+Cre12.g555400 CGLD32 Chloroplast
+Cre10.g447100 mitochondrial matrix Mitochondrion
+Cre-1.g2716955 rps4 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit.S4 29.2.1.1.1.1.4 Chloroplast
+Cre01.g028250 GEA1 lipid metabolism.lipid degradation.lipases.acylglycerol lipase 11.9.2.2
+Cre02.g107300 DPS1 amino acid metabolism.synthesis.aspartate family.lysine.dihydrodipicolinate synthase;amino acid metabolism.synthesis.aspartate family.lysine 13.1.3.5.1;13.1.3.5 lyase activity;metabolic process Chloroplast
+Cre12.g559450 protein binding
+Cre07.g338451 FBP1 gluconeogenesis / glyoxylate cycle 6 fructose 1,6-bisphosphate 1-phosphatase activity;gluconeogenesis;glycerol metabolic process
+Cre12.g495850 HBD1 misc.nitrilases, nitrile lyases, berberine bridge enzymes, reticuline oxidases, troponine reductases;misc.short chain dehydrogenase/reductase (SDR);lipid metabolism.FA synthesis and FA elongation.ACP oxoacyl reductase 26.8;26.22;11.1.4 Mitochondrion
+Cre01.g061077 CGL93 amino acid metabolism 13 Chloroplast
+Cre10.g428650 CDPKK1 protein.postranslational modification.kinase;protein.postranslational modification 29.4.1;29.4
+Cre16.g663600 PHT7 transport.phosphate;transport.sugars 34.7;34.2 transmembrane transport;integral component of membrane
+Cre02.g077350 HDH1 amino acid metabolism.synthesis.histidine.histidinol-phosphate aminotransferase;amino acid metabolism.synthesis.histidine 13.1.7.9;13.1.7 oxidation-reduction process;NAD binding;zinc ion binding;histidinol dehydrogenase activity;histidine biosynthetic process
+Cre13.g592200 GSN1 N-metabolism.ammonia metabolism.glutamate synthase.NADH dependent;N-metabolism.ammonia metabolism.glutamate synthase 12.2.1.2;12.2.1 oxidation-reduction process;oxidoreductase activity, acting on the CH-NH2 group of donors;oxidoreductase activity;glutamate synthase activity;metabolic process;nitrogen compound metabolic process;glutamate biosynthetic process Chloroplast
+Cre12.g540500 CGL108 cell.organisation 31.1 peroxisome fission;integral component of peroxisomal membrane
+Cre02.g092350 CYP51G1 hormone metabolism.brassinosteroid.synthesis-degradation.sterols.CYP51 17.3.1.2.3 oxidation-reduction process;heme binding;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen;iron ion binding Secretory pathway
+Cre10.g457650 Chloroplast
+Cre02.g143667 PLPA9 Chloroplast
+Cre17.g696850 hormone metabolism.abscisic acid.induced-regulated-responsive-activated 17.1.3 Mitochondrion
+Cre17.g721450 NSS4 transport.unspecified cations 34.14 transmembrane transport;membrane;transport;transporter activity
+Cre09.g395650
+Cre08.g376450 CPLD36
+Cre11.g479500 PRPL4 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit.L4 29.2.1.1.1.2.4 translation;ribosome;structural constituent of ribosome Chloroplast
+Cre09.g405450 Chloroplast
+Cre09.g397250 FAD5A lipid metabolism.FA desaturation.desaturase 11.2.1 lipid metabolic process Chloroplast
+Cre01.g033550 PDI2 redox.thioredoxin.PDIL;redox.thioredoxin 21.1.1;21.1 cell redox homeostasis;endoplasmic reticulum Secretory pathway
+Cre07.g325500 CHLH1 tetrapyrrole synthesis.magnesium chelatase;tetrapyrrole synthesis.glu-tRNA synthetase 19.10;19.1 magnesium chelatase activity;biosynthetic process Chloroplast
+Cre02.g095111 VSR1 protein.targeting.secretory pathway.vacuole 29.3.4.3 Secretory pathway
+Cre06.g251850
+Cre12.g524300 CGL71 not assigned.no ontology.tetratricopeptide repeat (TPR) 35.1.27 Chloroplast
+Cre01.g014000 Chloroplast
+Cre09.g393358 RNA.regulation of transcription.silencing group 27.3.70
+Cre-1.g2716995 psbL Chloroplast
+Cre12.g535950 NUOS1 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).localisation not clear;mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.2;9.1.1 oxidation-reduction process;iron-sulfur cluster binding;oxidoreductase activity, acting on NAD(P)H;oxidoreductase activity Mitochondrion
+Cre13.g577100 ACP2 lipid metabolism.FA synthesis and FA elongation.ACP protein 11.1.12 Chloroplast
+Cre10.g444550 SPP1A protein.degradation.serine protease;protein.degradation 29.5.5;29.5 peptidase activity;proteolysis Mitochondrion
+Cre07.g350750 PTOX1 PS.lightreaction.cyclic electron flow-chlororespiration 1.1.40 oxidation-reduction process;alternative oxidase activity
+Cre05.g244950 protein.targeting.secretory pathway.ER 29.3.4.1 integral component of membrane;endoplasmic reticulum Secretory pathway
+Cre10.g466850 FKB18 cell.cycle.peptidylprolyl isomerase;protein.folding.immunophilins (IMM).FKBPs 31.3.1;29.6.3.1 protein folding
+Cre13.g603500 Chloroplast
+Cre17.g729900 Mitochondrion
+Cre09.g399150 Mitochondrion
+Cre12.g537850 CCB2 Chloroplast
+Cre01.g024350 DNA.unspecified 28.99 integral component of membrane Secretory pathway
+Cre06.g259100 Chloroplast
+Cre06.g252650 LEU1S secondary metabolism.sulfur-containing.glucosinolates.synthesis.aliphatic.methylthioalkylmalate isomerase small subunit (MAM-IS);amino acid metabolism.degradation.branched chain group.leucine 16.5.1.1.1.4;13.2.4.4 metabolic process Chloroplast
+Cre16.g651923 secondary metabolism.isoprenoids.carotenoids.carotenoid isomerase 16.1.4.8 oxidation-reduction process;oxidoreductase activity Chloroplast
+Cre08.g362900 PSBP4 PS.lightreaction.photosystem II.PSII polypeptide subunits 1.1.1.2 extrinsic component of membrane;photosynthesis;photosystem II oxygen evolving complex;photosystem II;calcium ion binding Chloroplast
+Cre12.g549450 amino acid metabolism.degradation.aromatic aa.tyrosine 13.2.6.2 metabolic process;catalytic activity
+Cre01.g051500 ULP1 PS.lightreaction.unspecified 1.1.99 Chloroplast
+Cre17.g729800 ALB3.2 cell.division.plastid;protein.targeting.chloroplast 31.2.5;29.3.3 protein insertion into membrane;integral component of membrane Chloroplast.Stroma.Thylakoid.Membrane
+Cre02.g076900 FAP19 protein.postranslational modification;protein.synthesis.ribosome biogenesis 29.4;29.2.2
+Cre03.g199000 PHOT1 signalling.light;protein.postranslational modification 30.11;29.4 protein phosphorylation;protein kinase activity Chloroplast
+Cre02.g104900 FAP204 minor CHO metabolism.others 3.5 GTP binding
+Cre03.g203800 Chloroplast
+Cre02.g095092 PSY1 secondary metabolism.isoprenoids.carotenoids.phytoene synthase 16.1.4.1 transferase activity;biosynthetic process Chloroplast
+Cre10.g436350 SHKF1 amino acid metabolism.synthesis.aromatic aa.chorismate.shikimate kinase 13.1.6.1.5 Chloroplast
+Cre14.g614100 GTR26 protein.glycosylation;misc.misc2 29.7;26.1 protein N-linked glycosylation via asparagine;endoplasmic reticulum membrane Secretory pathway
+Cre12.g513200 PGH1 glycolysis.cytosolic branch.enolase 4.1.13 glycolytic process;phosphopyruvate hydratase activity;magnesium ion binding;phosphopyruvate hydratase complex
+Cre12.g501550 Chloroplast
+Cre08.g368700 RNA.regulation of transcription.SET-domain transcriptional regulator family 27.3.69 protein binding Chloroplast
+Cre08.g360900 RPS15 protein.synthesis.ribosomal protein.unknown.small subunit.S19;protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S15 29.2.1.99.1.19;29.2.1.2.1.15 translation;ribosome;structural constituent of ribosome
+Cre16.g691450 Secretory pathway
+Cre08.g378900 NUO3 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).localisation not clear;mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.2;9.1.1 oxidation-reduction process;NADH dehydrogenase (ubiquinone) activity Mitochondrion
+Cre10.g422201 CTP4 transport.metal 34.12 metal ion binding;metal ion transport;nucleotide binding Mitochondrion
+Cre10.g439000 transport.ABC transporters and multidrug resistance systems 34.16 ATPase activity;integral component of membrane;transport;ATP binding;transporter activity Chloroplast
+Cre01.g040000 RPL26 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L26 29.2.1.2.2.26 large ribosomal subunit;translation;structural constituent of ribosome Chloroplast
+Cre13.g588100 CYN19-3 cell.cycle.peptidylprolyl isomerase;protein.folding.immunophilins (IMM).cyclophilins 31.3.1;29.6.3.2 protein folding;peptidyl-prolyl cis-trans isomerase activity;protein peptidyl-prolyl isomerization
+Cre03.g167400 Chloroplast
+Cre05.g233800 TSG1 protein.aa activation.glycine-tRNA ligase 29.1.14 tRNA aminoacylation for protein translation;ATP binding;aminoacyl-tRNA ligase activity;nucleotide binding
+Cre09.g401293 SULTR3 transport.sulphate;misc.rhodanese 34.6;26.23 transmembrane transport;integral component of membrane;membrane;sulfate transmembrane transporter activity;sulfate transport;secondary active sulfate transmembrane transporter activity Chloroplast
+Cre10.g433600 C1-metabolism.methylenetetrahydrofolate reductase;C1-metabolism 25.6;25 oxidation-reduction process;methionine metabolic process;methylenetetrahydrofolate reductase (NAD(P)H) activity
+Cre16.g692751 PDI3 redox.thioredoxin.PDIL;redox.thioredoxin 21.1.1;21.1 cell redox homeostasis Secretory pathway
+Cre06.g284200 LHCBM9 PS.lightreaction.photosystem II.LHC-II 1.1.1.1 membrane;photosynthesis, light harvesting Chloroplast
+Cre17.g705000 FAP223 signalling.calcium;minor CHO metabolism.sugar alcohols;protein.postranslational modification 30.3;3.3;29.4 protein phosphorylation;ATP binding;protein binding;protein kinase activity
+Cre16.g659900 Chloroplast
+Cre-1.g2717006 rps2 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit.S2 29.2.1.1.1.1.2 Chloroplast
+Cre02.g107200
+Cre06.g306300 CHLI1 tetrapyrrole synthesis.magnesium chelatase;tetrapyrrole synthesis.glu-tRNA synthetase 19.10;19.1 magnesium chelatase activity;chlorophyll biosynthetic process;photosynthesis Chloroplast
+Cre03.g183900 Chloroplast
+Cre17.g709850 ACK2 major CHO metabolism.degradation.sucrose.fructokinase 2.2.1.1 phosphotransferase activity, carboxyl group as acceptor;phosphorylation;kinase activity;metabolic process;intracellular Mitochondrion
+Cre12.g522600 CYC2 mitochondrial electron transport / ATP synthesis.cytochrome c 9.6 heme binding;electron carrier activity
+Cre03.g154600 Chloroplast
+Cre06.g278195 Chloroplast
+Cre-1.g2716960 psbJ Chloroplast
+Cre16.g655150 PS.lightreaction.unspecified 1.1.99 Secretory pathway
+Cre06.g274700 OTU4 protein.degradation.cysteine protease 29.5.3 Chloroplast
+Cre03.g207000 Chloroplast
+Cre14.g608800 misc.short chain dehydrogenase/reductase (SDR) 26.22 Chloroplast
+Cre12.g494450 PRPS16 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit.S16 29.2.1.1.1.1.16 translation;ribosome;intracellular;structural constituent of ribosome Chloroplast
+Cre16.g657979
+Cre11.g467773 Chloroplast
+Cre10.g420550 TSP4 protein.degradation.serine protease 29.5.5 serine-type peptidase activity;proteolysis;protein binding Chloroplast
+Cre12.g512000 membrane Secretory pathway
+Cre17.g734100 nucleotide metabolism.synthesis.purine.adenylosuccinate synthase 23.1.2.20 purine nucleotide biosynthetic process;GTP binding;adenylosuccinate synthase activity Chloroplast
+Cre13.g586350 DNA.repair 28.2 Mitochondrion
+Cre12.g485550 amino acid metabolism.degradation.branched chain group.leucine 13.2.4.4 catalytic activity Mitochondrion
+Cre15.g643550 PDX1 Co-factor and vitamine metabolism 18 pyridoxal phosphate biosynthetic process;vitamin B6 biosynthetic process
+Cre06.g286250 MPC1 transport.metabolite transporters at the mitochondrial membrane 34.9
+Cre07.g336950 PHO2 major CHO metabolism.degradation.starch.starch phosphorylase 2.2.2.2 glycogen phosphorylase activity;carbohydrate metabolic process Chloroplast
+Cre17.g738751 Mitochondrion
+Cre06.g279850 protein.degradation 29.5 Chloroplast
+Cre13.g571150 NUOP1 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.1
+Cre12.g558600
+Cre06.g282500 RPL23A protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L23A;protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L23A 29.2.1.2.2.523;29.2.1.2.2.0523 translation;ribosome;structural constituent of ribosome
+Cre10.g445750 Mitochondrion
+Cre02.g084000 Chloroplast
+Cre12.g549300 MIP1 transport.major intrinsic proteins.TIP;transport.major intrinsic proteins.PIP 34.19.2;34.19.1 membrane;transport;transporter activity
+Cre06.g267350 Mitochondrion
+Cre06.g304500 ZYS4 cell.development.zygote 31.7.1 protein binding Secretory pathway
+Cre16.g684150 Chloroplast
+Cre11.g475850 ZNJ1 protein.folding;PS.lightreaction.photosystem I.biogenesis 29.6;1.1.2.3 Chloroplast.Stroma.Thylakoid.Lumen
+Cre02.g144850 CGLD26 Chloroplast
+Cre12.g497850 Chloroplast
+Cre02.g075700 RPL19 protein.synthesis.ribosomal protein.unknown.large subunit.L19;protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L19 29.2.1.99.2.19;29.2.1.2.2.19 translation;ribosome;intracellular;structural constituent of ribosome
+Cre09.g390615 FAP12 lipid metabolism.lipid degradation.lipases.triacylglycerol lipase 11.9.2.1 lipid metabolic process
+Cre12.g520350 ALD1 amino acid metabolism.degradation.glutamate family.proline 13.2.2.2 oxidation-reduction process;oxidoreductase activity;metabolic process Mitochondrion
+Cre10.g440450 PSB28 PS.lightreaction.photosystem II.biogenesis;PS.lightreaction.photosystem II.PSII polypeptide subunits 1.1.1.3;1.1.1.2 membrane;photosynthesis;photosystem II oxygen evolving complex;photosystem II Chloroplast.Stroma.Thylakoid.Membrane
+Cre06.g272950 RPS18 protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S18 29.2.1.2.1.18 translation;ribosome;intracellular;structural constituent of ribosome;RNA binding Chloroplast
+Cre17.g734644 SQE1 hormone metabolism.brassinosteroid.synthesis-degradation.sterols.other 17.3.1.2.99 FAD binding
+Cre11.g467597 transport.ABC transporters and multidrug resistance systems 34.16 ATPase activity;membrane;ATP binding
+Cre12.g494350 DNA.unspecified 28.99 integral component of membrane Secretory pathway
+Cre16.g678000 CPL22 Chloroplast
+Cre03.g153900 FMO11 FAD binding
+Cre16.g689087
+Cre03.g182450 C1-metabolism.methylenetetrahydrofolate dehydrogenase and methenyltetrahydrofolate cyclohydrolase 25.5 oxidation-reduction process;folic acid-containing compound biosynthetic process;methylenetetrahydrofolate dehydrogenase (NADP+) activity;catalytic activity Chloroplast
+Cre03.g208000 DNA.unspecified;DNA.synthesis/chromatin structure;RNA.regulation of transcription.unclassified 28.99;28.1;27.3.99 Chloroplast
+Cre08.g384000 CYP771A1 misc.cytochrome P450;misc.misc2;hormone metabolism.brassinosteroid.synthesis-degradation.BRs.metabolic regulation 26.10;26.1;17.3.1.1.5 oxidation-reduction process;heme binding;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen;iron ion binding Mitochondrion
+Cre13.g573900 NSS3 transport.unspecified cations 34.14 transmembrane transport;membrane;transport;transporter activity Secretory pathway
+Cre06.g278087 Chloroplast
+Cre07.g331550 PST1 amino acid metabolism.synthesis.serine-glycine-cysteine group.serine.phosphoserine aminotransferase 13.1.5.1.2 Chloroplast
+Cre01.g036850 PDY1 amino acid metabolism.degradation.glutamate family.proline 13.2.2.2 proline catabolic process;proline dehydrogenase activity Chloroplast
+Cre09.g402300 ASA8 mitochondrial electron transport / ATP synthesis.F1-ATPase 9.9
+Cre10.g464050 Chloroplast
+Cre17.g725400
+Cre08.g364800 nucleotide metabolism.synthesis.purine.FGAR amidotransferase 23.1.2.4 Chloroplast
+Cre02.g078507 photosystem II assembly Chloroplast
+Cre12.g536800 CGL52 Chloroplast
+Cre17.g707500 protein.targeting.chloroplast 29.3.3 Chloroplast
+Cre16.g685550 OASTL4 amino acid metabolism.synthesis.serine-glycine-cysteine group.cysteine.OASTL 13.1.5.3.1 Chloroplast
+Cre12.g508500 protein.degradation.metalloprotease 29.5.7 Secretory pathway
+Cre11.g467767 NUO13 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).localisation not clear;mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.2;9.1.1 membrane;electron carrier activity;NADH dehydrogenase (ubiquinone) activity
+Cre10.g422450 GGT1 misc.UDP glucosyl and glucoronyl transferases;major CHO metabolism.synthesis.starch 26.2;2.1.2 Secretory pathway
+Cre13.g576760 Chloroplast
+Cre11.g467769 Chloroplast
+Cre06.g298350 FAP224 protein.synthesis.initiation 29.2.3 protein binding
+Cre09.g393506 HCP3 redox.misc 21.99 oxidation-reduction process;oxidoreductase activity Chloroplast
+Cre-1.g2717008 ycf3 PS.lightreaction.photosystem I.biogenesis 1.1.2.3 Chloroplast
+Cre10.g459750 NUOA1
+Cre02.g082500 PSAN PS.lightreaction.photosystem I.PSI polypeptide subunits 1.1.2.2 thylakoid membrane;photosynthesis;photosystem I;calmodulin binding Chloroplast
+Cre08.g360950 Chloroplast
+Cre06.g278148 OPP.oxidative PP.6-phosphogluconate dehydrogenase;amino acid metabolism.synthesis.central amino acid metabolism.GABA.gamma-hydroxybutyrate DH 7.1.3;13.1.1.1.4 NAD binding Chloroplast
+Cre08.g365900 LHCSR1 PS.lightreaction.unspecified 1.1.99 membrane;photosynthesis, light harvesting Chloroplast
+Cre11.g467678 COP6 cell.eyespot;nucleotide metabolism.synthesis.purine;hormone metabolism.cytokinin.signal transduction 31.9;23.1.2;17.4.2 intracellular signal transduction;phosphorus-oxygen lyase activity;membrane;cyclic nucleotide biosynthetic process;signal transduction;phosphorelay signal transduction system;phosphorelay sensor kinase activity Chloroplast
+Cre03.g204650 NUOB4 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.1 Mitochondrion
+Cre04.g217933
+Cre17.g734612 MRP2 transport.ABC transporters and multidrug resistance systems 34.16 transmembrane transport;ATPase activity, coupled to transmembrane movement of substances;ATPase activity;integral component of membrane;transport;ATP binding
+Cre02.g085450 CPX1 tetrapyrrole synthesis.coproporphyrinogen III oxidase 19.8 oxidation-reduction process;porphyrin-containing compound biosynthetic process;coproporphyrinogen oxidase activity Chloroplast
+Cre-1.g2716994 psbF PS.lightreaction.photosystem II.PSII polypeptide subunits 1.1.1.2 Chloroplast
+Cre16.g675958 DNA.unspecified 28.99 integral component of membrane
+Cre08.g381702 TCA / organic transformation.other organic acid transformations.misc;secondary metabolism.N misc.betaine;amino acid metabolism.synthesis.central amino acid metabolism.GABA.SSADH 8.2.99;16.4.2;13.1.1.1.3 oxidation-reduction process;oxidoreductase activity;metabolic process Mitochondrion
+Cre01.g048150 HLA8 Chloroplast
+Cre12.g514050 GSF1 N-metabolism.ammonia metabolism.glutamate synthase.ferredoxin dependent 12.2.1.1 oxidation-reduction process;oxidoreductase activity, acting on the CH-NH2 group of donors;oxidoreductase activity;glutamate synthase activity;metabolic process;nitrogen compound metabolic process;glutamate biosynthetic process Chloroplast
+Cre16.g658526 transport.ABC transporters and multidrug resistance systems 34.16 ATPase activity;GTP binding;ATP binding Chloroplast
+Cre12.g490650 Mitochondrion
+Cre12.g490100 transport.sugars;transport.NDP-sugars at the ER 34.2;34.11
+Cre09.g400650 RPS6 protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S6 29.2.1.2.1.6 translation;ribosome;intracellular;structural constituent of ribosome
+Cre-1.g2716972 atpE PS.lightreaction.ATP synthase 1.1.4 Chloroplast
+Cre09.g391900 TRXH2 redox.thioredoxin 21.1 cell redox homeostasis;protein disulfide oxidoreductase activity;glycerol ether metabolic process
+Cre06.g268200 TGD1 transport.misc 34.99 ATP-binding cassette (ABC) transporter complex;transport Mitochondrion
+Cre04.g222700 transport.ABC transporters and multidrug resistance systems;protein.synthesis.elongation;protein.synthesis.ribosome biogenesis.export from nucleus 34.16;29.2.4;29.2.2.1 ATPase activity;ATP binding
+Cre16.g683750 CGL67 integral component of membrane Chloroplast
+Cre-1.g2716966 chlB tetrapyrrole synthesis.protochlorophyllide reductase 19.14 Chloroplast
+Cre02.g114450 Chloroplast
+Cre-1.g2716958 psaJ PS.lightreaction.photosystem I.PSI polypeptide subunits 1.1.2.2 Chloroplast
+Cre09.g404000 CPLD59 PS.lightreaction.unspecified 1.1.99 Chloroplast
+Cre09.g388200 RPL10 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L10 29.2.1.2.2.10 translation;ribosome;structural constituent of ribosome
+Cre09.g405050 ATPVD2 transport.p- and v-ATPases.H+-transporting two-sector ATPase.subunit D;transport.p- and v-ATPases.H+-transporting two-sector ATPase 34.1.1.3;34.1.1 ATPase activity, coupled to transmembrane movement of substances Chloroplast
+Cre06.g285401 FAP355 DNA binding Chloroplast
+Cre17.g702950 integral component of membrane
+Cre09.g386756
+Cre07.g348600 SULP1 membrane;transport Chloroplast
+Cre06.g272800 RPS8 protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S8 29.2.1.2.1.8 translation;ribosome;intracellular;structural constituent of ribosome
+Cre06.g292400 Chloroplast
+Cre07.g339150 CPN60B2 protein.folding.chaperones and co-chaperones.HSP60s;protein.folding;PS.calvin cycle.rubisco interacting 29.6.2.2;29.6;1.3.13 ATP binding Chloroplast.Stroma
+Cre03.g145207 CPLD33 Chloroplast
+Cre03.g187450 RPI1 OPP.non-reductive PP.ribose 5-phosphate isomerase;PS.calvin cycle.Rib5P Isomerase 7.2.4;1.3.10 pentose-phosphate shunt, non-oxidative branch;ribose-5-phosphate isomerase activity Chloroplast
+Cre02.g116500 CPY3 protein.degradation.serine protease 29.5.5 proteolysis;serine-type carboxypeptidase activity Secretory pathway
+Cre02.g103000 Secretory pathway
+Cre01.g000250 SNR1 integral component of membrane Mitochondrion
+Cre17.g720250 LHCB4 PS.lightreaction.photosystem II.LHC-II 1.1.1.1 membrane;photosynthesis, light harvesting
+Cre11.g468950 QCR9 mitochondrial electron transport / ATP synthesis.cytochrome c reductase 9.5 mitochondrial electron transport, ubiquinol to cytochrome c;mitochondrial respiratory chain complex III;mitochondrial inner membrane
+Cre06.g278188 NUOB18 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).localisation not clear;mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.2;9.1.1 NADH dehydrogenase (ubiquinone) activity;mitochondrion;NADH dehydrogenase activity
+Cre12.g494050 RPL9 protein.synthesis.ribosome biogenesis;protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L9 29.2.2;29.2.1.2.2.9 rRNA binding;translation;ribosome;structural constituent of ribosome
+Cre03.g206450
+Cre03.g158000 GSA1 tetrapyrrole synthesis.GSA 19.3 pyridoxal phosphate binding;transaminase activity Chloroplast
+Cre06.g278135 RPL21 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L21 29.2.1.2.2.21 translation;ribosome;intracellular;structural constituent of ribosome Chloroplast
+Cre03.g203850 ATS1 nucleotide metabolism.phosphotransfer and pyrophosphatases.adenylate kinase;S-assimilation.APS 23.4.1;14.1 sulfate adenylyltransferase (ATP) activity Chloroplast
+Cre01.g012500 PRA1 cell.vesicle transport;signalling.G-proteins;minor CHO metabolism.others 31.4;30.5;3.5
+Cre06.g295450 HPR1 amino acid metabolism.degradation.serine-glycine-cysteine group.glycine;amino acid metabolism.degradation.serine-glycine-cysteine group.serine;PS.photorespiration.hydroxypyruvate reductase 13.2.5.2;13.2.5.1;1.2.6 oxidation-reduction process;NAD binding;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;metabolic process Mitochondrion
+Cre-1.g2716963 psbC PS.lightreaction.photosystem II.PSII polypeptide subunits 1.1.1.2 Chloroplast
+Cre12.g528000 FAP303 Mitochondrion
+Cre03.g171350 SEC61A transport.misc;protein.targeting.secretory pathway.unspecified 34.99;29.3.4.99 membrane;protein transport Secretory pathway
+Cre04.g217929 S-assimilation.sulfite oxidase;N-metabolism.nitrate metabolism.NR 14.5;12.1.1 oxidation-reduction process;nitrate assimilation;molybdenum ion binding;oxidoreductase activity Mitochondrion
+Cre01.g047750 RPL18A protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L18A;protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L18A 29.2.1.2.2.518;29.2.1.2.2.0518 translation;ribosome;structural constituent of ribosome
+Cre12.g514900 TIM10 protein.targeting.mitochondria 29.3.2 protein import into mitochondrial inner membrane
+Cre-1.g2716987 psbA PS.lightreaction.photosystem II.PSII polypeptide subunits 1.1.1.2 Chloroplast
+Cre08.g382950 Mitochondrion
+Cre03.g182050 lipid metabolism.FA synthesis and FA elongation.long chain fatty acid CoA ligase 11.1.9 metabolic process;catalytic activity
+Cre01.g000350 PS.lightreaction.other electron carrier (ox/red).ferredoxin oxireductase 1.1.5.4 oxidation-reduction process;oxidoreductase activity
+Cre-1.g2717002 psbB PS.lightreaction.photosystem II.PSII polypeptide subunits 1.1.1.2 Chloroplast
+Cre14.g626750 PS.lightreaction.unspecified 1.1.99 Chloroplast
+Cre17.g702150 CCS5 protein.assembly and cofactor ligation;redox.thioredoxin 29.8;21.1 cell redox homeostasis;protein disulfide oxidoreductase activity;glycerol ether metabolic process Chloroplast
+Cre17.g747297 FAP37 aminoacyl-tRNA hydrolase activity Secretory pathway
+Cre14.g614600 Secretory pathway
+Cre12.g542350 stress 20 response to stress
+Cre08.g377150 catalytic activity Mitochondrion
+Cre-1.g2717021 petD PS.lightreaction.cytochrome b6/f 1.1.3 Chloroplast
+Cre01.g002300 CYN19-2 cell.cycle.peptidylprolyl isomerase;protein.folding.immunophilins (IMM).cyclophilins 31.3.1;29.6.3.2 protein folding;peptidyl-prolyl cis-trans isomerase activity;protein peptidyl-prolyl isomerization
+Cre02.g074950
+Cre-1.g2716983 atpF PS.lightreaction.ATP synthase 1.1.4 Chloroplast
+Cre05.g245900 BCA2 misc.aminotransferases.aminotransferase class IV family protein;Co-factor and vitamine metabolism.pantothenate.branched-chain amino acid aminotransferase;secondary metabolism.sulfur-containing.glucosinolates.synthesis.aliphatic.branched-chain amino acid aminotransferase (BCAT/MAAT);amino acid metabolism.synthesis.branched chain group.common.branched-chain-amino-acid aminotransferase 26.26.1;18.4.1;16.5.1.1.1.1;13.1.4.1.4 metabolic process;catalytic activity Chloroplast
+Cre03.g188650 PLAP2 cell.organisation 31.1 Chloroplast
+Cre06.g270200 signalling.phosphinositides.phosphoinositide phospholipase C 30.4.4 intracellular signal transduction;signal transduction;lipid metabolic process;protein binding;phosphatidylinositol phospholipase C activity
+Cre01.g002050 APT1 acid phosphatase activity Secretory pathway
+Cre07.g357850 RPL22 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L22 29.2.1.2.2.22 translation;ribosome;intracellular;structural constituent of ribosome
+Cre24.g755497 integral component of membrane
+Cre12.g551900
+Cre02.g109950 OHP1 Chloroplast
+Cre-1.g2716961 psbD PS.lightreaction.photosystem II.PSII polypeptide subunits 1.1.1.2 Chloroplast
+Cre12.g499350 EFH7 signalling.calcium;minor CHO metabolism.sugar alcohols 30.3;3.3 calcium ion binding Mitochondrion
+Cre12.g554650 REC8 protein binding;nuclear chromosome
+Cre06.g272850 PRPL10 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit.L10 29.2.1.1.1.2.10 ribosome biogenesis;intracellular Chloroplast
+Cre03.g172000 KAR1 misc.short chain dehydrogenase/reductase (SDR);lipid metabolism.FA synthesis and FA elongation.ACP oxoacyl reductase 26.22;11.1.4 Chloroplast
+Cre06.g257850 protein.postranslational modification 29.4 catalytic activity Chloroplast
+Cre12.g503350
+Cre16.g664600 NUOB16 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.1
+Cre01.g051900 RIP1 mitochondrial electron transport / ATP synthesis.cytochrome c reductase 9.5 oxidation-reduction process;2 iron, 2 sulfur cluster binding;oxidoreductase activity, acting on diphenols and related substances as donors;oxidoreductase activity;ubiquinol-cytochrome-c reductase activity Mitochondrion
+Cre07.g333900 NUOA8 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.1
+Cre10.g420700 ATP15 mitochondrial electron transport / ATP synthesis.F1-ATPase 9.9 proton-transporting ATPase activity, rotational mechanism;proton-transporting ATP synthase activity, rotational mechanism;ATP synthesis coupled proton transport;mitochondrial proton-transporting ATP synthase complex, catalytic core F(1)
+Cre03.g181500 STA11 major CHO metabolism.degradation.starch.D enzyme 2.2.2.4 carbohydrate metabolic process;4-alpha-glucanotransferase activity Chloroplast
+Cre03.g144627 CGS1 amino acid metabolism.synthesis.aspartate family.methionine.cystathionine gamma-synthase 13.1.3.4.1 pyridoxal phosphate binding Chloroplast
+Cre04.g213985
+Cre12.g494850 ADK3 nucleotide metabolism.phosphotransfer and pyrophosphatases.adenylate kinase 23.4.1 nucleobase-containing compound kinase activity;nucleobase-containing compound metabolic process;ATP binding Chloroplast
+Cre09.g397400 misc.short chain dehydrogenase/reductase (SDR) 26.22 oxidoreductase activity;metabolic process
+Cre02.g074100 Chloroplast
+Cre01.g049950 VLE1 protein.degradation.subtilases 29.5.1 proteolysis;serine-type endopeptidase activity Secretory pathway
+Cre10.g452050 LHCA4 PS.lightreaction.photosystem I.LHC-I 1.1.2.1 membrane;photosynthesis, light harvesting Chloroplast
+Cre16.g684750 minor CHO metabolism.others 3.5 Mitochondrion
+Cre12.g555250 NUOB14 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.1
+Cre02.g143050 RPP2 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.unknown 29.2.1.2.2.99
+Cre06.g298650 EIF4A protein.synthesis.initiation 29.2.3 ATP binding;nucleic acid binding Secretory pathway
+Cre05.g243050 TRXF2 redox.thioredoxin 21.1 cell redox homeostasis;protein disulfide oxidoreductase activity;glycerol ether metabolic process Chloroplast
+Cre06.g251150 OHP2 PS.lightreaction.unspecified;PS.lightreaction.photosystem I.LHC-I 1.1.99;1.1.2.1 Chloroplast
+Cre12.g498550 CHLM tetrapyrrole synthesis.magnesium protoporphyrin IX methyltransferase 19.11 Chloroplast
+Cre05.g248500 TRXO redox.thioredoxin 21.1 cell redox homeostasis;protein disulfide oxidoreductase activity;glycerol ether metabolic process Mitochondrion
+Cre11.g467668 NUOB22 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.1
+Cre09.g407700 CEP1 protein.degradation.cysteine protease 29.5.3 cysteine-type peptidase activity;proteolysis Secretory pathway
+Cre02.g082550 ZEP1 hormone metabolism.abscisic acid.synthesis-degradation.synthesis.zeaxanthin epoxidase 17.1.1.1.1 FAD binding;protein binding Chloroplast
+Cre06.g294950 ENR1 lipid metabolism.FA synthesis and FA elongation.enoyl ACP reductase 11.1.6 Chloroplast
+Cre01.g043350 CAO1 tetrapyrrole synthesis.chlorophyll b synthase 19.16 oxidation-reduction process;2 iron, 2 sulfur cluster binding;oxidoreductase activity;chlorophyllide a oxygenase [overall] activity Chloroplast
+Cre-1.g2716990 psbE PS.lightreaction.photosystem II.PSII polypeptide subunits 1.1.1.2 Chloroplast
+Cre04.g213250 protein.degradation 29.5 proteolysis
+Cre12.g507400 CGL105 lipid metabolism.FA synthesis and FA elongation.long chain fatty acid CoA ligase 11.1.9 metabolic process;catalytic activity Mitochondrion
+Cre12.g560950 PSAG PS.lightreaction.photosystem I.PSI polypeptide subunits 1.1.2.2 membrane;photosynthesis;photosystem I Chloroplast
+Cre01.g016514 TCA / organic transformation.TCA.pyruvate DH.E3;lipid metabolism.FA synthesis and FA elongation.pyruvate DH 8.1.1.3;11.1.31 oxidation-reduction process;flavin adenine dinucleotide binding;cell redox homeostasis;oxidoreductase activity;tRNA processing Chloroplast
+Cre14.g633550 Mitochondrion
+Cre02.g142246 Mitochondrion
+Cre06.g290100 SYP6 cell.vesicle transport 31.4 Golgi vesicle transport;membrane;protein binding
+Cre12.g484200 GGPS secondary metabolism.isoprenoids.non-mevalonate pathway.geranylgeranyl pyrophosphate synthase 16.1.1.10 isoprenoid biosynthetic process Chloroplast
+Cre12.g505950 TIM50 transport.metabolite transporters at the mitochondrial membrane;protein.targeting.unknown 34.9;29.3.99 protein transport;mitochondrial inner membrane presequence translocase complex;mitochondrial inner membrane Mitochondrion
+Cre12.g550750 Mitochondrion
+Cre12.g511100 protein.targeting.mitochondria 29.3.2 Mitochondrion
+Cre08.g372450 PSBQ PS.lightreaction.photosystem II.PSII polypeptide subunits 1.1.1.2 extrinsic component of membrane;photosynthesis;photosystem II oxygen evolving complex;photosystem II;calcium ion binding Chloroplast
+Cre16.g656400 SQD1 lipid metabolism.glycolipid synthesis.UDP-sulfoquinovose synthase 11.10.3 coenzyme binding;catalytic activity Chloroplast
+Cre12.g535851 RPL8 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L8 29.2.1.2.2.8 translation;ribosome;intracellular;structural constituent of ribosome Chloroplast
+Cre03.g204250 SAH1 amino acid metabolism.degradation.aspartate family.methionine 13.2.3.4 oxidation-reduction process;NAD binding;one-carbon metabolic process;adenosylhomocysteinase activity
+Cre05.g247450 CGL56 misc.rhodanese 26.23 Chloroplast
+Cre06.g283950 LHCBM4 PS.lightreaction.photosystem II.LHC-II 1.1.1.1 membrane;photosynthesis, light harvesting Chloroplast
+Cre01.g037150 transport.unspecified anions 34.18 transmembrane transport;membrane;chloride transport;voltage-gated chloride channel activity Chloroplast
+Cre16.g664700 SHY1 membrane Mitochondrion
+Cre16.g688850 HPT2 transport.misc 34.99 transmembrane transport;integral component of membrane Mitochondrion
+Cre12.g490350 HDS1 secondary metabolism.isoprenoids.non-mevalonate pathway.HDS 16.1.1.6 oxidation-reduction process;4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity;terpenoid biosynthetic process
+Cre06.g311900 RAB7 signalling.G-proteins;minor CHO metabolism.others 30.5;3.5 GTP binding
+Cre02.g110350 signalling.calcium;minor CHO metabolism.sugar alcohols 30.3;3.3 protein binding
+Cre12.g561000 CYN28 cell.cycle.peptidylprolyl isomerase;protein.folding.immunophilins (IMM).cyclophilins 31.3.1;29.6.3.2 protein folding;peptidyl-prolyl cis-trans isomerase activity;protein peptidyl-prolyl isomerization Chloroplast
+Cre02.g095122 FKB16-8 protein.folding.immunophilins (IMM).FKBPs;protein.folding 29.6.3.1;29.6 protein folding
+Cre08.g358540 Chloroplast
+Cre05.g233900 APX4 redox.ascorbate and glutathione.ascorbate 21.2.1 oxidation-reduction process;heme binding;response to oxidative stress;peroxidase activity Chloroplast
+Cre03.g168550 AOT3 transport.amino acids 34.3 Chloroplast
+Cre02.g146700 Chloroplast
+Cre03.g156250 FAP186
+Cre12.g540051 Secretory pathway
+Cre02.g107450 ATS2 S-assimilation.APS;PS.lightreaction.photosystem II.PSII polypeptide subunits 14.1;1.1.1.2 sulfate adenylyltransferase (ATP) activity Mitochondrion
+Cre17.g744897 regulation of transcription, DNA-templated;mitochondrion;double-stranded DNA binding Secretory pathway
+Cre13.g583550 VIPP1 RNA.regulation of transcription.unclassified;PS.lightreaction.unspecified 27.3.99;1.1.99 Chloroplast
+Cre06.g272050 PGM1 glycolysis.cytosolic branch.phosphoglycerate mutase 4.1.12 metal ion binding;manganese ion binding;glucose catabolic process;cytoplasm;phosphoglycerate mutase activity;catalytic activity
+Cre10.g423250 MDN2 TCA / organic transformation.other organic acid transformations.cyt MDH;TCA / organic transformation.TCA.malate DH;gluconeogenesis / glyoxylate cycle.malate dehydrogenase 8.2.9;8.1.9;6.3 oxidation-reduction process;carboxylic acid metabolic process;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;oxidoreductase activity
+Cre12.g492300 NUO10 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).localisation not clear;mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.2;9.1.1 oxidation-reduction process;iron-sulfur cluster binding
+Cre03.g199150 nucleotide metabolism 23 coenzyme binding;catalytic activity Mitochondrion
+Cre16.g660150 protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S20 29.2.1.2.1.20 translation;ribosome;structural constituent of ribosome
+Cre06.g302700 development.unspecified 33.99 protein binding Chloroplast
+Cre06.g308900 TOB55 protein.targeting.mitochondria 29.3.2 outer membrane
+Cre12.g486300 PSAL PS.lightreaction.photosystem I.PSI polypeptide subunits 1.1.2.2 photosynthesis;photosystem I reaction center;photosystem I Chloroplast
+Cre14.g630100 RPL13 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L13 29.2.1.2.2.13 translation;ribosome;intracellular;structural constituent of ribosome
+Cre06.g293582 protein.aa activation.leucine-tRNA ligase 29.1.4 tRNA aminoacylation for protein translation;ATP binding;aminoacyl-tRNA ligase activity;nucleotide binding
+Cre05.g240800 NUO17 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.1 Chloroplast
+Cre12.g534700 FKB19 protein.folding.immunophilins (IMM).FKBPs 29.6.3.1 protein folding Secretory pathway
+Cre02.g076250 EFG1 protein.synthesis.elongation 29.2.4 GTP binding Chloroplast
+Cre01.g016300 CAM3 Chloroplast
+Cre01.g044600 signalling.calcium;minor CHO metabolism.sugar alcohols 30.3;3.3
+Cre12.g532550 RPL13A protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L13A;protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L13A 29.2.1.2.2.513;29.2.1.2.2.0513 large ribosomal subunit;translation;ribosome;structural constituent of ribosome
+Cre09.g392867 FMG2 cell.motility.eukaryotes.flagellar membrane proteins 31.6.1.8 Secretory pathway
+Cre03.g189300 PLAP10 cell.organisation 31.1 Chloroplast
+Cre12.g555150 NUOB10 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.1
+Cre16.g666050 CPLD49 oxidation-reduction process;oxidoreductase activity Chloroplast
+Cre17.g745097 Secretory pathway
+Cre11.g467691 Secretory pathway
+Cre14.g617826
+Cre06.g273700 HCF136 protein.assembly and cofactor ligation;PS.lightreaction.photosystem II.biogenesis 29.8;1.1.1.3 Chloroplast.Stroma.Thylakoid.Membrane
+Cre10.g436050 FSD1 redox.dismutases and catalases 21.6 oxidation-reduction process;metal ion binding;superoxide metabolic process;superoxide dismutase activity Chloroplast
+Cre12.g508000 TIC40 protein.targeting.chloroplast 29.3.3 Chloroplast.Membrane.Inner
+Cre10.g451900 THS1 amino acid metabolism.synthesis.aspartate family.threonine.threonine synthase 13.1.3.2.1 Chloroplast
+Cre06.g294450 minor CHO metabolism.others 3.5 Chloroplast
+Cre11.g467573 LHCA3 PS.lightreaction.photosystem I.LHC-I 1.1.2.1 membrane;photosynthesis, light harvesting Chloroplast
+Cre10.g461050 ATPVA1 transport.p- and v-ATPases.H+-transporting two-sector ATPase;transport.p- and v-ATPases 34.1.1;34.1 ATP metabolic process;proton-transporting two-sector ATPase complex, catalytic domain;hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances;proton transport;ATP hydrolysis coupled proton transport;ATP binding
+Cre07.g325734 FAP340 nucleotide metabolism.phosphotransfer and pyrophosphatases.nucleoside diphosphate kinase 23.4.10 CTP biosynthetic process;UTP biosynthetic process;GTP biosynthetic process;nucleoside diphosphate phosphorylation;nucleoside diphosphate kinase activity Chloroplast
+Cre02.g101350 RPL10A protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L10A;protein.synthesis.ribosomal protein.prokaryotic.unknown organellar.50S subunit.L10A;protein.synthesis.ribosomal protein.prokaryotic.unknown organellar.50S subunit.L10A 29.2.1.2.2.510;29.2.1.1.3.2.510;29.2.1.1.3.2.0510
+Cre06.g259450 Chloroplast
+Cre05.g243800 PSB27 PS.lightreaction.photosystem II.biogenesis;PS.lightreaction.photosystem II.PSII polypeptide subunits 1.1.1.3;1.1.1.2 photosystem II assembly Chloroplast.Stroma.Thylakoid.Lumen
+Cre13.g577850 FKB20 protein.folding.immunophilins (IMM).FKBPs;PS.lightreaction.photosystem II.biogenesis 29.6.3.1;1.1.1.3 Chloroplast.Stroma.Thylakoid.Lumen
+Cre01.g048950 PYR5 nucleotide metabolism.synthesis.pyrimidine.uridine 5'-monophosphate synthase 23.1.1.5 nucleoside metabolic process;'de novo' pyrimidine nucleobase biosynthetic process;orotidine-5'-phosphate decarboxylase activity Chloroplast
+Cre03.g154950 misc.glutathione S transferases 26.9 protein binding Secretory pathway
+Cre11.g478800
+Cre12.g496750 NUO8 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).localisation not clear;mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.2;9.1.1 Mitochondrion
+Cre03.g198950 CGL30 PS.lightreaction.photosystem II.PSII polypeptide subunits 1.1.1.2 extrinsic component of membrane;photosynthesis;photosystem II oxygen evolving complex;photosystem II;calcium ion binding Chloroplast
+Cre07.g318450 SEC61B protein.targeting.secretory pathway.unspecified 29.3.4.99 intracellular protein transport;Sec61 translocon complex Chloroplast
+Cre13.g584250 Chloroplast
+Cre12.g493150 VKE1 PS.lightreaction.photosystem II.biogenesis 1.1.1.3 Chloroplast.Stroma.Thylakoid.Membrane
+Cre17.g741850 HNR1 RNA.RNA binding 27.4
+Cre10.g432750
+Cre13.g567950 STA1 major CHO metabolism.synthesis.starch.AGPase 2.1.2.1 nucleotidyltransferase activity;biosynthetic process Chloroplast
+Cre01.g035350 lipid metabolism.exotics (steroids, squalene etc).trans-2-enoyl-CoA reductase (NADPH) 11.8.7 oxidation-reduction process;oxidoreductase activity;zinc ion binding
+Cre03.g185550 SEBP1 PS.calvin cycle.sedoheptulose bisphosphatase 1.3.9 phosphoric ester hydrolase activity;fructose 1,6-bisphosphate 1-phosphatase activity;carbohydrate metabolic process Chloroplast
+Cre02.g086850 Chloroplast
+Cre11.g469150 Chloroplast
+Cre07.g327400 NUO9 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).localisation not clear;mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.2;9.1.1 oxidation-reduction process;NADH dehydrogenase (ubiquinone) activity Mitochondrion
+Cre09.g396213 PSBO PS.lightreaction.photosystem II.PSII polypeptide subunits 1.1.1.2 photosystem II stabilization;extrinsic component of membrane;photosynthesis;photosystem II oxygen evolving complex;photosystem II;calcium ion binding Chloroplast
+Cre-1.g2717031 psbN PS.lightreaction.photosystem II.biogenesis 1.1.1.3 Chloroplast
+Cre12.g546150 PETM PS.lightreaction.cytochrome b6/f 1.1.3 cytochrome b6f complex Chloroplast
+Cre03.g178250 NUOS6 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).localisation not clear;mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.2;9.1.1
+Cre14.g628350 HSLV1 protein.degradation.ubiquitin.proteasom 29.5.11.20 proteolysis involved in cellular protein catabolic process;proteasome core complex;threonine-type endopeptidase activity Mitochondrion
+Cre08.g373100 CYP97C3 secondary metabolism.isoprenoids.carotenoids.carotenoid epsilon ring hydroxylase 16.1.4.7 oxidation-reduction process;heme binding;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen;iron ion binding Chloroplast
+Cre02.g111450 TEF4 PS.lightreaction.unspecified.TEF 1.1.99.1 Chloroplast
+Cre02.g100200 NUOP3 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).localisation not clear;mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.2;9.1.1 Mitochondrion
+Cre06.g268750 MME1 TCA / organic transformation.other organic acid transformations.malic 8.2.10 oxidation-reduction process;NAD binding;malate dehydrogenase (decarboxylating) (NAD+) activity Mitochondrion
+Cre17.g715500 oxidation-reduction process;oxidoreductase activity;antioxidant activity Chloroplast
+Cre10.g433950 CURTL2 PS.lightreaction.unspecified 1.1.99 Chloroplast
+Cre03.g199423 PYR4 nucleotide metabolism.synthesis.pyrimidine.dihydroorotate dehydrogenase 23.1.1.4 oxidation-reduction process;oxidoreductase activity, acting on the CH-CH group of donors;cytoplasm
+Cre05.g245450 COQ5A Co-factor and vitamine metabolism.ubiquinone;Co-factor and vitamine metabolism 18.8;18 methyltransferase activity;metabolic process Mitochondrion
+Cre09.g405850 NUO7 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).localisation not clear;mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.2;9.1.1 oxidation-reduction process;NAD binding;quinone binding;oxidoreductase activity, acting on NAD(P)H Mitochondrion
+Cre12.g498500 DEG1C protein.degradation.serine protease 29.5.5 proteolysis;protein binding;serine-type endopeptidase activity Mitochondrion
+Cre03.g177350 development.unspecified 33.99 Chloroplast
+Cre01.g038400 CRT2 signalling.calcium;minor CHO metabolism.sugar alcohols 30.3;3.3 unfolded protein binding;protein folding;endoplasmic reticulum;calcium ion binding Secretory pathway
+Cre06.g267300 Mitochondrion
+Cre01.g044400 Chloroplast
+Cre12.g538950
+Cre03.g146167 TEF10a PS.lightreaction.unspecified.TEF 1.1.99.1 Chloroplast.Stroma.Thylakoid.Membrane
+Cre06.g262700 QCR7 mitochondrial electron transport / ATP synthesis.cytochrome c reductase 9.5 mitochondrial electron transport, ubiquinol to cytochrome c;mitochondrial respiratory chain complex III
+Cre03.g177500 hormone metabolism.abscisic acid.induced-regulated-responsive-activated;hormone metabolism.abscisic acid.synthesis-degradation 17.1.3;17.1.1
+Cre17.g702900 integral component of membrane
+Cre-1.g2717007 rps18 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit.S18 29.2.1.1.1.1.18 Chloroplast
+Cre01.g045100 Secretory pathway
+Cre01.g049600 CGLD22 PS.lightreaction.ATP synthase 1.1.4 Chloroplast
+Cre12.g508750 LHCA2 PS.lightreaction.photosystem I.LHC-I 1.1.2.1 membrane;photosynthesis, light harvesting Chloroplast
+Cre13.g586300 FKBP12 cell.cycle.peptidylprolyl isomerase;protein.folding.immunophilins (IMM).FKBPs;protein.folding 31.3.1;29.6.3.1;29.6 protein folding
+Cre01.g010900 GAP3 glycolysis.cytosolic branch.glyceraldehyde 3-phosphate dehydrogenase (GAP-DH);PS.calvin cycle.GAP 4.1.8;1.3.4 oxidation-reduction process;oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor Chloroplast
+Cre09.g402552 NUO11 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.1 oxidation-reduction process;ATP synthesis coupled electron transport;oxidoreductase activity, acting on NAD(P)H Mitochondrion
+Cre01.g027000 RPL11 protein.synthesis.ribosomal protein.unknown.large subunit.L5;protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L16;protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L11 29.2.1.99.2.5;29.2.1.2.2.16;29.2.1.2.2.11
+Cre03.g158900 DLA2 TCA / organic transformation.TCA.pyruvate DH.E2;lipid metabolism.FA synthesis and FA elongation.pyruvate DH 8.1.1.2;11.1.31 transferase activity, transferring acyl groups;metabolic process Chloroplast
+Cre13.g581650 PRPL7 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit.L12 29.2.1.1.1.2.12 translation;structural constituent of ribosome Chloroplast
+Cre09.g402950 CGL21 Chloroplast
+Cre04.g228450 CPL10 mitochondrial electron transport / ATP synthesis.cytochrome c oxidase 9.7 Chloroplast
+Cre02.g146250 NFS1 amino acid metabolism.synthesis.serine-glycine-cysteine group.cysteine 13.1.5.3 Mitochondrion
+Cre06.g293850 CAG2 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I.carbonic anhydrase 9.1.1.5 Mitochondrion
+Cre10.g434450 NUOA9 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).localisation not clear;lipid metabolism.exotics (steroids, squalene etc) 9.1.2;11.8 Mitochondrion
+Cre17.g734500 ATPVE transport.p- and v-ATPases.H+-transporting two-sector ATPase.subunit E;transport.p- and v-ATPases.H+-transporting two-sector ATPase 34.1.1.4;34.1.1 proton-transporting ATPase activity, rotational mechanism;proton-transporting two-sector ATPase complex, catalytic domain;transferase activity, transferring acyl groups other than amino-acyl groups;ATP hydrolysis coupled proton transport
+Cre17.g734200 DPA1 amino acid metabolism.synthesis.aspartate family.lysine.LL-diaminopimelic acid aminotransferase 13.1.3.5.3 pyridoxal phosphate binding;biosynthetic process Chloroplast
+Cre06.g291150 HEL29 RNA.processing.RNA helicase;RNA.processing;hormone metabolism.ethylene.induced-regulated-responsive-activated 27.1.2;27.1;17.5.3 ATP binding;nucleic acid binding Mitochondrion
+Cre01.g049900
+Cre12.g554103 CGL74 protein binding Mitochondrion
+Cre10.g465550 CLPD1 stress.abiotic.heat 20.2.1 protein metabolic process;ATPase activity;ATP binding Chloroplast
+Cre09.g387726 AST1 amino acid metabolism.synthesis.central amino acid metabolism.aspartate.aspartate aminotransferase 13.1.1.2.1 pyridoxal phosphate binding;biosynthetic process;transaminase activity;cellular amino acid metabolic process Mitochondrion
+Cre09.g394436 transport.H+ transporting pyrophosphatase;transport.amino acids 34.30;34.3 membrane;proton transport;hydrogen-translocating pyrophosphatase activity;inorganic diphosphatase activity Secretory pathway
+Cre13.g562750 CGLD38 Chloroplast
+Cre12.g559800 misc.glutathione S transferases 26.9
+Cre06.g303700 Secretory pathway
+Cre02.g080900 PRX4 redox.peroxiredoxin 21.5 oxidoreductase activity Mitochondrion
+Cre05.g247950 Mitochondrion
+Cre10.g424100 IPY1 nucleotide metabolism.phosphotransfer and pyrophosphatases.misc 23.4.99 phosphate-containing compound metabolic process;cytoplasm;inorganic diphosphatase activity;magnesium ion binding Chloroplast
+Cre02.g117500 HXK1 major CHO metabolism.degradation.sucrose.hexokinase 2.2.1.4 carbohydrate phosphorylation;phosphotransferase activity, alcohol group as acceptor;carbohydrate metabolic process;glucose binding;ATP binding;hexokinase activity;cellular glucose homeostasis Secretory pathway
+Cre05.g234637 protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S15A 29.2.1.2.1.515 translation;ribosome;structural constituent of ribosome
+Cre-1.g2717038 psaB PS.lightreaction.photosystem I.PSI polypeptide subunits 1.1.2.2 Chloroplast
+Cre02.g088900 PRPL1 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit.L1 29.2.1.1.1.2.1 Chloroplast
+Cre07.g330200 RSP9 cell.motility.eukaryotes.radial spoke.head 31.6.1.5.1 Secretory pathway
+Cre06.g308250 RPS4 protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S4 29.2.1.2.1.4 translation;ribosome;intracellular;structural constituent of ribosome;RNA binding
+Cre02.g088200 RB60 redox.thioredoxin.PDIL;redox.thioredoxin;PS.lightreaction.photosystem II.biogenesis 21.1.1;21.1;1.1.1.3 cell redox homeostasis Secretory pathway
+Cre06.g293150 PGM12 Secretory pathway
+Cre10.g439850 DNA.unspecified 28.99 integral component of membrane Secretory pathway
+Cre10.g422600 NUO6 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).localisation not clear;mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.2;9.1.1 4 iron, 4 sulfur cluster binding Mitochondrion
+Cre08.g365692 SIR4 S-assimilation.sulfite redox 14.3 oxidation-reduction process;iron-sulfur cluster binding;heme binding;oxidoreductase activity Chloroplast
+Cre01.g031100 TEF30 PS.lightreaction.photosystem II 1.1.1 Chloroplast.Stroma.Thylakoid.Membrane
+Cre11.g468800 PHC71 Chloroplast
+Cre09.g393173 ELI2 PS.lightreaction.unspecified 1.1.99 Chloroplast
+Cre10.g458550 Chloroplast
+Cre08.g377000
+Cre01.g000850 CPLD38 Chloroplast
+Cre10.g425900 LHCA5 PS.lightreaction.photosystem I.LHC-I 1.1.2.1 membrane;photosynthesis, light harvesting Chloroplast
+Cre14.g630550 DEG1B protein.degradation.serine protease 29.5.5 protein binding Chloroplast
+Cre06.g278215 amino acid metabolism.degradation.aromatic aa.tryptophan;amino acid metabolism.degradation.aspartate family.lysine 13.2.6.3;13.2.3.5 metabolic process;catalytic activity
+Cre06.g267200 NUO21 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).localisation not clear;mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.2;9.1.1
+Cre14.g611950 Chloroplast
+Cre11.g467400 Chloroplast
+Cre16.g663200 FAP295 protein.postranslational modification;protein.synthesis.ribosome biogenesis 29.4;29.2.2 protein phosphorylation;protein kinase activity
+Cre09.g415850 CAG3 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I.carbonic anhydrase 9.1.1.5
+Cre06.g294750 CHLG tetrapyrrole synthesis.chlorophyll synthase 19.15 integral component of membrane;prenyltransferase activity Chloroplast
+Cre09.g404100 CLV3 transport.unspecified anions 34.18 transmembrane transport;membrane;chloride transport;voltage-gated chloride channel activity
+Cre06.g256250 TEF14 PS.lightreaction.unspecified.TEF 1.1.99.1 Chloroplast
+Cre11.g468300 SAR1 signalling.G-proteins;minor CHO metabolism.others;protein.targeting.secretory pathway.unspecified 30.5;3.5;29.3.4.99
+Cre06.g282800 ICL1 gluconeogenesis / glyoxylate cycle.isocitrate lyase 6.9
+Cre17.g742300 FAP179 protein binding
+Cre12.g550702 TEF13 PS.lightreaction.unspecified.TEF 1.1.99.1 Chloroplast
+Cre14.g615050 lipid metabolism.exotics (steroids, squalene etc).trans-2-enoyl-CoA reductase (NADPH) 11.8.7 oxidoreductase activity, acting on the CH-CH group of donors;integral component of membrane;lipid metabolic process;cytoplasm;protein binding
+Cre01.g019850 FTSH3 protein.degradation.AAA type;protein.degradation.metalloprotease 29.5.9;29.5.7 integral component of membrane;zinc ion binding;proteolysis;ATP binding;metalloendopeptidase activity Mitochondrion
+Cre01.g066917 LHCBM1 PS.lightreaction.photosystem II.LHC-II 1.1.1.1 membrane;photosynthesis, light harvesting Chloroplast
+Cre14.g617900 RPL35 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L35 29.2.1.2.2.35 translation;ribosome;intracellular;structural constituent of ribosome
+Cre06.g300700 Chloroplast
+Cre07.g344400 amino acid metabolism.synthesis.serine-glycine-cysteine group.serine.phosphoglycerate dehydrogenase 13.1.5.1.1 oxidation-reduction process;NAD binding;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;metabolic process;phosphogluconate dehydrogenase (decarboxylating) activity Chloroplast
+Cre06.g261750 Chloroplast
+Cre10.g450500 major CHO metabolism 2 starch binding Chloroplast
+Cre03.g174300 Secretory pathway
+Cre09.g394850 TEF24 PS.lightreaction.unspecified.TEF 1.1.99.1
+Cre04.g221700 COX3 mitochondrial electron transport / ATP synthesis.cytochrome c oxidase 9.7 aerobic electron transport chain;membrane;heme-copper terminal oxidase activity Mitochondrion
+Cre06.g278213 LHCA6 PS.lightreaction.photosystem I.LHC-I 1.1.2.1 membrane;photosynthesis, light harvesting Chloroplast
+Cre10.g450400 NUO5 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).localisation not clear;mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.2;9.1.1 Mitochondrion
+Cre13.g569750 Mitochondrion
+Cre12.g537550 Mitochondrion
+Cre02.g079400 RNA.RNA binding 27.4 nucleic acid binding Mitochondrion
+Cre12.g501050 ALD6 RNA.processing 27.1
+Cre16.g659350 CYB1 redox.misc;redox.ascorbate and glutathione;N-metabolism.nitrate metabolism.NR 21.99;21.2;12.1.1
+Cre12.g556250 cell.division 31.2 GTP binding
+Cre09.g409150 QCR10
+Cre02.g142206 Chloroplast
+Cre17.g732250 Chloroplast
+Cre07.g353450 ACS3 major CHO metabolism.degradation.sucrose.invertases;secondary metabolism.phenylpropanoids.lignin biosynthesis.4CL;lipid metabolism.FA synthesis and FA elongation.acyl CoA ligase 2.2.1.3;16.2.1.3;11.1.8 metabolic process;catalytic activity
+Cre07.g328200 PSBP6 PS.lightreaction.photosystem II.PSII polypeptide subunits 1.1.1.2 extrinsic component of membrane;photosynthesis;photosystem II oxygen evolving complex;photosystem II;calcium ion binding Chloroplast
+Cre06.g272650 LHCA8 PS.lightreaction.photosystem I.LHC-I 1.1.2.1 membrane;photosynthesis, light harvesting Chloroplast
+Cre16.g688800
+Cre09.g411200 TEF5 misc.other Ferredoxins and Rieske domain;PS.lightreaction.photosystem II.biogenesis 26.30;1.1.1.3 Chloroplast.Stroma.Thylakoid.Membrane
+Cre15.g638500 CYC1 mitochondrial electron transport / ATP synthesis.cytochrome c;mitochondrial electron transport / ATP synthesis.cytochrome c reductase 9.6;9.5 heme binding;electron carrier activity Mitochondrion
+Cre12.g523850 MPPB mitochondrial electron transport / ATP synthesis.cytochrome c reductase;protein.targeting.mitochondria 9.5;29.3.2 Mitochondrion
+Cre12.g485150 GAP1 glycolysis.plastid branch.glyceraldehyde 3-phosphate dehydrogenase (GAP-DH);glycolysis.cytosolic branch.glyceraldehyde 3-phosphate dehydrogenase (GAP-DH) 4.2.8;4.1.8 oxidation-reduction process;oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor Chloroplast
+Cre11.g480150 RPS14 protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S14 29.2.1.2.1.14 translation;ribosome;structural constituent of ribosome
+Cre13.g569250 CGLD9 Chloroplast
+Cre02.g104850 Mitochondrion
+Cre06.g257500 FTT2 cell.motility.eukaryotes.basal bodies;signalling.14-3-3 proteins;minor CHO metabolism.sugar kinases 31.6.1.1;30.7;3.7 protein domain specific binding
+Cre17.g721700 CPLD44 not assigned.no ontology.pentatricopeptide (PPR) repeat-containing protein 35.1.5 Chloroplast
+Cre10.g459400
+Cre10.g435500 EFT2 protein.synthesis.elongation 29.2.4 translational elongation;intracellular;translation elongation factor activity Mitochondrion
+Cre06.g257450 ATPVL1 transport.p- and v-ATPases.H+-transporting two-sector ATPase.subunit C;transport.p- and v-ATPases.H+-transporting two-sector ATPase 34.1.1.2;34.1.1 proton-transporting two-sector ATPase complex, proton-transporting domain;ATP hydrolysis coupled proton transport;hydrogen ion transmembrane transporter activity Mitochondrion
+Cre01.g049350 protein.degradation 29.5 proteolysis;metalloendopeptidase activity Chloroplast
+Cre03.g213313 lipid metabolism.FA synthesis and FA elongation.ACP oxoacyl reductase 11.1.4 Mitochondrion
+Cre12.g505850 CPN23 protein.co-chaperones;protein.folding.chaperones and co-chaperones.co-chaperones;protein.folding 29.9;29.6.2.6;29.6 protein folding;cytoplasm Chloroplast
+Cre12.g483950 MDN4 TCA / organic transformation.TCA.malate DH;gluconeogenesis / glyoxylate cycle.malate dehydrogenase 8.1.9;6.3 oxidation-reduction process;carboxylic acid metabolic process;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;steroid biosynthetic process;3-beta-hydroxy-delta5-steroid dehydrogenase activity Chloroplast
+Cre16.g687900 LHCA7 PS.lightreaction.photosystem I.LHC-I 1.1.2.1 membrane;photosynthesis, light harvesting Chloroplast
+Cre11.g468550 ATPVG transport.p- and v-ATPases 34.1 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances;vacuolar proton-transporting V-type ATPase complex;proton transport
+Cre17.g728800 IDH1 TCA / organic transformation.other organic acid transformations.IDH;TCA / organic transformation.TCA.IDH 8.2.4;8.1.4 oxidation-reduction process;NAD binding;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;magnesium ion binding Mitochondrion
+Cre01.g011000 RPL6 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L6 29.2.1.2.2.6 translation;ribosome;intracellular;structural constituent of ribosome
+Cre08.g358526 AAA1 transport.misc;transport.metabolite transporters at the mitochondrial membrane;transport.metabolite transporters at the envelope membrane 34.99;34.9;34.8 integral component of membrane;transport;ATP binding;ATP:ADP antiporter activity Chloroplast
+Cre-1.g2717000 psaA PS.lightreaction.photosystem I.PSI polypeptide subunits 1.1.2.2 Chloroplast
+Cre02.g113100 mitochondrial pyruvate transport;mitochondrial inner membrane
+Cre12.g530300 FKB16-3 protein.folding.immunophilins (IMM).FKBPs;protein.folding 29.6.3.1;29.6 protein folding Chloroplast
+Cre09.g398900 GP1 PS.carbon concentrating mechanism 1.5 Chloroplast
+Cre06.g260450 LCI20 transport.metabolite transporters at the mitochondrial membrane 34.9 transmembrane transport;integral component of membrane Chloroplast
+Cre09.g415950 PRPL6 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit.L6 29.2.1.1.1.2.6 rRNA binding;translation;ribosome;structural constituent of ribosome Chloroplast
+Cre03.g175200 TOC75 protein.targeting.chloroplast 29.3.3 outer membrane Chloroplast
+Cre03.g156950 QCR8 mitochondrial electron transport / ATP synthesis.cytochrome c reductase 9.5 respiratory chain;electron transport chain;mitochondrial inner membrane
+Cre10.g418450 Secretory pathway
+Cre09.g416350 DNA.synthesis/chromatin structure 28.1 nucleosome assembly;nucleus
+Cre17.g723650 ATO1 amino acid metabolism.degradation.branched chain group.shared 13.2.4.1 transferase activity, transferring acyl groups other than amino-acyl groups;metabolic process Mitochondrion
+Cre12.g537050
+Cre12.g509750 MPPA2 protein.degradation;protein.targeting.mitochondria 29.5;29.3.2 Mitochondrion
+Cre05.g233950 CGL129 Chloroplast
+Cre16.g675500 FKB16-5 cell.cycle.peptidylprolyl isomerase;protein.assembly and cofactor ligation;protein.folding.immunophilins (IMM).FKBPs 31.3.1;29.8;29.6.3.1 protein folding Chloroplast
+Cre06.g261000 PSBR PS.lightreaction.photosystem II.PSII polypeptide subunits 1.1.1.2 thylakoid membrane;photosynthesis;photosystem II oxygen evolving complex;photosystem II Chloroplast
+Cre11.g467725 Secretory pathway
+Cre04.g232104 LHCBM3 PS.lightreaction.photosystem II.LHC-II 1.1.1.1 membrane;photosynthesis, light harvesting Chloroplast
+Cre09.g393765 LMR1 Chloroplast
+Cre06.g283050 LHCA1 PS.lightreaction.photosystem I.LHC-I 1.1.2.1 membrane;photosynthesis, light harvesting Chloroplast
+Cre11.g474800 OTA1 tetrapyrrole synthesis.GSA;amino acid metabolism.degradation.glutamate family.arginine;amino acid metabolism.synthesis.glutamate family.proline.ornithine aminotransferase 19.3;13.2.2.3;13.1.2.2.10 pyridoxal phosphate binding;transaminase activity Mitochondrion
+Cre12.g538700 CPLD62 Chloroplast
+Cre11.g479750 SRP54L protein.targeting.secretory pathway.unspecified;protein.targeting.chloroplast 29.3.4.99;29.3.3 signal recognition particle;7S RNA binding;SRP-dependent cotranslational protein targeting to membrane;GTP binding;GTPase activity Chloroplast
+Cre06.g285250 LHCBM6 PS.lightreaction.photosystem II.LHC-II 1.1.1.1 membrane;photosynthesis, light harvesting Chloroplast
+Cre12.g529651 RPL7A protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L7A 29.2.1.2.2.57
+Cre03.g184500 Chloroplast
+Cre02.g141100 CPL23 development.unspecified;PS.lightreaction.unspecified 33.99;1.1.99 Chloroplast
+Cre01.g042800 DVR1 tetrapyrrole synthesis.divinyl chlorophyllide-a 8-vinyl-reductase 19.13 Chloroplast
+Cre11.g481450 ATPG PS.lightreaction.ATP synthase.subunit B (ATPX);PS.lightreaction.ATP synthase 1.1.4.9;1.1.4 proton-transporting ATP synthase complex, coupling factor F(o);ATP synthesis coupled proton transport;hydrogen ion transmembrane transporter activity Chloroplast
+Cre07.g323600 Chloroplast
+Cre02.g143567
+Cre05.g237400 DAE1 amino acid metabolism.synthesis.aspartate family.lysine.diaminopimelate epimerase 13.1.3.5.4 lysine biosynthetic process via diaminopimelate;diaminopimelate epimerase activity Chloroplast
+Cre03.g178150 CAM1 cell.motility.eukaryotes.central pair.C1a;signalling.calcium;minor CHO metabolism.sugar alcohols 31.6.1.6.1;30.3;3.3
+Cre11.g477950 minor CHO metabolism.callose;protein.postranslational modification 3.6;29.4 Secretory pathway
+Cre02.g141400 PCK1 gluconeogenesis / glyoxylate cycle.phosphoenolpyruvate carboxykinase (PEPCK) 6.4 gluconeogenesis;ATP binding;phosphoenolpyruvate carboxykinase (ATP) activity Chloroplast
+Cre03.g156900 LHCBM5 PS.lightreaction.photosystem II.LHC-II 1.1.1.1 membrane;photosynthesis, light harvesting Chloroplast
+Cre06.g294650 AGT1 amino acid metabolism.synthesis.serine-glycine-cysteine group.glycine.serine glyoxylate aminotransferase;amino acid metabolism.synthesis.central amino acid metabolism.alanine.alanine-glyoxylate aminotransferase;PS.photorespiration.aminotransferases peroxisomal 13.1.5.2.3;13.1.1.3.11;1.2.3 Chloroplast
+Cre03.g145507 Chloroplast
+Cre10.g434200
+Cre06.g274650 NUOAF4 signalling.light 30.11 Chloroplast
+Cre08.g371650 TATB protein transport;protein transporter activity Chloroplast
+Cre06.g284250 LHCBM8 PS.lightreaction.photosystem II.LHC-II 1.1.1.1 membrane;photosynthesis, light harvesting Chloroplast
+Cre02.g076350 ATPVB transport.p- and v-ATPases.H+-transporting two-sector ATPase.subunit B;transport.p- and v-ATPases.H+-transporting two-sector ATPase 34.1.1.1;34.1.1 ATP metabolic process;proton-transporting two-sector ATPase complex, catalytic domain;hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances;proton transport;ATP hydrolysis coupled proton transport;ATP binding
+Cre02.g080650 HSP90B protein.folding.chaperones and co-chaperones.HSP90s;stress.abiotic.heat 29.6.2.4;20.2.1 unfolded protein binding;response to stress;protein folding;ATP binding EndoplasmicReticulum
+Cre17.g732850 SCO1 mitochondrial electron transport / ATP synthesis.cytochrome c oxidase 9.7 oxidation-reduction process;oxidoreductase activity;antioxidant activity Mitochondrion
+Cre02.g113550 Mitochondrion
+Cre06.g280650 CGL59 Chloroplast
+Cre03.g182150 TEF8 PS.lightreaction.unspecified.TEF 1.1.99.1 Chloroplast
+Cre07.g325600 GRX5 redox.glutaredoxins 21.4 cell redox homeostasis;protein disulfide oxidoreductase activity;electron carrier activity Mitochondrion
+Cre05.g232200 NDA3 mitochondrial electron transport / ATP synthesis.NADH-DH (type II).external;mitochondrial electron transport / ATP synthesis.NADH-DH.type II.internal matrix;mitochondrial electron transport / ATP synthesis.NADH-DH.type II.external 9.2.2;9.2.1.4;9.2.1.2 oxidation-reduction process;oxidoreductase activity Chloroplast
+Cre16.g673109 ACP1 lipid metabolism.FA synthesis and FA elongation.ACP protein 11.1.12 Mitochondrion
+Cre10.g430000 Chloroplast
+Cre13.g562850 THF1 protein.targeting;PS.lightreaction.photosystem II 29.3;1.1.1 photosynthesis;photosystem II assembly Chloroplast.Stroma.Thylakoid.Membrane
+Cre11.g468750 CPLD48 Chloroplast
+Cre12.g514200 misc.nitrilases, nitrile lyases, berberine bridge enzymes, reticuline oxidases, troponine reductases 26.8 oxidation-reduction process;flavin adenine dinucleotide binding;oxidoreductase activity, acting on CH-OH group of donors Chloroplast
+Cre09.g409100 UROS1 tetrapyrrole synthesis.uroporphyrinogen III synthase 19.6 tetrapyrrole biosynthetic process;uroporphyrinogen-III synthase activity Chloroplast
+Cre11.g482900 RAB20 signalling.G-proteins;minor CHO metabolism.others 30.5;3.5 GTP binding
+Cre05.g242400 PGR5 PS.lightreaction.cyclic electron flow-chlororespiration 1.1.40 Chloroplast
+Cre01.g002500 COP1 signalling.light 30.11
+Cre09.g390763 FAP354 signalling.G-proteins;minor CHO metabolism.others 30.5;3.5 GTP binding
+Cre19.g750247 transport.unspecified cations 34.14 Chloroplast
+Cre01.g055408 ACS2 major CHO metabolism.degradation.sucrose.invertases;lipid metabolism.FA synthesis and FA elongation.acyl CoA ligase 2.2.1.3;11.1.8 metabolic process;catalytic activity Chloroplast
+Cre07.g349200
+Cre03.g145887 TATC protein.targeting.chloroplast 29.3.3 integral component of membrane Chloroplast
+Cre03.g164300 lipid metabolism.lipid degradation.lysophospholipases.carboxylesterase 11.9.3.2 Chloroplast
+Cre10.g432800 RPSA protein.synthesis.ribosomal protein.eukaryotic.40S subunit.SA 29.2.1.2.1.31 small ribosomal subunit;translation;ribosome;intracellular;structural constituent of ribosome
+Cre-1.g2717030 psbH PS.lightreaction.photosystem II.PSII polypeptide subunits 1.1.1.2 Chloroplast
+Cre12.g560150 FAP353 signalling.G-proteins;minor CHO metabolism.others 30.5;3.5 GTP binding
+Cre16.g665250 TEF6 PS.lightreaction.unspecified.TEF;PS 1.1.99.1;1 Chloroplast
+Cre01.g022500 MME5 TCA / organic transformation.other organic acid transformations.malic 8.2.10 oxidation-reduction process;NAD binding;malate dehydrogenase (decarboxylating) (NAD+) activity Mitochondrion
+Cre13.g590500 FAD6 lipid metabolism.FA desaturation.omega 6 desaturase 11.2.4 lipid metabolic process Chloroplast
+Cre17.g700750 integral component of membrane
+Cre-1.g2717034 atpB PS.lightreaction.ATP synthase 1.1.4 Chloroplast
+Cre05.g238332 PSAD PS.lightreaction.photosystem I.PSI polypeptide subunits 1.1.2.2 photosynthesis;photosystem I reaction center;photosystem I Chloroplast
+Cre02.g094250 transport.metabolite transporters at the mitochondrial membrane;transport.peroxisomes 34.9;34.17
+Cre17.g722150 PKS3 secondary metabolism.wax;lipid metabolism.FA synthesis and FA elongation.fatty acid elongase;lipid metabolism.FA synthesis and FA elongation.beta ketoacyl CoA synthase 16.7;11.1.11;11.1.10 transferase activity, transferring acyl groups other than amino-acyl groups;membrane;fatty acid biosynthetic process
+Cre02.g108850 PRPL17 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit.L17 29.2.1.1.1.2.17 translation;ribosome;intracellular;structural constituent of ribosome Chloroplast
+Cre04.g225050 protein.targeting.chloroplast 29.3.3 Chloroplast
+Cre09.g393200 HSP70C protein.folding.chaperones and co-chaperones.HSP70s;stress.abiotic.heat 29.6.2.3;20.2.1 Mitochondrion.Matrix
+Cre12.g484050 RPL36 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L36 29.2.1.2.2.36 translation;ribosome;intracellular;structural constituent of ribosome
+Cre07.g344350 TPP1 protein.targeting.chloroplast 29.3.3 membrane;serine-type peptidase activity;proteolysis Chloroplast
+Cre01.g042750 ACH1 TCA / organic transformation.TCA.aconitase 8.1.3 metabolic process Chloroplast
+Cre17.g707900 Secretory pathway
+Cre09.g410700 MDN5 TCA / organic transformation.other organic acid transformations.cyt MDH 8.2.9 oxidation-reduction process;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;malate dehydrogenase activity;oxidoreductase activity;malate metabolic process Chloroplast
+Cre06.g278179
+Cre02.g099150 SNAPA1 protein.targeting.secretory pathway.unspecified 29.3.4.99 intracellular protein transport
+Cre03.g144164 RSEP2 protein.degradation.metalloprotease 29.5.7 proteolysis;metalloendopeptidase activity Chloroplast
+Cre06.g262050 AEP1 minor CHO metabolism.others 3.5 isomerase activity;carbohydrate metabolic process Secretory pathway
+Cre16.g695100 amino acid metabolism.degradation.branched chain group.leucine;lipid metabolism.lipid degradation.beta-oxidation.acyl CoA DH 13.2.4.4;11.9.4.2 oxidation-reduction process;flavin adenine dinucleotide binding;oxidoreductase activity, acting on the CH-CH group of donors;metabolic process;acyl-CoA dehydrogenase activity Mitochondrion
+Cre07.g340200 PGRL1 PS.lightreaction.unspecified.TEF;PS.lightreaction.cyclic electron flow-chlororespiration 1.1.99.1;1.1.40 Chloroplast
+Cre02.g115200 RPL27A protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L27A;protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L27A 29.2.1.2.2.527;29.2.1.2.2.0527
+Cre12.g532100
+Cre12.g517400 RAB5 signalling.G-proteins;minor CHO metabolism.others 30.5;3.5 GTP binding Secretory pathway
+Cre09.g405550 TIM21 protein.targeting.mitochondria 29.3.2 protein import into mitochondrial matrix;mitochondrial inner membrane presequence translocase complex Mitochondrion
+Cre03.g171550 SSA13 Mitochondrion
+Cre03.g193750 GCST amino acid metabolism.degradation.serine-glycine-cysteine group.glycine;PS.photorespiration.glycine cleavage.T subunit 13.2.5.2;1.2.4.2 Mitochondrion
+Cre02.g097400 EIF5A protein.synthesis.initiation 29.2.3 positive regulation of translational termination;positive regulation of translational elongation;ribosome binding;translational frameshifting;translation elongation factor activity;RNA binding
+Cre12.g516450 CAG1 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I.carbonic anhydrase 9.1.1.5 Mitochondrion
+Cre05.g244901 NUOB12 electron transport chain;mitochondrial respiratory chain complex I;mitochondrion
+Cre06.g250200 METM metal handling.binding, chelation and storage;amino acid metabolism.synthesis.aspartate family.methionine.S-adenosylmethionine synthetase;amino acid metabolism.synthesis.aspartate family.methionine 15.2;13.1.3.4.11;13.1.3.4 S-adenosylmethionine biosynthetic process;ATP binding;methionine adenosyltransferase activity
+Cre03.g172500 PTOX2 PS.lightreaction.cyclic electron flow-chlororespiration 1.1.40 oxidation-reduction process;alternative oxidase activity Chloroplast
+Cre12.g500150 ALD5 fermentation.aldehyde dehydrogenase;fermentation.LDH;secondary metabolism.N misc.betaine.betaine-aldehyde dehydrogenase 5.10;5.1;16.4.2.1 oxidation-reduction process;oxidoreductase activity;metabolic process Mitochondrion
+Cre12.g534250 Chloroplast
+Cre03.g176250 ATPVD1 transport.p- and v-ATPases.H+-transporting two-sector ATPase 34.1.1 proton-transporting V-type ATPase, V0 domain;ATP hydrolysis coupled proton transport;hydrogen ion transmembrane transporter activity
+Cre03.g171100 Chloroplast
+Cre12.g550850 PSBP1 PS.lightreaction.photosystem II.PSII polypeptide subunits 1.1.1.2 extrinsic component of membrane;photosynthesis;photosystem II oxygen evolving complex;photosystem II;calcium ion binding Chloroplast
+Cre10.g451950 AAT1 amino acid metabolism.synthesis.serine-glycine-cysteine group.glycine.glycine transaminase;amino acid metabolism.synthesis.central amino acid metabolism.alanine.alanine aminotransferase;PS.photorespiration.aminotransferases peroxisomal 13.1.5.2.2;13.1.1.3.1;1.2.3 pyridoxal phosphate binding;biosynthetic process Mitochondrion
+Cre15.g641875 methyltransferase activity;metabolic process Chloroplast
+Cre12.g484000 BCX1 lipid metabolism.FA synthesis and FA elongation.acetyl CoA carboxylation.heteromeric complex.beta carboxyltransferase 11.1.1.2.2 Chloroplast
+Cre06.g252200 TOC34 signalling.G-proteins;protein.targeting.chloroplast 30.5;29.3.3 GTP binding
+Cre12.g488173 Chloroplast
+Cre02.g081250 Chloroplast
+Cre13.g602650 misc.rhodanese 26.23 Chloroplast
+Cre01.g027550 misc.cytochrome P450 26.1 oxidation-reduction process;heme binding;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen;iron ion binding
+Cre07.g344550 amino acid metabolism.synthesis.serine-glycine-cysteine group.serine.phosphoglycerate dehydrogenase 13.1.5.1.1 oxidation-reduction process;NAD binding;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;metabolic process Chloroplast
+Cre12.g528750 RPL12 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L12 29.2.1.2.2.12 translation;ribosome;structural constituent of ribosome
+Cre02.g114600 PRX2 redox.peroxiredoxin.BAS1;redox.peroxiredoxin 21.5.1;21.5 oxidation-reduction process;peroxiredoxin activity;oxidoreductase activity
+Cre-1.g2717041 atpA PS.lightreaction.ATP synthase 1.1.4 Chloroplast
+Cre06.g257950 AST4 amino acid metabolism.synthesis.central amino acid metabolism.aspartate.aspartate aminotransferase 13.1.1.2.1 pyridoxal phosphate binding;biosynthetic process;transaminase activity;cellular amino acid metabolic process Secretory pathway
+Cre01.g047550 RAB6 signalling.G-proteins;minor CHO metabolism.others 30.5;3.5 GTP binding
+Cre09.g386740 Mitochondrion
+Cre12.g498900 RPS7 protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S7 29.2.1.2.1.7 translation;ribosome;intracellular;structural constituent of ribosome
+Cre16.g687200 Chloroplast
+Cre15.g635600 FAP357 cell.unspecified;protein.synthesis.elongation 31.99;29.2.4
+Cre43.g760497 protein.degradation.serine protease 29.5.5 protein metabolic process Chloroplast
+Cre10.g434750 AAI1 amino acid metabolism.synthesis.branched chain group.common.ketol-acid reductoisomerase;amino acid metabolism.synthesis.branched chain group.common 13.1.4.1.2;13.1.4.1 oxidation-reduction process;oxidoreductase activity;branched-chain amino acid biosynthetic process;ketol-acid reductoisomerase activity Chloroplast
+Cre13.g568900 RPL17 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L17 29.2.1.2.2.17 large ribosomal subunit;translation;ribosome;structural constituent of ribosome
+Cre14.g621751 USP cell wall.precursor synthesis.NDP sugar pyrophosphorylase.multiple NDP-Sugars 10.1.1.20 uridylyltransferase activity;metabolic process
+Cre03.g206929 EGY1 protein.degradation 29.5 proteolysis;metalloendopeptidase activity Chloroplast
+Cre08.g358562 CPN20 protein.co-chaperones;protein.folding.chaperones and co-chaperones.co-chaperones;protein.folding 29.9;29.6.2.6;29.6 protein folding;cytoplasm Chloroplast
+Cre17.g734450 PRPL19 protein.synthesis.ribosomal protein.unknown.large subunit.L19;protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit.L19 29.2.1.99.2.19;29.2.1.1.1.2.19 translation;ribosome;intracellular;structural constituent of ribosome Chloroplast
+Cre02.g081050 FAP24 cell.motility.eukaryotes.flagellar associated proteins 31.6.1.10 Secretory pathway
+Cre05.g230850 Chloroplast
+Cre04.g231026 SRP43 protein.targeting.chloroplast;DNA.synthesis/chromatin structure 29.3.3;28.1 signal recognition particle, chloroplast targeting;protein import into chloroplast thylakoid membrane;chloroplast;response to light stimulus Chloroplast
+Cre01.g010400 FAP380 Secretory pathway
+Cre16.g694400 TGD2 protein.targeting.chloroplast 29.3.3
+Cre06.g276001 TOM5
+Cre08.g372100 HSP70A protein.folding.chaperones and co-chaperones.HSP70s;protein.folding;stress.abiotic.heat 29.6.2.3;29.6;20.2.1 Cytosol
+Cre07.g344950 LHCA9 PS.lightreaction.photosystem I.LHC-I 1.1.2.1 membrane;photosynthesis, light harvesting Chloroplast
+Cre06.g273750 SABC transport.ABC transporters and multidrug resistance systems 34.16 ATPase activity;ATP binding Chloroplast
+Cre12.g510400 CPLD30 protein.assembly and cofactor ligation 29.8 Chloroplast
+Cre13.g586050 development.unspecified 33.99 protein binding Chloroplast
+Cre06.g288700 GYD1 PS.photorespiration.glycolate oxydase 1.2.2 oxidation-reduction process;flavin adenine dinucleotide binding;oxidoreductase activity;catalytic activity Mitochondrion
+Cre07.g314150 ZDS1 secondary metabolism.isoprenoids.carotenoids.zeta-carotene desaturase;secondary metabolism.isoprenoids.carotenoids 16.1.4.3;16.1.4 Chloroplast
+Cre11.g476750 FNR1 OPP.electron transfer;PS.lightreaction.other electron carrier (ox/red).ferredoxin reductase 7.3;1.1.5.3 oxidation-reduction process;oxidoreductase activity Chloroplast
+Cre13.g591900 PLD1 Mitochondrion
+Cre04.g214500 IDH3 TCA / organic transformation.TCA.IDH 8.1.4 oxidation-reduction process;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;isocitrate metabolic process;isocitrate dehydrogenase (NADP+) activity Mitochondrion
+Cre08.g378050 NUOP5 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).localisation not clear;mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.2;9.1.1
+Cre02.g084350 CGLD1 membrane Secretory pathway
+Cre10.g436550 LCI5 PS.carbon concentrating mechanism.algal 1.5.3 Chloroplast.Stroma
+Cre16.g681900 SECY1 protein.targeting.chloroplast 29.3.3 membrane;protein transport Chloroplast
+Cre12.g537450 COX13 mitochondrial electron transport / ATP synthesis.cytochrome c oxidase 9.7 Mitochondrion
+Cre12.g537800 RPL7 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L7 29.2.1.2.2.7
+Cre07.g330250 PSAH PS.lightreaction.photosystem I.PSI polypeptide subunits 1.1.2.2 photosynthesis;photosystem I reaction center;photosystem I Chloroplast
+Cre06.g296400 amino acid metabolism.degradation.branched chain group.leucine 13.2.4.4 oxidation-reduction process;flavin adenine dinucleotide binding;oxidoreductase activity, acting on the CH-CH group of donors;metabolic process;acyl-CoA dehydrogenase activity Mitochondrion
+Cre16.g695050 HCD1 lipid metabolism.lipid degradation.beta-oxidation.multifunctional 11.9.4.9 oxidation-reduction process;oxidoreductase activity;fatty acid metabolic process;3-hydroxyacyl-CoA dehydrogenase activity Secretory pathway
+Cre07.g337650 PDC1 TCA / organic transformation.TCA.pyruvate DH.E1 8.1.1.1 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor;metabolic process Mitochondrion
+Cre09.g387838 membrane
+Cre04.g229300 RCA1 PS.calvin cycle.rubisco interacting 1.3.13 ATP binding Chloroplast
+Cre12.g558900 PETO PS.lightreaction.cytochrome b6/f 1.1.3 Chloroplast
+Cre06.g260400 FAP287
+Cre07.g325736 cell.organisation 31.1 Chloroplast
+Cre07.g349350 Mitochondrion
+Cre06.g272450 MBI1 Mitochondrion
+Cre10.g444800 CGL63
+Cre03.g190150 CGL1 Chloroplast
+Cre06.g250902 METH amino acid metabolism.synthesis.aspartate family.methionine.homocysteine S-methyltransferase 13.1.3.4.12 metal ion binding;pteridine-containing compound metabolic process;cobalamin binding;methionine biosynthetic process;methionine synthase activity;intracellular
+Cre16.g657350 protein.postranslational modification.kinase;protein.postranslational modification 29.4.1;29.4 protein phosphorylation;ATP binding;protein kinase activity Chloroplast
+Cre01.g071662 ACS1 major CHO metabolism.degradation.sucrose.invertases;lipid metabolism.FA synthesis and FA elongation.acyl CoA ligase 2.2.1.3;11.1.8 metabolic process;catalytic activity
+Cre17.g731200 Chloroplast
+Cre07.g315900 transport.misc;protein.targeting.secretory pathway 34.99;29.3.4 integral component of membrane;transport
+Cre03.g180750 METE amino acid metabolism.synthesis.aspartate family.methionine.methionine synthase;amino acid metabolism.synthesis.aspartate family.methionine 13.1.3.4.3;13.1.3.4 methionine biosynthetic process;cellular amino acid biosynthetic process;zinc ion binding;5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity
+Cre12.g556050 PRPL9 protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit.L9 29.2.1.1.1.2.9 translation;ribosome;intracellular;structural constituent of ribosome Chloroplast
+Cre10.g417700 RPL3 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L3 29.2.1.2.2.3 translation;ribosome;intracellular;structural constituent of ribosome Chloroplast
+Cre16.g691000 EFP1 protein.synthesis.elongation 29.2.4 peptide biosynthetic process;translational elongation;cytoplasm;translation elongation factor activity Chloroplast
+Cre09.g397697 RPL4 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L4/L1 29.2.1.2.2.141 translation;ribosome;structural constituent of ribosome
+Cre06.g259900 ATPC PS.lightreaction.ATP synthase.gamma chain;PS.lightreaction.ATP synthase 1.1.4.4;1.1.4 proton-transporting ATPase activity, rotational mechanism;proton-transporting ATP synthase activity, rotational mechanism;proton-transporting ATP synthase complex, catalytic core F(1);ATP synthesis coupled proton transport Chloroplast
+Cre12.g487850 CGL49 protein.targeting.secretory pathway.unspecified 29.3.4.99 small GTPase mediated signal transduction;GTP binding
+Cre03.g206600 AAD1 amino acid metabolism.synthesis.branched chain group 13.1.4 metabolic process;catalytic activity Chloroplast
+Cre10.g430150 LPA1 not assigned.no ontology.pentatricopeptide (PPR) repeat-containing protein;PS.lightreaction.photosystem II.biogenesis 35.1.5;1.1.1.3 Chloroplast.Stroma.Thylakoid.Membrane
+Cre03.g189800 CYN38 protein.folding.immunophilins (IMM).cyclophilins;protein.folding 29.6.3.2;29.6 protein folding;peptidyl-prolyl cis-trans isomerase activity;protein peptidyl-prolyl isomerization Chloroplast
+Cre07.g319950 Chloroplast
+Cre-1.g2717046 psaC PS.lightreaction.photosystem I.PSI polypeptide subunits 1.1.2.2 Chloroplast
+Cre-1.g2717009 ycf4 PS.lightreaction.photosystem I.biogenesis 1.1.2.3 Chloroplast
+Cre12.g549350 Chloroplast
+Cre03.g152150
+Cre11.g467350 lipid metabolism.lipid degradation.beta-oxidation.acyl CoA DH 11.9.4.2 oxidation-reduction process;fatty acid beta-oxidation;peroxisome;acyl-CoA oxidase activity;acyl-CoA dehydrogenase activity Chloroplast
+Cre12.g484700
+Cre01.g020350 SDH3 TCA / organic transformation.TCA.succinate dehydrogenase 8.1.7 oxidoreductase activity, acting on the CH-CH group of donors Mitochondrion
+Cre12.g492350
+Cre01.g007850 TEF29 PS.lightreaction.unspecified.TEF 1.1.99.1 Mitochondrion
+Cre17.g727100
+Cre06.g300550
+Cre13.g575000 CCS1 mitochondrial electron transport / ATP synthesis.cytochrome c 9.6
+Cre16.g663900 PBGD1 tetrapyrrole synthesis.porphobilinogen deaminase 19.5 tetrapyrrole biosynthetic process;hydroxymethylbilane synthase activity Chloroplast
+Cre13.g573400 Chloroplast
+Cre13.g605150 MSD2 redox.dismutases and catalases 21.6 oxidation-reduction process;metal ion binding;superoxide metabolic process;superoxide dismutase activity Mitochondrion
+Cre12.g552200 STA4 major CHO metabolism.degradation.starch.starch phosphorylase 2.2.2.2 glycogen phosphorylase activity;carbohydrate metabolic process Chloroplast
+Cre03.g164000 ANR1 PS.lightreaction.cyclic electron flow-chlororespiration 1.1.40 Chloroplast
+Cre01.g037200 Chloroplast
+Cre12.g483650 protein.postranslational modification;PS.lightreaction.state transition 29.4;1.1.30 protein phosphorylation;ATP binding;protein kinase activity
+Cre17.g724300 PSAK PS.lightreaction.photosystem I.PSI polypeptide subunits 1.1.2.2 membrane;photosynthesis;photosystem I Chloroplast
+Cre07.g356350 DXS1 secondary metabolism.isoprenoids.non-mevalonate pathway.DXS 16.1.1.1 terpenoid biosynthetic process;1-deoxy-D-xylulose-5-phosphate synthase activity;metabolic process;catalytic activity Chloroplast
+Cre06.g304350 COX12 mitochondrial electron transport / ATP synthesis.cytochrome c oxidase 9.7 mitochondrion;cytochrome-c oxidase activity
+Cre17.g701650 RPL27 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.L27 29.2.1.2.2.27 translation;ribosome;intracellular;structural constituent of ribosome
+Cre12.g509050 PSBP3 PS.lightreaction.photosystem II.PSII polypeptide subunits 1.1.1.2 extrinsic component of membrane;photosynthesis;photosystem II oxygen evolving complex;photosystem II;calcium ion binding Chloroplast
+Cre16.g677500 APK1 S-assimilation.AKN 14.15 ATP binding;adenylylsulfate kinase activity;sulfate assimilation
+Cre09.g402775
+Cre12.g498950
+Cre01.g038600 FAD7 lipid metabolism.FA desaturation.omega 3 desaturase 11.2.3 oxidation-reduction process;oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water;lipid metabolic process Chloroplast
+Cre10.g424450 TOM40 transport.metabolite transporters at the mitochondrial membrane;transport.porins;protein.targeting.mitochondria 34.9;34.20;29.3.2 transmembrane transport;mitochondrial outer membrane
+Cre12.g547300 transport.ABC transporters and multidrug resistance systems 34.16 ATPase activity;membrane;ATP binding Chloroplast
+Cre12.g519100 ACC1 secondary metabolism.unspecified;lipid metabolism.FA synthesis and FA elongation.acetyl CoA carboxylation.heteromeric complex.alpha carboxyltransferase 16.99;11.1.1.2.1 Chloroplast
+Cre06.g254400 FUM1 TCA / organic transformation.TCA.fumarase 8.1.8 hydro-lyase activity;lyase activity Mitochondrion
+Cre13.g602450 Chloroplast
+Cre06.g279500 CPL6 Chloroplast
+Cre08.g361850 Chloroplast
+Cre03.g189250 RAB11 signalling.G-proteins;minor CHO metabolism.others 30.5;3.5 GTP binding
+Cre09.g416800
+Cre10.g464600 CAM14 calcium ion binding Chloroplast
+Cre02.g145800 MDN3 TCA / organic transformation.other organic acid transformations.cyt MDH 8.2.9 oxidation-reduction process;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;malate dehydrogenase activity;oxidoreductase activity;malate metabolic process
+Cre12.g537200 OGD1 TCA / organic transformation.TCA.2-oxoglutarate dehydrogenase 8.1.5 oxidation-reduction process;thiamine pyrophosphate binding;oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor;metabolic process;tricarboxylic acid cycle;oxoglutarate dehydrogenase (succinyl-transferring) activity Mitochondrion
+Cre11.g481126 redox.misc 21.99 oxidation-reduction process;oxidoreductase activity Mitochondrion
+Cre03.g144807 MAS1 gluconeogenesis / glyoxylate cycle.malate synthase 6.2 glyoxylate cycle;malate synthase activity
+Cre-1.g2716979 tufA protein.synthesis.elongation 29.2.4 Chloroplast
+Cre18.g750047 FMG1 cell.motility.eukaryotes.flagellar membrane proteins 31.6.1.8 Secretory pathway
+Cre16.g696000 minor CHO metabolism.others;misc.UDP glucosyl and glucoronyl transferases;cell wall.precursor synthesis 3.5;26.2;10.1 uridylyltransferase activity;metabolic process Secretory pathway
+Cre03.g179800 LCI24 PS.carbon concentrating mechanism.algal 1.5.3 Chloroplast
+Cre12.g490500 CGL78 Chloroplast
+Cre08.g370450 MGE1 protein.co-chaperones;protein.folding.chaperones and co-chaperones.co-chaperones;protein.folding 29.9;29.6.2.6;29.6 chaperone binding;protein homodimerization activity;protein folding;adenyl-nucleotide exchange factor activity Mitochondrion
+Cre13.g572200 transport.amino acids 34.3 amino acid transmembrane transport Mitochondrion
+Cre12.g493250 FAP358 protein.postranslational modification;protein.synthesis.ribosome biogenesis 29.4;29.2.2 protein phosphorylation;protein kinase activity
+Cre06.g259150 EFG8 protein.synthesis.elongation 29.2.4 GTP binding Mitochondrion
+Cre03.g146247 NUOS4 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).localisation not clear;mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.2;9.1.1 electron transport chain;oxidoreductase activity, acting on NAD(P)H
+Cre08.g382500 RPS25 protein.synthesis.ribosomal protein.unknown.small subunit.S25;protein.synthesis.ribosomal protein.eukaryotic.40S subunit.S25 29.2.1.99.1.25;29.2.1.2.1.25
+Cre06.g263250
+Cre03.g199652 Chloroplast
+Cre11.g481126 redox.misc 21.99 oxidation-reduction process;oxidoreductase activity Mitochondrion
+Cre13.g567450 HON1 DNA.synthesis/chromatin structure.histone 28.1.3 nucleosome assembly;nucleus;DNA binding;nucleosome
+Cre03.g185600 OGD3
+Cre03.g194200 PDH2 TCA / organic transformation.TCA.pyruvate DH.E1;lipid metabolism.FA synthesis and FA elongation.pyruvate DH 8.1.1.1;11.1.31 metabolic process;catalytic activity Chloroplast
+Cre03.g145247 TEF11 PS.lightreaction.unspecified.TEF 1.1.99.1 Chloroplast
+Cre13.g567600 COX4 mitochondrial electron transport / ATP synthesis.cytochrome c oxidase 9.7 mitochondrial envelope;cytochrome-c oxidase activity Mitochondrion
+Cre-2.g801499 nad1 Mitochondrion
+Cre12.g520500 RPP0 protein.synthesis.ribosomal protein.eukaryotic.60S subunit.P0 29.2.1.2.2.80 ribosome biogenesis;intracellular
+Cre-2.g801492 nad5 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I 9.1.1 Mitochondrion
+Cre06.g251900 ALB3.1 protein.targeting.chloroplast 29.3.3 protein insertion into membrane;integral component of membrane
+Cre-2.g801495 cox1 Mitochondrion
+Cre02.g143250 IDH2 TCA / organic transformation.other organic acid transformations.IDH 8.2.4 oxidation-reduction process;NAD binding;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;magnesium ion binding
+Cre03.g194850 MDN1 TCA / organic transformation.other organic acid transformations.cyt MDH;TCA / organic transformation.TCA.malate DH;gluconeogenesis / glyoxylate cycle.malate dehydrogenase 8.2.9;8.1.9;6.3 oxidation-reduction process;carboxylic acid metabolic process;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;oxidoreductase activity Chloroplast
+Cre11.g467689 PETC PS.lightreaction.cytochrome b6/f 1.1.3 oxidation-reduction process;2 iron, 2 sulfur cluster binding;thylakoid membrane;oxidoreductase activity, acting on diphenols and related substances as donors;oxidoreductase activity;plastoquinol--plastocyanin reductase activity Chloroplast
+Cre01.g034400 PGL1 OPP.oxidative PP.6-phosphogluconolactonase 7.1.2 carbohydrate metabolic process Chloroplast
+Cre01.g015350 POR1 tetrapyrrole synthesis.protochlorophyllide reductase 19.14 oxidoreductase activity;metabolic process Chloroplast
+Cre12.g534600 TOM20 protein.targeting.mitochondria 29.3.2 protein import into mitochondrial outer membrane;mitochondrial outer membrane translocase complex
+Cre03.g199535 LHL3 RNA.regulation of transcription.unclassified;RNA.regulation of transcription.heat-shock transcription factor family (HSF);PS.lightreaction.unspecified 27.3.99;27.3.23;1.1.99 Chloroplast
+Cre13.g571700 signalling.calcium;minor CHO metabolism.sugar alcohols;protein.postranslational modification.kinase;protein.postranslational modification 30.3;3.3;29.4.1;29.4 protein phosphorylation;ATP binding;protein kinase activity Mitochondrion
+Cre01.g005150 SGA1 amino acid metabolism.synthesis.serine-glycine-cysteine group.glycine.serine glyoxylate aminotransferase;amino acid metabolism.synthesis.central amino acid metabolism.alanine.alanine-glyoxylate aminotransferase;PS.photorespiration.aminotransferases peroxisomal 13.1.5.2.3;13.1.1.3.11;1.2.3 Mitochondrion
+Cre02.g114850 carbon-nitrogen ligase activity, with glutamine as amido-N-donor;protein binding Mitochondrion
+Cre06.g278750 UCP1 mitochondrial electron transport / ATP synthesis.uncoupling protein 9.8 Mitochondrion
+Cre10.g437950 mannosidase activity;zinc ion binding;mannose metabolic process;carbohydrate metabolic process;alpha-mannosidase activity;hydrolase activity, hydrolyzing O-glycosyl compounds
+Cre02.g077150 CPLD14 Chloroplast
+Cre12.g529100 ATPVL2 transport.p- and v-ATPases.H+-transporting two-sector ATPase.subunit C;transport.p- and v-ATPases.H+-transporting two-sector ATPase 34.1.1.2;34.1.1 proton-transporting two-sector ATPase complex, proton-transporting domain;ATP hydrolysis coupled proton transport;hydrogen ion transmembrane transporter activity
+Cre12.g514750 CIS1 TCA / organic transformation.TCA.CS 8.1.2 transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer Mitochondrion
+Cre06.g264350 PRPL13 protein.synthesis.ribosomal protein.prokaryotic.non-organellar.50S subunit;protein.synthesis.ribosomal protein.prokaryotic.unknown organellar.50S subunit.L13;protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit.L13 29.2.1.1.4.2;29.2.1.1.3.2.13;29.2.1.1.1.2.13 translation;ribosome;structural constituent of ribosome Chloroplast
+Cre12.g527550
+Cre02.g078300 GPX1 oxidation-reduction process;response to oxidative stress;glutathione peroxidase activity
+Cre16.g675650 ALD8 amino acid metabolism.degradation.branched chain group.valine 13.2.4.3 oxidation-reduction process;oxidoreductase activity;metabolic process Mitochondrion
+Cre-1.g2717017 petB PS.lightreaction.cytochrome b6/f 1.1.3 Chloroplast
+Cre05.g232752 Mitochondrion
+Cre12.g559250 FTT1 cell.motility.eukaryotes.basal bodies;signalling.14-3-3 proteins;minor CHO metabolism.sugar kinases 31.6.1.1;30.7;3.7 protein domain specific binding
+Cre02.g074650 lipid metabolism.FA synthesis and FA elongation.acyl-CoA binding protein 11.1.13 protein binding;fatty-acyl-CoA binding
+Cre10.g420350 PSAE PS.lightreaction.photosystem I.PSI polypeptide subunits 1.1.2.2 photosynthesis;photosystem I reaction center;photosystem I Chloroplast
+Cre03.g157700 COX5C mitochondrial electron transport / ATP synthesis.cytochrome c oxidase 9.7
+Cre06.g299350 FBB15
+Cre12.g539000 ECT1 development.unspecified;cell.division;lipid metabolism.phospholipid synthesis.choline-phosphate cytidylyltransferase 33.99;31.2;11.3.6 biosynthetic process;catalytic activity Secretory pathway
+Cre05.g245550 PIK1 signalling.phosphinositides.phosphatidylinositol 4-kinase;signalling.phosphinositides 30.4.2;30.4 phosphatidylinositol-mediated signaling;phosphatidylinositol phosphorylation;phosphotransferase activity, alcohol group as acceptor Mitochondrion
+Cre16.g664550 SHMT1 C1-metabolism.glycine hydroxymethyltransferase;C1-metabolism;PS.photorespiration.serine hydroxymethyltransferase 25.1;25;1.2.5 transferase activity Mitochondrion
+Cre01.g045550 transport.metabolite transporters at the envelope membrane;major CHO metabolism.degradation.starch.transporter 34.8;2.2.2.6 integral component of membrane;membrane Chloroplast
+Cre06.g263300 cell.organisation;protein.targeting.peroxisomes 31.1;29.3.5 peroxisome fission;integral component of peroxisomal membrane
+Cre14.g619133 SDH1 TCA / organic transformation.TCA.succinate dehydrogenase 8.1.7 oxidation-reduction process;oxidoreductase activity Mitochondrion
+Cre16.g677026 PDH1 TCA / organic transformation.TCA.pyruvate DH.E1 8.1.1.1 metabolic process;catalytic activity
+Cre07.g340350 ASA1 mitochondrial electron transport / ATP synthesis.F1-ATPase 9.9 Mitochondrion
+Cre09.g390604
+Cre01.g020305 SDH4
+Cre16.g683550 misc.cytochrome P450;misc.misc2;secondary metabolism.phenylpropanoids 26.10;26.1;16.2 oxidation-reduction process;oxidoreductase activity;FMN binding Secretory pathway
+Cre12.g510050 CTH1 tetrapyrrole synthesis.magnesium-protoporphyrin IX monomethyl ester (oxidative) cyclase 19.12 oxidation-reduction process;metal ion binding;oxidoreductase activity Chloroplast
+Cre03.g183100 TIM22B protein.targeting.mitochondria 29.3.2
+Cre10.g452450 TIC110 protein.targeting.chloroplast 29.3.3 Chloroplast
+Cre02.g099850 PDC2 TCA / organic transformation.TCA.pyruvate DH.E1 8.1.1.1 thiamine pyrophosphate binding;catalytic activity
+Cre01.g044800 PFL1 metabolic process;catalytic activity Chloroplast
+Cre06.g251400 MME6 TCA / organic transformation.other organic acid transformations.malic 8.2.10 oxidation-reduction process;NAD binding;malate dehydrogenase (decarboxylating) (NAD+) activity Mitochondrion
+Cre03.g154350 COX2A mitochondrial electron transport / ATP synthesis.cytochrome c oxidase 9.7 electron transport chain;integral component of membrane Mitochondrion
+Cre02.g107150 Chloroplast
+Cre03.g160500 TSK1 protein.aa activation.lysine-tRNA ligase 29.1.6 tRNA aminoacylation for protein translation;ATP binding;aminoacyl-tRNA ligase activity;nucleic acid binding;nucleotide binding
+Cre02.g093650 oxidation-reduction process;2 iron, 2 sulfur cluster binding;oxidoreductase activity Chloroplast
+Cre12.g509650 PDS1 secondary metabolism.isoprenoids.carotenoids.phytoene dehydrogenase 16.1.4.2 Chloroplast
+Cre11.g467770 PGK1 glycolysis.cytosolic branch.3-phosphoglycerate kinase (PGK);PS.calvin cycle.phosphoglycerate kinase 4.1.11;1.3.3 glycolytic process;phosphoglycerate kinase activity Chloroplast
+Cre11.g467707 ATP4 mitochondrial electron transport / ATP synthesis.F1-ATPase 9.9 proton-transporting ATPase activity, rotational mechanism;proton-transporting ATP synthase activity, rotational mechanism;proton-transporting ATP synthase complex, catalytic core F(1);ATP synthesis coupled proton transport Mitochondrion
+Cre09.g386750 HSP90A protein.folding.chaperones and co-chaperones.HSP90s;stress.abiotic.heat 29.6.2.4;20.2.1 unfolded protein binding;response to stress;protein folding;ATP binding Cytosol;Chloroplast
+Cre17.g703700 SCLB1 TCA / organic transformation.TCA.succinyl-CoA ligase 8.1.6 metabolic process;catalytic activity Mitochondrion
+Cre16.g674950 secondary metabolism.isoprenoids.carotenoids 16.1.4 oxidation-reduction process;oxidoreductase activity Chloroplast
+Cre01.g054500 oxidation-reduction process;NADP binding;integral component of membrane;NAD(P)+ transhydrogenase (AB-specific) activity Mitochondrion
+Cre02.g119550 NIP1 PS.lightreaction.unspecified 1.1.99
+Cre03.g193850 SCLA1 TCA / organic transformation.TCA.succinyl-CoA ligase 8.1.6 cofactor binding;metabolic process;catalytic activity Mitochondrion
+Cre06.g250100 HSP70B protein.folding.chaperones and co-chaperones.HSP70s;stress.abiotic.heat 29.6.2.3;20.2.1 Chloroplast
+Cre09.g396300 PPX1 tetrapyrrole synthesis.protoporphyrin IX oxidase 19.9 Chloroplast
+Cre16.g659700 Chloroplast
+Cre09.g417150 CAT1 redox.dismutases and catalases 21.6 oxidation-reduction process;heme binding;response to oxidative stress;catalase activity
+Cre02.g080200 TRK1 OPP.non-reductive PP.transketolase;PS.calvin cycle.transketolase 7.2.1;1.3.8 metabolic process;catalytic activity Chloroplast
+Cre06.g264200 SDH2 TCA / organic transformation.TCA.succinate dehydrogenase 8.1.7 iron-sulfur cluster binding;electron carrier activity Mitochondrion
+Cre06.g309100 CPN60C protein.folding.chaperones and co-chaperones.HSP60s;protein.folding 29.6.2.2;29.6 ATP binding Mitochondrion
+Cre05.g241950 VDAC2 transport.metabolite transporters at the mitochondrial membrane;transport.unspecified anions 34.9;34.18 transmembrane transport;mitochondrial outer membrane
+Cre09.g401350 Chloroplast
+Cre02.g079800 ASA6 Mitochondrion
+Cre17.g720050 FTSH2 protein.degradation.metalloprotease 29.5.7 proteolysis;ATP binding;metalloendopeptidase activity Chloroplast
+Cre15.g635067 Secretory pathway
+Cre08.g358538 secondary metabolism.isoprenoids.carotenoids.lycopene beta cyclase 16.1.4.5 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen;carotenoid biosynthetic process Chloroplast
+Cre11.g467640
+Cre15.g641200 MCP28 mitochondrial electron transport / ATP synthesis.uncoupling protein;transport.metabolite transporters at the mitochondrial membrane 9.8;34.9
+Cre16.g691850 COX90 mitochondrial electron transport / ATP synthesis.cytochrome c oxidase 9.7
+Cre09.g412100 PSAF PS.lightreaction.photosystem I.PSI polypeptide subunits 1.1.2.2 photosynthesis;photosystem I reaction center;photosystem I Chloroplast
+Cre09.g401886 redox.ascorbate and glutathione.ascorbate 21.2.1 oxidation-reduction process;heme binding;response to oxidative stress;peroxidase activity Mitochondrion
+Cre03.g149100 CIS2 gluconeogenesis / glyoxylate cycle.citrate synthase 6.1 transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer Mitochondrion
+Cre02.g079600 TSF2 protein.aa activation.phenylalanine-tRNA ligase 29.1.20 tRNA aminoacylation;tRNA processing;phenylalanyl-tRNA aminoacylation;cytoplasm;ATP binding;phenylalanine-tRNA ligase activity;aminoacyl-tRNA ligase activity;magnesium ion binding;tRNA binding Chloroplast
+Cre10.g452350 Chloroplast
+Cre01.g018800 ATP6 mitochondrial electron transport / ATP synthesis.F1-ATPase;transport.p- and v-ATPases.H+-transporting two-sector ATPase 9.9;34.1.1 ATP synthesis coupled proton transport;hydrogen ion transmembrane transporter activity Mitochondrion
+Cre16.g680000 ATP5 mitochondrial electron transport / ATP synthesis.F1-ATPase 9.9 proton-transporting ATP synthase activity, rotational mechanism;ATP synthesis coupled proton transport Mitochondrion
+Cre12.g485800 FTSH1 protein.degradation.metalloprotease 29.5.7 proteolysis;ATP binding;metalloendopeptidase activity Chloroplast
+Cre02.g073550 DNA.synthesis/chromatin structure 28.1 nucleosome assembly;nucleus Chloroplast
+Cre16.g672650 MCP14 transport.metabolite transporters at the mitochondrial membrane 34.9
+Cre12.g505150 OPR52 Mitochondrion
+Cre03.g146187 amino acid metabolism.synthesis.glutamate family.arginine.N-acetylglutamate-5-P reductase;amino acid metabolism.synthesis.glutamate family.arginine 13.1.2.3.3;13.1.2.3 oxidation-reduction process;NAD binding;protein dimerization activity;oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor;cellular amino acid biosynthetic process;cytoplasm;N-acetyl-gamma-glutamyl-phosphate reductase activity Chloroplast
+Cre11.g467569 ATPD PS.lightreaction.ATP synthase.delta chain;PS.lightreaction.ATP synthase 1.1.4.7;1.1.4 proton-transporting ATP synthase activity, rotational mechanism;ATP synthesis coupled proton transport Chloroplast
+Cre12.g514850 HSP90C protein.folding.chaperones and co-chaperones.HSP90s;stress.abiotic.heat 29.6.2.4;20.2.1 unfolded protein binding;response to stress;protein folding;ATP binding Chloroplast.Stroma
+Cre03.g144967 protein.degradation.AAA type;protein.degradation.ubiquitin.proteasom 29.5.9;29.5.11.20 ATP binding Mitochondrion
+Cre01.g050950 GGR1 secondary metabolism.isoprenoids.non-mevalonate pathway 16.1.1 FAD binding Chloroplast
+Cre16.g682000 Chloroplast
+Cre01.g049500 COX2B mitochondrial electron transport / ATP synthesis.cytochrome c oxidase 9.7 membrane;copper ion binding;cytochrome-c oxidase activity
+Cre17.g698000 ATP2 mitochondrial electron transport / ATP synthesis.F1-ATPase 9.9 proton-transporting ATP synthase activity, rotational mechanism;ATP metabolic process;proton-transporting two-sector ATPase complex, catalytic domain;hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances;proton transport;ATP hydrolysis coupled proton transport;ATP synthesis coupled proton transport;ATP binding Mitochondrion
+Cre09.g415550 ASA2 mitochondrial electron transport / ATP synthesis.F1-ATPase 9.9 Mitochondrion
+Cre17.g721300 ASA5 mitochondrial electron transport / ATP synthesis.F1-ATPase 9.9
+Cre09.g416150 ASA7 mitochondrial electron transport / ATP synthesis.F1-ATPase 9.9 Mitochondrion
+Cre14.g618700 MRPS7 translation Mitochondrion
+Cre03.g172300 MPC5 transport.metabolite transporters at the mitochondrial membrane 34.9 Mitochondrion
+Cre12.g519350 PHB2 cell.cycle;cell.division 31.3;31.2 membrane
+Cre13.g568400 FTSH4 protein.degradation.metalloprotease 29.5.7 ATPase activity;proteolysis;ATP binding;metalloendopeptidase activity
+Cre03.g187650 Chloroplast
+Cre07.g338050 ASA3 mitochondrial electron transport / ATP synthesis.F1-ATPase 9.9 Mitochondrion
+Cre17.g722750
+Cre-1.g2716989 petA PS.lightreaction.cytochrome b6/f 1.1.3 Chloroplast
+Cre02.g088000 PHB1 mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I;cell.motility.eukaryotes.basal bodies;cell.cycle 9.1.1;31.6.1.1;31.3 membrane Mitochondrion
+Cre17.g727300 NFO2 hormone metabolism.jasmonate.synthesis-degradation.12-oxophytodienoate reductase 3 17.7.1.5 oxidation-reduction process;oxidoreductase activity;FMN binding Chloroplast
+Cre-1.g000035 ORF1995 Chloroplast
+Cre03.g164700 Chloroplast
+Cre12.g534800 GCSP C1-metabolism;amino acid metabolism.degradation.serine-glycine-cysteine group.glycine;PS.photorespiration.glycine cleavage.P subunit 25;13.2.5.2;1.2.4.1 oxidation-reduction process;glycine catabolic process;glycine dehydrogenase (decarboxylating) activity Mitochondrion
+Cre12.g499800
+Cre02.g092400 protein.targeting.nucleus 29.3.1 transport;intracellular
+Cre17.g729450 CLV2 transport.unspecified anions 34.18 transmembrane transport;membrane;chloride transport;voltage-gated chloride channel activity Chloroplast
diff --git a/workflows/alignData_3_v7.fsx b/workflows/alignData_3_v7.fsx
deleted file mode 100644
index ece070bd60c64a3b707407a39b7cab40b53bd084..0000000000000000000000000000000000000000
--- a/workflows/alignData_3_v7.fsx
+++ /dev/null
@@ -1,1510 +0,0 @@
-
-
-
-#r "nuget: Plotly.NET,2.0.0-alpha2"
-#r "nuget: BioFSharp,2.0.0-beta4"
-#r "nuget: BioFSharp.BioDB,2.0.0-beta4"
-#r "nuget: FSharp.Stats,0.3.0-beta"
-#r "nuget: FSharpAux,1.0.0"
-#r "netstandard.dll"
-
-open System
-open Plotly.NET
-open Plotly.NET.Axis
-open BioFSharp
-open FSharp.Stats
-open StyleParam
-open FSharpAux
-open Fitting.LinearRegression.OrdinaryLeastSquares
-
-#time
-
-FSharp.Stats.ServiceLocator.setEnvironmentPathVariable @"C:\Users\bvenn\source\repos\FSharp.Stats\lib"
-FSharp.Stats.Algebra.LinearAlgebra.Service()
-
-let myAxis name = LinearAxis.init(Title=name,Mirror=StyleParam.Mirror.All,Ticks=StyleParam.TickOptions.Inside,Showgrid=false,Showline=true)
-let myAxisWODes name = LinearAxis.init(Title=name,Mirror=StyleParam.Mirror.All,Ticks=StyleParam.TickOptions.Inside,Showgrid=false,Showline=true,Tickfont=Font.init(StyleParam.FontFamily.Arial,Size=6.))
-let myAxisRange name range = LinearAxis.init(Title=name,Range=StyleParam.Range.MinMax(range), Mirror=StyleParam.Mirror.All,Ticks=StyleParam.TickOptions.Inside,Showgrid=false,Showline=true)
-let myAxisRangeWODes name range = LinearAxis.init(Title=name,Range=StyleParam.Range.MinMax(range), Mirror=StyleParam.Mirror.All,Ticks=StyleParam.TickOptions.Inside,Showgrid=false,Showline=true,Tickfont=Font.init(StyleParam.FontFamily.Arial,Size=6.))
-let myAxisLog name = LinearAxis.init(AxisType=AxisType.Log,Title=name, Mirror=StyleParam.Mirror.All,Ticks=StyleParam.TickOptions.Inside,Showgrid=false,Showline=true)
-let styleChart x y chart = chart |> Chart.withX_Axis (myAxis x) |> Chart.withY_Axis (myAxis y)
-let styleChartwR x y (min,max) chart = chart |> Chart.withX_Axis (myAxisRange x (min,max)) |> Chart.withY_Axis (myAxis y)
-
-
-let getReg (vec:Vector<float>) rep = vec.[0..rep]
-Vector.init 2 (fun _ -> 2.)
-
-let fst3 (a,b,c) = a
-let snd3 (a,b,c) = b
-let trd3 (a,b,c) = c
-
-let rnd = System.Random()
-
-
-module Annotation =
-
- open FSharpAux
-
- type ChlamyMapping =
- {
- JGI43full :string
- JGI55full :string
- JGI43 :string
- JGI55 :string
- MapManGMM :string []
- MapManDescription :string []
- GOTerm :string []
- GODescription :string []
- Synonym :string
- SubLocTerm :string
- SubLoc :string
- }
- let createChlamyMapping (str:string) =
- let tmp = str.Split([|'\t'|])
- {
- JGI43full = tmp.[0]
- JGI55full = tmp.[1]
- JGI43 = tmp.[2]
- JGI55 = tmp.[3]
- MapManGMM = tmp.[4].Split([|'|'|])
- MapManDescription = tmp.[5].Split([|'|'|])
- GOTerm = tmp.[6].Split([|'|'|])
- GODescription = tmp.[7].Split([|'|'|])
- Synonym = tmp.[8]
- SubLocTerm = tmp.[9]
- SubLoc = tmp.[10]
- }
-
- //Translate JGI4.3.1 to JGI5.5 and contains further annotations for each cre number
- let readJGIMapping =
- System.IO.File.ReadAllLines(@"\\fp0.uni-kl.de\DFS\tu\bio\biotech\Organisation\AG Muehlhaus\Annotation\Chlamy\chlamyMapping_jgi431_jgi55.txt")
- |> Array.tail
- |> Array.map (fun x ->
- createChlamyMapping x
- )
-
-
- ///Map to translate MapManGmm-Term to MapManDescription for most of MapManBins
- let gmm2Des =
- readJGIMapping
- |> Array.map (fun x ->
- let zip = Array.zip x.MapManGMM x.MapManDescription
- zip
- |> Array.map (fun (gmm,des) ->
- let tmp1 = gmm.Split('.') |> Array.scanReduce (fun acc elem -> acc + "." + elem)
- let tmp2 = des.Split('.') |> Array.scanReduce (fun acc elem -> acc + "." + elem)
- Array.zip tmp1 tmp2
- )
- )
- |> Array.concat
- |> Array.concat
- |> Array.distinct
- |> Map.ofArray
-
- let gmmDesToJGI55 str =
- readJGIMapping
- |> Array.filter (fun x ->
- x.MapManDescription
- |> Array.exists (fun des -> des.StartsWith str)
- )
- |> Array.map (fun x -> x.JGI55)
-
-
- //Map to translate MapManGmm-Term to MapManDescription for most of MapManBins
- let jgi55ToInfo =
- readJGIMapping
- |> Array.map (fun x ->
- x.JGI55,(sprintf "%s\t%s\t%s\t%s\t%s\t%s" x.JGI55 (x.MapManGMM|> String.concat ";") (x.MapManDescription|> String.concat ";") (x.GODescription|> String.concat ";") x.SubLoc x.Synonym)
- )
- |> Map.ofArray
-
- //Map to translate MapManGmm-Term to MapManDescription for most of MapManBins
- let jgi55ToDes =
- readJGIMapping
- |> Array.map (fun x ->
- x.JGI55,(x.MapManDescription|> String.concat ";").Replace("\"",""))
- |> Map.ofArray
-
- let jgi55ToDesStr (str :string)=
- let str = (str.Split '.').[0..1] |> String.concat "."
- if jgi55ToDes.ContainsKey str then jgi55ToDes.[str] else ""
-
- //Map to translate MapManGmm-Term to MapManDescription for most of MapManBins
- let jgi55ToGODes =
- readJGIMapping
- |> Array.map (fun x ->
- x.JGI55,(x.GODescription|> String.concat ";").Replace("\"",""))
- |> Map.ofArray
-
- let jgi55ToGODesStr (str :string)=
- let truncatedStr = (str.Split '.').[0..1] |> String.concat "."
- if jgi55ToGODes.ContainsKey truncatedStr then jgi55ToGODes.[truncatedStr] else ""
-
- //Map to translate MapManGmm-Term to MapManDescription for most of MapManBins
- let jgi55ToSyn =
- readJGIMapping
- |> Array.map (fun x ->
- x.JGI55,x.Synonym.Replace("\"",""))
- |> Map.ofArray
-
- let jgi55ToSynStr (str :string) =
- let truncatedStr = (str.Split '.').[0..1] |> String.concat "."
- //if jgi55ToSyn.ContainsKey truncatedStr then
- // jgi55ToSyn.[truncatedStr]
- //else
- let bioDBQuery = BioDB.FaToolDb.Queries.getSynonyms truncatedStr
- if bioDBQuery = [] then
- ""
- else bioDBQuery |> List.map snd |> String.concat ";"
-
- //Map to translate MapManGmm-Term to MapManDescription for most of MapManBins
- let jgi55ToLoc =
- readJGIMapping
- |> Array.map (fun x ->
- x.JGI55,x.SubLoc
- )
- |> Map.ofArray
-
- let jgi55ToLocStr (str:string) =
- let str' = (str.Split '.').[0..1] |> String.concat "."
- if jgi55ToLoc.ContainsKey str' then jgi55ToLoc.[str'] else ""
-
-module DTW =
-
- type warpingPaths = {
- Distance: float
- Paths : Matrix<float>
- }
-
- //window: see : Only allow for shifts up to this amount away from the two diagonals.
- //maxDist: see : Stop if the returned distance measure will be larger than this value.
- //maxStep: see : Do not allow steps larger than this value.
- //maxLengthDiff : Return infinity if difference in length of two series is larger.
- //penalty : Penalty to add if compression or expansion is applied (on top of the distance).
- //psi : Relaxation to ignore begin and/or end of sequences (for cylical sequencies)
- ///Dynamic Time Warping.
- ///The full matrix of all warping paths is build.
- ///x: First sequence
- ///y: Second sequence
- ///returns: (DTW distance, DTW matrix)
- let warp window maxDist maxStep maxLengthDiff penalty psi (x:array<float>) (y:array<float>) =
- let r,c = x.Length, y.Length
- match maxLengthDiff with
- | Some x when abs(r-c) > x -> None
- | _ ->
- let window =
- match window with
- | Some x -> x
- | None -> max r c
- let maxStep =
- match maxStep with
- | Some x -> Some (x**2.)
- | None -> None
- let maxDist =
- match maxDist with
- | Some x -> Some (x**2.)
- | None -> None
- let penalty =
- match penalty with
- | Some x -> (x**2.)
- | None -> 0.
- let psi =
- match psi with
- | Some x -> x
- | None -> 0
- let dtw =
- let tmp = Matrix.create (r+1) (c+1) infinity
- for i = 0 to psi do
- tmp.[0,i] <- 0.
- tmp.[i,0] <- 0.
- tmp
- ///
- let rec innerLoop upper prevLastUnderMaxDist lastUnderMaxDis i0 i1 i j =
- if j = upper then
- i+1, lastUnderMaxDis
- else
- /// euclidean distance is used
- let d = (x.[i] - y.[j])**2.
- match maxStep with
- | Some x when d > x ->
- innerLoop upper prevLastUnderMaxDist lastUnderMaxDis i0 i1 i (j+1)
- | _ ->
- /// cost function
- dtw.[i1,j+1] <- d + (List.min [ dtw.[i0, j];dtw.[i0, j + 1] + penalty;dtw.[i1, j] + penalty])
- match maxDist with
- | Some x when dtw.[i1, j + 1] <= x ->
- innerLoop upper prevLastUnderMaxDist (j) i0 i1 i (j+1)
- | Some x ->
- dtw.[i1, j + 1] <- infinity
- if prevLastUnderMaxDist < (j+1) then
- (i+1, lastUnderMaxDis)
- else
- innerLoop upper prevLastUnderMaxDist lastUnderMaxDis i0 i1 i (j+1)
- | None ->
- innerLoop upper prevLastUnderMaxDist lastUnderMaxDis i0 i1 i (j+1)
- ///
- let rec outerLoop lastUnderMaxDist i =
- if i = r then Some (dtw,i)
- else
- let prevLastUnderMaxDist =
- if lastUnderMaxDist = -1 then
- infinity |> int |> (*) -1
- else
- lastUnderMaxDist
- let last_under_max_dist, i0, i1 = -1, i, i+1
- let lower =
- let tmp = i - (max 0 (r - c)) - window + 1
- max 0 tmp
- let upper =
- let tmp = i + (max 0 (c - r)) + window
- min c tmp
- let nextIdx,prevLastUnderMaxDist = innerLoop upper prevLastUnderMaxDist lastUnderMaxDist i0 i1 i lower
- match maxDist with
- | Some x when lastUnderMaxDist = -1 ->
- None
- | Some x ->
- outerLoop lastUnderMaxDist (i+1)
- | None ->
- outerLoop lastUnderMaxDist (i+1)
- let (dtw') = outerLoop 0 0
- match dtw' with
- | None ->
- Some ({Distance=infinity;Paths=dtw})
- | Some (dtw',i1) ->
- Matrix.inplace_mapi (fun m n x -> sqrt x) dtw' |> ignore
- let d =
- //if psi = 0 then
- //take the cumulated error in the furthers corner (when square, that last cell)
- dtw.[i1, (min c (c + window - 1))]
- // else
- // let ir = i1
- // let ic = min (c + window - 1)
- // vr = dtw.get[ir-psi:ir+1, ic]
- // vc = dtw[ir, ic-psi:ic+1]
- // mir = np.argmin(vr)
- // mic = np.argmin(vc)
- // if vr[mir] < vc[mic]:
- // dtw[ir-psi+mir+1:ir+1, ic] = -1
- // d = vr[mir]
- // else:
- // dtw[ir, ic - psi + mic + 1:ic+1] = -1
- // d = vc[mic]
- Some ({Distance=d;Paths=dtw})
-
- open FSharpAux
-
-//DTW.warp None None None None None None [|0.1;4.1;0.1;0.1;0.1;|] [|0.1;0.1;0.1;6.1;0.1;|]
-//DTW.warp None None None None None None [|1.;2.;4.;2.;5.;3.;2.;3.;2.;5.;|] [|1.;1.;2.;4.;3.;5.;3.;2.;3.;2.;|]
-
-
- /// Returns the best warping path.
- let bestPath (paths:Matrix<float>) =
- let m,n =
- let m',n' = paths.Dimensions
- m'-1,n'-1
- let pInit = if paths.[m,n] <> -1. then [m-1,n-1] else []
- let rec loop m n path =
- if m <= 0 || n <= 0 then
- match path with
- | h::t -> t
- | [] -> []
- else
- let pos = [|paths.[m - 1, n - 1]; paths.[m - 1, n]; paths.[m, n - 1]|]
- let c = Array.foldi (fun i acc x -> if x < pos.[acc] then i else acc ) 0 pos
- let m',n' =
- if c = 0 then
- (m-1),(n-1)
- elif c = 1 then
- (m-1),(n)
- else
- (m),(n-1)
- if paths.[m',n'] <> -1. then
- loop m' n' ((m'-1,n'-1)::path)
- else loop m' n' (path)
- loop m n pInit
-
- ///
- let warping_Path window maxDist maxStep maxLengthDiff penalty psi (x:array<float>) (y:array<float>) =
- let res = warp window maxDist maxStep maxLengthDiff penalty psi x y
- match res with
- | Some x -> bestPath x.Paths
- | None -> failwith "Warping not possible."
-
- ///
- let distance window maxDist maxStep maxLengthDiff penalty psi (x:array<float>) (y:array<float>) =
- let res = warp window maxDist maxStep maxLengthDiff penalty psi x y
- match res with
- | Some x -> x.Distance
- | None -> failwith "Warping not possible."
-
- let distanceDefault (x:seq<float>) (y:seq<float>) =
- distance None None None None None None (x|> Array.ofSeq) (y|> Array.ofSeq)
-
- /// Aligns source to target. Given a sourceX it returns the mapping of the xVal closest to
- /// sourceX to its targetX counterPart after alignment.
- let align (target:(float*float)[]) (source:(float*float)[]) =
- let xt,yt = target |> Array.unzip
- let xs,ys = source |> Array.unzip
- let optimalPath = warping_Path None None None None None None yt ys
- List.map (fun (ytIdx,ysIdx) -> xt.[ytIdx],ys.[ysIdx]) optimalPath
-
- /// Aligns source to target. Given a sourceX it returns the mapping of the xVal closest to
- /// sourceX to its targetX counterPart after alignment.
- let align' (target:(float*float)[]) (source:(float*float)[]) sourceX =
- let xt,yt = target |> Array.unzip
- let xs,ys = source |> Array.unzip
- let optimalPath = warping_Path None None None None None None yt ys
- List.map (fun (ytIdx,ysIdx) -> xs.[ysIdx],xt.[ytIdx]) optimalPath
- |> List.minBy (fun (xs,xt) -> abs(xs-sourceX))
-
- let s1 =
- [|0.;1.;2.;3.;2.;1.;0.;0.;0.;0.;0.;0.;0.;0.;0.;0.;0.;0.;1.;2.;1.;0.|]
- |> Array.mapi (fun i x -> float i,x)
-
- let s2 =
- [|0.;0.;0.;0.;0.;1.;2.;2.5;2.;1.;0.;0.;0.;0.;0.;0.;0.;0.;0.;0.;0.1;0.2;0.1;0.;0.;0.5;1.;0.5;0.|]
- |> Array.mapi (fun i x -> float i + 20.,x)
-
- let s2' =
- align s1 s2
-
-
- let zNorm (y:float []) =
- let m = Seq.mean y
- let s = Seq.stDev y
- y
- |> Array.map (fun x -> (x-m)/s)
-
-
-
-type Protein = {
- ID : string
- MajorID : string
- MolWeight: float
- //Qvalue : float
- //Score : float
- Intensities: float []
- IBaq : float []
- LFQ : float []
- } with static member create id majID weight inten ibaq lfq=
- {
- ID = id
- MajorID = majID
- MolWeight = weight
- Intensities = inten
- IBaq = ibaq
- LFQ = lfq
- }
-
-type IntMeasurement =
- | Intensity
- | LFQ
- | IBAQ
-
-let getIntensity intensityType transform (x:Protein) =
- match intensityType with
- | IBAQ -> Array.map transform x.IBaq
- | Intensity -> Array.map transform x.Intensities
- | LFQ -> Array.map transform x.LFQ
-
-let readFrame foldername =
- System.IO.File.ReadAllLines(@"C:\Users\bvenn\OneDrive - tukl\Projects\Benni\data\Fred\CPLXome LPA2\20180420 MS " + foldername + " txt\proteinGroups.txt")
- |> Array.tail
- |> Array.map (fun x ->
- let tmp = x.Split '\t'
- let id = tmp.[0]
- let majid = tmp.[1]
- let molWeight = tmp.[121] |> float
- let qValue = tmp.[124]
- let score = tmp.[125]
- let intensity = tmp.[163..198] |> Array.map float
- let iBAQ = tmp.[200..235] |> Array.map float
- let LFQ = tmp.[236..271] |> Array.map float
- //String.concat "\t" [id;majid;molWeight;qValue;score;String.concat "\t" intensity;String.concat "\t"iBAQ;String.concat "\t"LFQ]
- Protein.create id majid molWeight intensity iBAQ LFQ
- )
- |> Array.filter (fun x ->
- not (x.ID.Contains "CON") && not (x.ID.Contains "REV" )
- //&& (x.ID |> String.filter (fun s -> s = 'C') |> fun c -> c.Length = 1)
- )
-
-
-
-let wt1 = readFrame "JBbnAida001"
-let wt2 = readFrame "JBbnBida001"
-let wt3 = readFrame "JBbnCida001"
-let mut1 = readFrame "JBbnDida001"
-let mut2 = readFrame "JBbnEida001"
-let mut3 = readFrame "JBbnFida001"
-
-let datasets = [|wt1;wt2;wt3;mut1;mut2;mut3|]
-let colors= [|"F25930";"FABB01";"FFEA48";"48BCD7";"0081C7";"0B3D6F";|]
-let laneHeader = [|"wt1";"wt2";"wt3";"mut1";"mut2";"mut3"|]
-
-
-
-
-
-
-
-
-
-
-module Normalization =
-
-
- /// defines proteins existing in every lane and are unique in protein group
- let intersUnique =
- [
- wt1 |> Array.map (fun x -> x.ID) |> Array.filter (fun x -> (x.Split ';').Length = 1) |> Set.ofArray
- wt2 |> Array.map (fun x -> x.ID) |> Array.filter (fun x -> (x.Split ';').Length = 1) |> Set.ofArray
- wt3 |> Array.map (fun x -> x.ID) |> Array.filter (fun x -> (x.Split ';').Length = 1) |> Set.ofArray
- mut1 |> Array.map (fun x -> x.ID) |> Array.filter (fun x -> (x.Split ';').Length = 1) |> Set.ofArray
- mut2 |> Array.map (fun x -> x.ID) |> Array.filter (fun x -> (x.Split ';').Length = 1) |> Set.ofArray
- mut3 |> Array.map (fun x -> x.ID) |> Array.filter (fun x -> (x.Split ';').Length = 1) |> Set.ofArray
- ]
- |> Set.intersectMany
-
-
- let plotLaneIntensities (transform:float -> float) name (datasets:Protein[] []) intType =
- datasets
- |> Array.map (fun lane ->
- lane
- //|> Array.filter (fun protein -> inters.Contains protein.ID)
- |> Array.sumBy (fun t -> Array.sum (Array.map transform (getIntensity intType transform t)))
- )
- |> Array.mapi (fun i x ->
- //printfn "%f" x
- laneHeader.[i],x)
- //|> Chart.Combine
- |> Chart.Line
- |> styleChart "lane" "intensity sum"
- |> Chart.withTitle name
- |> Chart.Show
-
-
- //plotLaneIntensities (fun si -> if si = 0. then 0. else log si) "intersect proteins, log lfq sum" [|wt1;wt2;wt3;mut1;mut2;mut3|] IntMeasurement.LFQ
- plotLaneIntensities id "all proteins, lfq sum" [|wt1;wt2;wt3;mut1;mut2;mut3|] IntMeasurement.LFQ
- plotLaneIntensities id "all proteins, IBAq sum" [|wt1;wt2;wt3;mut1;mut2;mut3|] IntMeasurement.IBAQ
- plotLaneIntensities id "all proteins, intensity sum" [|wt1;wt2;wt3;mut1;mut2;mut3|] IntMeasurement.Intensity
-
- let plotSliceIntensities (transform :float -> float) name aggregator (datasets:Protein[] []) intType =
- datasets
- |> Array.map (fun x -> x (*|> Array.filter (fun x -> inters.Contains x.ID)*) |> Array.sortBy (fun x -> x.ID) |> Array.map (fun x -> Array.map transform (getIntensity intType transform x)))
- |> Array.mapi (fun i x ->
- x
- |> JaggedArray.transpose
- |> Array.map aggregator
- |> Array.indexed
- |> Chart.Line
- |> Chart.withTraceName laneHeader.[i])
- |> Chart.Combine
- |> styleChart "slice" "intensity sum"
- |> Chart.withTitle name
- |> Chart.withSize (1100.,750.)
- |> Chart.Show
-
- //plotSliceIntensities (fun si -> if si = 0. then 0. else log si) "All proteins, log intensities sum" Array.sum [|wt1;wt2;wt3;mut1;mut2;mut3|]
- //plotSliceIntensities id "All proteins, intensities sum" Array.sum [|wt1;wt2;wt3;mut1;mut2;mut3|]
-
- let correctedValues intType transform =
- // summed lane intensities
- let summedlanes =
- [|wt1;wt2;wt3;mut1;mut2;mut3|]
- |> Array.map (fun lane ->
- lane
- //|> Array.filter (fun protein -> inters.Contains protein.ID)
- |> Array.sumBy (fun t -> Array.sum (getIntensity intType transform t))
- )
- let laneSumsMean = Seq.mean summedlanes
- let laneSumsCorrection =
- summedlanes
- |> Array.map (fun x -> x/laneSumsMean)
-
- let corrected =
- [|wt1;wt2;wt3;mut1;mut2;mut3|]
- |> Array.mapi (fun laneIndex lane ->
- lane
- |> Array.map (fun protein ->
- let corrected =
- (getIntensity intType transform protein)
- |> Array.mapi (fun sliceIndex slice ->
- slice/laneSumsCorrection.[laneIndex])
- match intType with
- | IntMeasurement.LFQ -> {protein with LFQ = corrected; Intensities = [||]; IBaq = [||]}
- | IntMeasurement.Intensity -> {protein with LFQ = [||]; Intensities = corrected; IBaq = [||]}
- | IntMeasurement.IBAQ -> {protein with LFQ = [||]; Intensities = [||]; IBaq = corrected}
- )
- )
- corrected
-
-let correctedLFQs = Normalization.correctedValues IntMeasurement.LFQ id
-let correctedIBAQss = Normalization.correctedValues IntMeasurement.IBAQ id
-let correctedIntensities = Normalization.correctedValues IntMeasurement.Intensity id
-
-let writeDataFrame (input:Protein[][]) outputPath =
- input
- |> Array.mapi (fun j sample ->
- sample
- //|> Array.take 5
- |> Array.filter (fun x -> not (x.ID.Contains "iRT"))
- |> Array.mapi (fun i x ->
- if i%50=0 then printfn "%i_%i" j i
- //let truncID =
- // x.ID.Split '.'
- // |> fun s ->
- // if s.Length > 4 then printfn "Warning %s" x.ID
- // s.[0..1] |> String.concat "."
- //let syn = Annotation.jgi55ToSynStr truncID
- //let (mapMan,mapManDes) =
- // (BioFSharp.BioDB.FaToolDb.Queries.getOntologyterms BioDB.FaToolDb.MapManOntology truncID).OntologyGroups |> List.unzip |> fun (a,b) -> (a |> String.concat ";").Replace("GMM:",""),b |> String.concat ";"
- //let annotationGO = (BioFSharp.BioDB.FaToolDb.Queries.getOntologyterms BioDB.FaToolDb.GeneOntology truncID).OntologyGroups |> List.map snd |> String.concat ";"
- //let annotationLoc = (BioFSharp.BioDB.FaToolDb.Queries.getOntologyterms BioDB.FaToolDb.SubCellularLocalisationOntology truncID).OntologyGroups |> List.map snd |> String.concat ";"
- //sprintf "%s\t%s\t%f\t%s\t%s\t%s\t%s\t%s" x.ID syn x.MolWeight mapMan mapManDes annotationGO annotationLoc (x.Intensities |> Array.map string |> String.concat "\t")
- sprintf "%s\t%f\t%s" x.ID x.MolWeight (x.Intensities |> Array.map string |> String.concat "\t")
-
-
- )
- )
- |> Array.mapi (fun i sample ->
- let intensityHeader = Array.init 36 (fun x -> sprintf "Intensity_%02i" (x+1)) |> String.concat "\t"
- //let header = sprintf "Identifier\tTrivialName\tMolWeight\tMapMan\tMapManDescription\tGO\tLocalization\t%s" intensityHeader
- let header = sprintf "Identifier\tMolWeight\t%s" intensityHeader
- let rows = Array.append [|header|] sample
- System.IO.File.WriteAllLines(outputPath + laneHeader.[i] + ".txt",rows)
- )
-
-writeDataFrame datasets @"C:\Users\bvenn\OneDrive - tukl\Projects\Benni\results\forMichael_v9\intensitiesRaw_"
-writeDataFrame correctedIntensities @"C:\Users\bvenn\OneDrive - tukl\Projects\Benni\results\forMichael_v9\intensitiesNormed_"
-
-correctedIntensities
-|> Array.map (fun x -> x |> Array.map (fun x -> x.Intensities))
-|> Array.concat
-|> Array.concat
-|> Array.filter (fun x -> x <> 0.)
-|> Array.map log10
-|> Chart.Histogram
-|> styleChart "log10(intensity)" "count"
-|> Chart.Show
-
-Colors.Table.Office.lightOrange
-
-let plotRelativeIntensity cre=
- let getWtMeanIntensity =
- datasets.[0..2] |> Array.concat |> Array.filter (fun x -> not (x.ID.Contains ";"))
- |> Array.filter (fun x -> x.ID.StartsWith cre)
- |> Array.map (fun x -> x.Intensities |> Array.sum)
- |> Seq.mean
- |> fun x -> Shape.init(ShapeType.Line,log10 x,log10 x,0.,350.,Line=Line.init(Color="ED7D31"))
-
- let getMuMeanIntensity =
- datasets.[3..5] |> Array.concat |> Array.filter (fun x -> not (x.ID.Contains ";"))
- |> Array.filter (fun x -> x.ID.StartsWith cre)
- |> Array.map (fun x -> x.Intensities |> Array.sum)
- |> Seq.mean
- |> fun x -> Shape.init(ShapeType.Line,log10 x,log10 x,0.,350.,Line=Line.init(Color="5B9BD5"))
-
- datasets
- |> Array.map (fun x -> x |> Array.map (fun x -> x.Intensities |> Array.sum) )
- |> Array.concat
- |> Array.filter (fun x -> x <> 0.)
- |> Array.map log10
- |> Chart.Histogram
- |> styleChart "log10(protein intensity)" "count"
- |> Chart.withShapes [getWtMeanIntensity;getMuMeanIntensity]
- |> Chart.withTitle cre
- |> Chart.Show
-
-plotRelativeIntensity "Cre01.g042200"
-plotRelativeIntensity "Cre03.g151200"
-plotRelativeIntensity "Cre06.g278245"
-plotRelativeIntensity "Cre06.g272450"
-plotRelativeIntensity "Cre02.g105650"
-plotRelativeIntensity "Cre-1.g2717030"
-plotRelativeIntensity "Cre02.g073850"
-
-Normalization.plotLaneIntensities id "lane ibaq sums (after intensity sum correction)" correctedIBAQss IntMeasurement.IBAQ
-Normalization.plotSliceIntensities id "slice ibaq sums (after intensity sum correction)" Array.sum correctedIBAQss IntMeasurement.IBAQ
-
-Normalization.plotLaneIntensities id "lane intensity sums (after intensity sum correction)" correctedIntensities IntMeasurement.Intensity
-Normalization.plotSliceIntensities id "slice intensity sums (after intensity sum correction)" Array.sum correctedIntensities IntMeasurement.Intensity
-
-
-
-
-///////////////////////////
-/////////////////////////// single warping
-///////////////////////////
-///plot bestPaths and warping
-module Warping =
- correctedIntensities
- |> Array.mapi (fun laneIndex lane ->
- lane
- |> Array.map (fun protein ->
- laneIndex,(protein.MolWeight,protein.ID),protein.LFQ
- )
- )
- |> Array.concat
- |> Array.groupBy (snd3 >> snd)
- |> Array.filter (fun (identifier,items) ->
- not (identifier.Contains ";") &&
- items.Length = 6 &&
- not (identifier.StartsWith "CON")
- )
- |> Array.map (fun (i,x) -> Array.map trd3 x)
- |> Array.item 1
- |> fun z ->
- let median =
- z |> JaggedArray.transpose |> Array.map Seq.median
- |> Array.mapi (fun i x -> float (i+1),x)
-
- z
- |> Array.map (fun lane ->
- let laneSeq = lane |> Array.mapi (fun i x -> float (i+1),x)
- let maxSliceIndex = laneSeq |> Array.maxBy snd |> fst
- let xt,yt = median |> Array.unzip
- let xs,ys = laneSeq |> Array.unzip
- let optimalPath = DTW.warping_Path None None None None None None yt ys
- let newtrace = List.map (fun (ytIdx,ysIdx) -> xt.[ytIdx],ys.[ysIdx]) optimalPath
- let maxSliceIndex_new = newtrace |> Seq.maxBy snd |> fst
-
- newtrace
- |> fun x -> Chart.Line(x,"warped",Color=colors.[5])
- |> fun x ->
- Chart.Combine [Chart.Line(laneSeq,"signal",Color=colors.[3]);Chart.Line(median,"mean",Color=colors.[1]);x],
- optimalPath
- )
- |> Array.unzip
- |> fun (a,b) ->
- a
- |> Chart.Stack 2
- |> Chart.withSize(1000.,800.)
- |> Chart.Show
- b
- |> Array.map (Chart.Line)
- |> Chart.Combine
- |> Chart.Show
-
-
-
- ///plot WARPING boxplots
- correctedIntensities
- |> Array.mapi (fun laneIndex lane ->
- lane
- |> Array.map (fun protein ->
- {|LaneIndex = laneIndex; Weight = protein.MolWeight;ID= protein.ID;LFQ=protein.LFQ|}
- )
- )
- |> Array.concat
- |> Array.groupBy (fun x -> x.ID)
- |> Array.filter (fun (identifier,items) ->
- not (identifier.Contains ";") &&
- items.Length = 6 &&
- not (identifier.StartsWith "CON")
- )
- |> Array.mapi (fun proteinIndex (identifier,x) -> proteinIndex,x |> Array.map (fun z -> z.LFQ))
- //|> Array.item 1
- |> Array.map (fun (proteinIndex,z) ->
- //median trace of this protein
- let median =
- z
- |> JaggedArray.transpose
- |> Array.map Seq.median
- |> Array.mapi (fun i x -> float (i+1),x)
-
- z
- |> Array.mapi (fun laneIndex trace ->
- let traceSeq = trace |> Array.mapi (fun i x -> float (i+1),x)
- let maxSliceIndex = traceSeq |> Array.maxBy snd |> fst
- let xt,yt = median |> Array.unzip
- let xs,ys = traceSeq |> Array.unzip
- let optimalPath = DTW.warping_Path None None None None None None yt ys
- let newtrace = List.map (fun (ytIdx,ysIdx) -> xt.[ytIdx],ys.[ysIdx]) optimalPath
- let maxSliceIndex_new = newtrace |> Seq.maxBy snd |> fst
-
- let peakOffset = maxSliceIndex - maxSliceIndex_new
- {|Lane=laneIndex;MaxIntSlice=maxSliceIndex;PeakOffset=peakOffset|}
- )
- )
- |> Array.concat
- |> Array.groupBy (fun x -> x.Lane)
- |> fun x ->
- printfn "%i" x.Length
- x
- |> Array.map (fun (laneIndex,items) ->
- //everything for one lane
- items
- |> Array.groupBy (fun x -> x.MaxIntSlice)
- |> Array.map (fun (sliceIndex,d) ->
- //everything for one slice within one lane
- d
- |> Array.map (fun x -> x.PeakOffset)
- |> fun s -> Chart.BoxPlot(y=s,Name = string sliceIndex,Color=colors.[laneIndex%6])
- )
- |> Chart.Combine
- )
- |> Chart.Combine
- |> styleChart "sliceIndex" "offset to warped (maxLFQSliceIndex - warpedSliceIndex"
- |> Chart.withSize (1000.,900.)
- |> Chart.Show
-
-///////////////////////////
-/////////////////////////// offset Plots
-///////////////////////////
-module OffsetPlots =
- correctedIntensities
- |> Array.mapi (fun i lane ->
- lane
- |> Array.filter (fun x -> Normalization.intersUnique.Contains x.ID)
- |> Array.mapi (fun j protein ->
- i,protein.ID,protein.LFQ |> Array.indexed |> Array.maxBy snd |> fst
- )
- )
- |> Array.concat
- |> Array.groupBy (fun (lane,id,maxIntSliceIndex) -> id)
- |> Array.map (fun (id,items) ->
- let medianSlice = items |> Seq.map trd3 |> Seq.median
- items
- |> Array.map (fun (lane,_,maxIntSliceIndex) ->
- lane,maxIntSliceIndex,maxIntSliceIndex-medianSlice
- )
- )
- |> Array.concat
- |> Array.groupBy fst3
- |> Array.map (fun (lane,items) ->
- items
- |> Array.map (fun (_,b,c) -> b,c)
- |> Array.groupBy fst
- |> Array.sortBy fst
- |> Array.map (fun (slice,it) ->
- let offset = it|> Array.map snd
- let xAx = "sl " + string slice
- Chart.BoxPlot(y=offset,Name=xAx,Color=colors.[lane])
- )
- |> Chart.Combine
- )
- |> Chart.Combine
- |> styleChart "sliceIndex" "offset to median (maxLFQSliceIndex - medianSliceIndex)"
- |> Chart.withSize (1000.,900.)
- |> Chart.Show
-
-
- correctedIntensities
- |> Array.map (Array.filter (fun x -> Normalization.intersUnique.Contains x.ID) >> Array.sortBy (fun x -> x.ID))
- |> JaggedArray.transpose
- |> Array.filter (fun lanes ->
- lanes
- |> Array.filter (fun x -> Seq.median x.LFQ = 0.)
- |> Array.length
- |> fun reallySignalCount -> reallySignalCount > 4
- )
- |> Array.concat
- //1.
- |> Array.groupBy (fun x -> x.ID)
- |> Array.filter (fun (_,it) -> it.Length = 6)
- |> Array.map (fun (id,items) ->
- //get median trace
- let mediantrace =
- items
- |> Array.map (fun x -> x.LFQ)
- |> JaggedArray.transpose
- |> Array.map Seq.mean //here median?
-
- let indexMaxLFQMean =
- mediantrace
- |> Array.indexed
- |> Array.maxBy snd
- |> fst
-
- let indicesOfMaxLFQ =
- items
- |> Array.map (fun x -> x.LFQ |> Array.indexed |> Array.maxBy snd |> fst)
-
- indicesOfMaxLFQ
- |> Array.mapi (fun laneIndex single ->
- let offset = single - indexMaxLFQMean
- {|LaneID=laneIndex;SliceID=single;SliceOffset=offset|}
- )
- )
- |> Array.concat
- |> Array.groupBy (fun x -> x.LaneID)
- |> Array.sortBy fst
- |> Array.map (fun (laneID,items) ->
- items
- |> Array.groupBy (fun t -> t.SliceID)
- |> Array.sortBy fst
- |> Array.map (fun (sliceID,items) ->
- let offsets = items |> Array.map (fun x -> x.SliceOffset)
- printfn "%i\t%i\t%i\t" laneID sliceID items.Length
- Chart.BoxPlot(y=offsets,Name="sI " + string sliceID,Color=colors.[laneID])//|> Chart.withTraceName (sprintf "%i" items.Length)
- )
- )
- |> Array.concat
- |> Chart.Combine
- |> styleChart "sliceIndex" "offset to mean (maxLFQSliceIndex - medianSliceIndex)"
- |> Chart.withSize (1000.,900.)
- |> Chart.Show
-
-
-
-
- //////////////////////////////////
- ////////////////////////////////// plot peak coverage
- //////////////////////////////////
- //////////////////////////////////
-
- correctedIntensities
- |> Array.mapi (fun i lane ->
- lane
- |> Array.map (fun protein ->
- let maxIntens = protein.LFQ |> Array.max
- protein.LFQ |> Array.filter (fun x -> x > 0.2*maxIntens)
- |> Array.length
- |> fun x -> float x
- )
- |> fun j -> Chart.BoxPlot(y=j,Jitter=0.2,Boxpoints=Boxpoints.All,Boxmean=BoxMean.True,Color=colors.[i])
- )
- |> Chart.Combine
- |> styleChart "" "signal / lane"
- |> Chart.Show
-
-
- let getPeakWidths signal percentageForMinIntensity =
- let minSig = signal |> Array.max |> fun x -> x * percentageForMinIntensity
- let rec loop i acc current =
- if i = signal.Length-1 then
- if signal.[i] > minSig then
- if current = 0 then
- 1::acc
- else (current+1)::acc
- else
- if current = 0 then acc else (current)::acc
- else
- if current <> 0 then
- if signal.[i] < minSig then
- loop (i+1) (current::acc) 0
- else loop (i+1) acc (current+1)
- else
- if signal.[i] > minSig then
- loop (i+1) acc 1
- else loop (i+1) acc 0
- loop 0 [] 0
-
- let plotPeaksPerLane percentageForMinIntensity =
- correctedIntensities
- |> Array.mapi (fun i lane ->
- lane
- |> Array.map (fun protein ->
- getPeakWidths protein.LFQ percentageForMinIntensity
- |> Seq.length
- )
- |> fun j -> Chart.BoxPlot(y=j,Name=laneHeader.[i],Jitter=0.2,Boxpoints=Boxpoints.All,Boxmean=BoxMean.True,Color=colors.[i])
- )
- |> Chart.Combine
- |> styleChart "" "peaks / lane"
- |> Chart.withTitle (string (int (10. * percentageForMinIntensity)) + "% threshold" )
-
- let plotPeaksPerLaneHisto percentageForMinIntensity =
- correctedIntensities
- |> Array.mapi (fun i lane ->
- lane
- |> Array.map (fun protein ->
- getPeakWidths protein.LFQ percentageForMinIntensity
- |> Seq.length
- )
- )
- |> Array.concat
- |> fun x -> Chart.Histogram(x,HistNorm=HistNorm.Probability,Color="grey")
- |> styleChart "" "peaks / lane"
- |> Chart.withTitle (string (int (10. * percentageForMinIntensity)) + "% threshold" )
-
-
-
- let plotPeaksWidth percentageForMinIntensity =
- correctedIntensities
- |> Array.mapi (fun i lane ->
- lane
- |> Array.map (fun protein ->
- getPeakWidths protein.LFQ percentageForMinIntensity
- )
- |> Seq.concat
- |> fun j -> Chart.BoxPlot(y=j,Name=laneHeader.[i],Jitter=0.2,Boxpoints=Boxpoints.All,Boxmean=BoxMean.True,Color=colors.[i])
- )
- |> Chart.Combine
- |> styleChart "" "peakwidth / lane"
- |> Chart.withTitle (string (int (100. * percentageForMinIntensity)) + "% threshold" )
-
- let plotPeaksWidthHisto percentageForMinIntensity =
- correctedIntensities
- |> Array.mapi (fun i lane ->
- lane
- |> Array.map (fun protein ->
- getPeakWidths protein.LFQ percentageForMinIntensity
- )
- |> Seq.concat
- )
- |> Seq.concat
- |> fun x -> Chart.Histogram(x,HistNorm=HistNorm.Probability,Color="grey")
- |> styleChart "" "peakwidth / lane"
- |> Chart.withTitle (string (int (100. * percentageForMinIntensity)) + "% threshold" )
-
- [
- plotPeaksPerLane 0.05
- plotPeaksPerLane 0.1
- plotPeaksPerLane 0.2
- plotPeaksWidth 0.05
- plotPeaksWidth 0.1
- plotPeaksWidth 0.2
- ]
- |> Chart.Stack 3
- |> Chart.withSize (1500.,1000.)
- |> Chart.withTitle ("5% (left), 10% (middle) and 20% (right) threshold" )
- |> Chart.Show
-
- [
- plotPeaksPerLaneHisto 0.05
- plotPeaksPerLaneHisto 0.1
- plotPeaksPerLaneHisto 0.2
- plotPeaksWidthHisto 0.05
- plotPeaksWidthHisto 0.1
- plotPeaksWidthHisto 0.2
- ]
- |> Chart.Stack 3
- |> Chart.withSize (1500.,1000.)
- |> Chart.withTitle ("5% (left), 10% (middle) and 20% (right) threshold" )
- |> Chart.Show
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-//////////////////////////////////
-////////////////////////////////// distances
-//////////////////////////////////
-//////////////////////////////////
-
-
-
-
-let getDTWeuc (x:float []) (y:float []) =
- let dtw = DTW.distanceDefault x y
- let euc = ML.DistanceMetrics.euclidean x y
- let meanInt = max (Seq.mean x) (Seq.mean y)
- //(dtw + euc) / meanInt
-
- euc / meanInt
-
-
-
-
-let getWarpDistancesOfSignals (input:float [] []) =
- let inputCount = input.Length
- let normedInput =
- //input |> Array.map DTW.zNorm
- //input |> Array.map (fun x -> x |> Array.map (fun sx -> sx / (Seq.average x)))
- input
- let rec loop i acc =
- if i >= inputCount-1 then
- acc
- else
- normedInput.[(i+1)..]
- |> Array.map (fun x ->
- //let dtwDist = DTW.distanceDefault x normedInput.[i]
- //let euc = ML.DistanceMetrics.euclidean x normedInput.[i]
- //dtwDist + euc
- //log(dtwDist)
- //log(dtwDist + euc)
- getDTWeuc x normedInput.[i]
- )
- |> fun distances ->
- loop (i+1) (distances::acc)
- loop 0 []
- |> Array.concat
-
-
-
-
-//////////////////////////////////
-////////////////////////////////// Writer (combined Funktion)
-//////////////////////////////////
-//////////////////////////////////
-
-let combinedFunction intMeasurement=
- let getPeaks signal (percentageForMinIntensity :float) =
- let minSig = signal |> Array.max |> fun x -> x * percentageForMinIntensity
- let sigLength = signal.Length
- [for i=1 to signal.Length - 2 do
- let currSignal = signal.[i]
- if currSignal > signal.[i-1] && currSignal > signal.[i+1] && currSignal > minSig then yield (i+1)]
- |> fun acc -> if signal.[0] > signal.[1] && signal.[0] > minSig then 1::acc else acc
- |> fun acc -> if signal.[sigLength-1] > signal.[sigLength-2] && signal.[sigLength-1]> minSig then sigLength::acc else acc
-
- let dataset =
- match intMeasurement with
- | IntMeasurement.LFQ -> correctedLFQs |> Array.map (fun lane -> lane |> Array.filter (fun x -> not (x.ID.Contains ";") && not (x.ID.Contains "iRT")))
- | IntMeasurement.IBAQ -> correctedIBAQss |> Array.map (fun lane -> lane |> Array.filter (fun x -> not (x.ID.Contains ";") && not (x.ID.Contains "iRT")))
- | IntMeasurement.Intensity -> correctedIntensities |> Array.map (fun lane -> lane |> Array.filter (fun x -> not (x.ID.Contains ";") && not (x.ID.Contains "iRT")))
-
- dataset
- |> Array.mapi (fun laneIndex lane ->
- lane
- //|> Array.filter (fun protein -> Normalization.intersUniqueMin2.Contains protein.ID)
- //|> Array.filter (fun protein -> Normalization.intersUnique.Contains protein.ID)
- |> Array.map (fun x ->
- let intensities =
- match intMeasurement with
- | IntMeasurement.LFQ -> x.LFQ
- | IntMeasurement.IBAQ -> x.IBaq
- | IntMeasurement.Intensity -> x.Intensities
- laneIndex,x.ID,intensities)
- )
- |> Array.concat
- |> Array.groupBy snd3
- //|> Array.sortByDescending (fun (id,it) -> it|> Array.map snd|> JaggedArray.transpose |> Array.map Seq.mean |> Seq.indexed |> Seq.maxBy snd |> fst)
- |> Array.map (fun (id,x) ->
- let id' = (id.Split '.').[0..1] |> String.concat "."
- let (wt,wtCount) =
- let empty :float [] []= Array.init 3 (fun _ -> Array.zeroCreate 36)
- let intensities = x |> Array.filter (fun (lI,id,lfq) -> lI <=2)
- for elem in intensities do empty.[fst3 elem] <- trd3 elem
- //for i=0 to intensities.Length-1 do empty.[i] <- intensities.[i]
- empty,(intensities |> Array.map trd3 |> Array.filter (fun x -> (Array.exists (fun t -> t>0.) x))).Length
- let wtMeans = wt |> JaggedArray.transpose |> Array.map Seq.mean
- let (mut,mutCount) =
- let empty :float [] []= Array.init 3 (fun _ -> Array.zeroCreate 36)
- let intensities = x |> Array.filter (fun (lI,id,lfq) -> lI >=3)
- for elem in intensities do empty.[fst3 elem - 3] <- trd3 elem
- //for i=0 to intensities.Length-1 do empty.[i] <- intensities.[i]
- empty,(intensities |> Array.map trd3 |> Array.filter (fun x -> (Array.exists (fun t -> t>0.) x))).Length
- let mutMeans = mut |> JaggedArray.transpose |> Array.map Seq.mean
- let ttestSums =
- let wtSums = (wt |> Array.map Seq.sum |> vector)
- let mutSums = (mut |> Array.map Seq.sum |> vector)
- //printfn "%A %A" wtSums mutSums
- if Seq.mean wtSums = 0. then
- if Seq.mean mutSums = 0. then nan
- else (Testing.TTest.twoSample false mutSums wtSums).PValue
- else (Testing.TTest.twoSample false wtSums mutSums).PValue
-
- let dH0_wt = getWarpDistancesOfSignals wt
- let dH0_mut = getWarpDistancesOfSignals mut
- let combinedH0Distances = Array.append dH0_wt dH0_mut
- [id' + " wt";id' + " mu"],[wtMeans;mutMeans;(*x.[0..2] |> Array.map snd |> JaggedArray.transpose |> Array.map Seq.mean*)],(combinedH0Distances,ttestSums,(wtCount,mutCount))
- )
- |> Array.unzip3
- |> fun (rowNames,heatmapdata,h0andTests) ->
- //log of distance + euclidean
- let (h0Distances,pVal,replicates) =
- Array.unzip3 h0andTests
-
- let (listString,distances) =
- heatmapdata
- |> Array.mapi (fun i x ->
- let d = getDTWeuc x.[0] x.[1]
- let string = sprintf "%s\t%f" ((rowNames.[i].[0].Split ' ').[0]) d
- string,d)
- |> Array.unzip
-
- let sortedIndices =
- distances
- |> Array.indexed
- |> Array.sortBy snd
- |> Array.map fst
-
- let sortedRownames =
- sortedIndices
- |> Array.map (fun i -> rowNames.[i])
-
- let pValSorted =
- sortedIndices
- |> Array.map (fun i -> pVal.[i])
-
- let replicateSorted =
- sortedIndices
- |> Array.map (fun i -> replicates.[i])
-
-
- let distanceHeatmap =
- distances
- |> Array.sort
- |> Array.map (fun x -> [|[|x|];[|x|]|])
- |> Seq.concat
- |> fun x ->
- Chart.Heatmap(x,RowNames=(sortedRownames|> Seq.concat))
- |> Chart.withX_Axis(LinearAxis.init(Showticklabels=false,Tickfont=Font.init(Color="white"),Ticks=TickOptions.Empty))
-
-
- let traces =
- sortedIndices
- |> Array.map (fun i -> heatmapdata.[i])
- |> Array.map (fun x -> [| DTW.zNorm x.[0];DTW.zNorm x.[1]|])
- //DTW.zNorm [|0.;0.;0.;|]
-
- let peaks =
- sortedIndices
- |> Array.map (fun i -> heatmapdata.[i])
- |> Array.map (fun x ->
- "[" + (getPeaks x.[0] 0.1 |> List.map string |> String.concat ";") + ";]",
- "[" + (getPeaks x.[1] 0.1 |> List.map string |> String.concat ";") + ";]"
- )
-
- //let rplicateCount =
- // sortedIndices
- // |> Array.map (fun i -> heatmapdata.[i])
- // |> Array.map (fun x -> x.[0] x.[1]|])
-
- let tracesOrig =
- sortedIndices
- |> Array.map (fun i -> heatmapdata.[i])
- |> Array.map (fun x -> [|x.[0];x.[1]|])
-
- let traceHeatmap =
- Chart.Heatmap((traces|> Array.concat),ColNames=[1..36],RowNames=(sortedRownames|> Seq.concat),Showlegend=false,Colorbar=false)
- |> Chart.withColorBarStyle("int",Side.Left)
- |> Chart.withX_AxisStyle "Slice index"
-
- let h0Distances = h0Distances |> Array.concat
- let h0Size = h0Distances.Length
- let cutOffIndex =0.95 * (float h0Size)
- let cutOffThreshold = (h0Distances |> Array.sort).[int cutOffIndex]
-
- //distances
- //|> Array.sort
- //|> Array.iteri (fun i difference ->
- // if difference > cutOffThreshold then
- // printfn "%s\t%f\t%s\t%s\t%s" sortedRownames.[i].[0] difference (Annotation.jgi55ToSynStr sortedRownames.[i].[0]) (traces.[i].[0] |> Array.map string |> String.concat "\t") (traces.[i].[1]|> Array.map string |> String.concat "\t")
- // )
-
- distances
- |> Array.sort
- |> Array.mapi (fun i difference ->
- if i%10=0 then printfn "%i" i
- let name = (sortedRownames.[i].[0].Split ' ').[0]
- let synonym = "test"//(Annotation.jgi55ToSynStr name)
- let wtmeans = tracesOrig.[i].[0]
- let mutmeans = tracesOrig.[i].[1]
- let wtMeanSum = Seq.sum wtmeans
- let mutMeanSum = Seq.sum mutmeans
- let wtMeansStr= wtmeans |> Array.map string |> String.concat "\t"
- let mutMeansStr= mutmeans |> Array.map string |> String.concat "\t"
- let pValSums = pValSorted.[i]
- let dtweucAdj = getDTWeuc wtmeans mutmeans
- let dtw = DTW.distanceDefault wtmeans mutmeans
- let euc = ML.DistanceMetrics.euclidean wtmeans mutmeans
- let maxMean = max (Seq.mean wtmeans) (Seq.mean mutmeans)
- //printfn "%s\t%f\t%s\t%s\t%s" sortedRownames.[i].[0] difference (Annotation.jgi55ToSynStr sortedRownames.[i].[0]) (traces.[i].[0] |> Array.map string |> String.concat "\t")
- let (mapMan,mapManDes) =
- "test","test"//(BioFSharp.BioDB.FaToolDb.Queries.getOntologyterms BioDB.FaToolDb.MapManOntology name).OntologyGroups |> List.unzip |> fun (a,b) -> (a |> String.concat ";").Replace("GMM:",""),b |> String.concat ";"
- let annotationGO = "test"//(BioFSharp.BioDB.FaToolDb.Queries.getOntologyterms BioDB.FaToolDb.GeneOntology name).OntologyGroups |> List.map snd |> String.concat ";"
- let annotationLoc = "test"//(BioFSharp.BioDB.FaToolDb.Queries.getOntologyterms BioDB.FaToolDb.SubCellularLocalisationOntology name).OntologyGroups |> List.map snd |> String.concat ";"
- //sprintf $"{name}\t{synonym}\t{annotation}\t{pValSums}\t{difference}\t{dtw}\t{euc}\t{maxMean}\t{wtMeansStr}\t{mutMeansStr}"
-
- //let linkToFile = "=HYPERLINK(LEFT(CELL(\"filename\", $A$1), FIND(\"[\",CELL(\"filename\",$A$1))-1) & \"plots\LFQ\\" + synonym + "_" + name + ".html\",\"" + name + "\")"
- let linkToFile =
- match intMeasurement with
- | IntMeasurement.LFQ -> "=HYPERLINK(LEFT(CELL(\"filename\", $A$1), FIND(\"[\",CELL(\"filename\",$A$1))-1) & \"plots\LFQ\\" + synonym + "_" + name + ".html\",\"" + name + "\")"
- | IntMeasurement.Intensity -> "=HYPERLINK(LEFT(CELL(\"filename\", $A$1), FIND(\"[\",CELL(\"filename\",$A$1))-1) & \"plots\\" + synonym + "_" + name + ".html\",\"" + name + "\")"
- sprintf $"{linkToFile}\t{synonym}\t{mapManDes}\t{mapMan}\t{annotationGO}\t{annotationLoc}\t{fst replicateSorted.[i]}\t{snd replicateSorted.[i]}\t{pValSums}\t{difference}\t{dtw}\t{euc}\t{maxMean}\t{fst peaks.[i]}\t{snd peaks.[i]}\t{wtMeansStr}\t{mutMeansStr}"
- )
- |> fun x ->
- printfn "Name\tSynonym\tMapMan\tMapManTerm\tGO\tSubLoc\treplicatesWT\treplicatesMut\tpValSum\tdiff_adj\tdtw\teuc\tmaxMean\tpeaksWT\tpeaksMut\twtMean1\twtMean2\twtMean3\twtMean4\twtMean5\twtMean6\twtMean7\twtMean8\twtMean9\twtMean10\twtMean11\twtMean12\twtMean13\twtMean14\twtMean15\twtMean16\twtMean17\twtMean18\twtMean19\twtMean20\twtMean21\twtMean22\twtMean23\twtMean24\twtMean25\twtMean26\twtMean27\twtMean28\twtMean29\twtMean30\twtMean31\twtMean32\twtMean33\twtMean34\twtMean35\twtMean36\tmutMean1\tmutMean2\tmutMean3\tmutMean4\tmutMean5\tmutMean6\tmutMean7\tmutMean8\tmutMean9\tmutMean10\tmutMean11\tmutMean12\tmutMean13\tmutMean14\tmutMean15\tmutMean16\tmutMean17\tmutMean18\tmutMean19\tmutMean20\tmutMean21\tmutMean22\tmutMean23\tmutMean24\tmutMean25\tmutMean26\tmutMean27\tmutMean28\tmutMean29\tmutMean30\tmutMean31\tmutMean32\tmutMean33\tmutMean34\tmutMean35\tmutMean36"
-
- x |> Array.iter (printfn "%s")
-
- let shape() = Shape.init(ShapeType.Line,cutOffThreshold,cutOffThreshold,0.,0.05)
- [
- h0Distances
- |> fun x -> Chart.Histogram(x,HistNorm=HistNorm.Probability)
- |> Chart.withShape (shape())
- |> Chart.withTraceName "h0_distances"
- |> styleChartwR "" "count" (0.,100.)
- distances
- |> fun x -> Chart.Histogram(x,HistNorm=HistNorm.Probability)
- //|> Chart.withShape (shape())
- |> Chart.withTraceName "vs distances"
- |> styleChartwR "DWTeuc_adj" "count" (0.,100.)
- ]
- |> Chart.Stack 1
- |> Chart.Show
-
- [[
- traceHeatmap
- distanceHeatmap
- ]]
- |> fun c -> Chart.Grid(c,true)
- |> Chart.withSize (900.,900.)
- |> Chart.withMarginSize (150.)
- |> Chart.withTitle "Migration distances of WT vs Mut"
- |> Chart.ShowWithDescription {Heading ="Interactive chart of migration distances";Text="(left) zNormed intensities of wild type and mutant.<br>(right) Adjusted euclidean distance of each protein pair.<br><br>Note: Distance is 36 if signal of WT or Mut is missing. Click and zoom vertically for more details"}
-
- listString
-
-combinedFunction IntMeasurement.Intensity
-
-
-
-
-
-//////////////////////////////////
-////////////////////////////////// plot signals
-//////////////////////////////////
-//////////////////////////////////
-let plotSignals save weight cre intmeasure =
-
- let synonym = Annotation.jgi55ToSynStr cre
- let original =
- datasets
- |> Array.map (Array.filter (fun x -> (x.ID |> String.filter (fun s -> s = 'C') |> fun c -> c.Length = 1))) //new
- |> Array.mapi (fun laneIndex x ->
- x
- |> Array.map (fun x -> x)
- |> Array.filter (fun (x) -> x.ID.StartsWith cre)
- |> fun x ->
- if x = [||] then
- laneIndex,Array.init 36 (fun _ -> 0.)
- else
- if x.Length > 2 then printfn "WARNING: %A" x
- match intmeasure with
- | IntMeasurement.LFQ -> laneIndex,x.[0].LFQ
- | IntMeasurement.Intensity -> laneIndex,x.[0].Intensities
- | IntMeasurement.IBAQ -> laneIndex,x.[0].IBaq
- )
-
- let originalChart =
- original
- |> Array.map (fun (j,x) -> x |> Seq.mapi (fun i x-> i+1,x) |> fun x -> Chart.Line(x,Name=laneHeader.[j] + " raw",Color=colors.[j]))
- |> Chart.Combine
-
- let normed =
- let normedData =
- match intmeasure with
- | IntMeasurement.LFQ -> correctedLFQs
- | IntMeasurement.Intensity -> correctedIntensities
- | IntMeasurement.IBAQ -> correctedIBAQss
-
- normedData
- |> Array.map (Array.filter (fun x -> (x.ID |> String.filter (fun s -> s = 'C') |> fun c -> c.Length = 1))) //new
- |> Array.mapi (fun laneIndex x ->
- x
- |> Array.map (fun x -> x)
- |> Array.filter (fun (x) -> x.ID.StartsWith cre)
- |> fun x ->
- if x = [||] then
- laneIndex,Array.init 36 (fun _ -> 0.)
- else
- if x.Length > 2 then printfn "WARNING: %A" x
- match intmeasure with
- | IntMeasurement.LFQ -> laneIndex,x.[0].LFQ
- | IntMeasurement.Intensity -> laneIndex,x.[0].Intensities
- | IntMeasurement.IBAQ -> laneIndex,x.[0].IBaq
- )
- //|> Array.concat
- //|> Array.mapi (fun j (laneIndex,x) -> laneIndex,x.LFQ)
-
- let normedChart =
- normed
- |> Array.map (fun (j,x) -> x |> Seq.mapi (fun i x-> i+1,x) |> fun x -> Chart.Line(x,Name=laneHeader.[j] + " norm",Color=colors.[j]) )
- |> Chart.Combine
-
- let wtTraces = (normed |> Array.filter (fun (i,x) -> i <= 2) |> Array.map snd)
- let mutTraces = (normed |> Array.filter (fun (i,x) -> i >= 3) |> Array.map snd)
- //let h0Distances =
- // Array.append
- // (getWarpDistancesOfSignals wtTraces)
- // (getWarpDistancesOfSignals mutTraces )
- // |> Array.map (sprintf "%.2f") |> String.concat ", "
-
- let wt = wtTraces |> JaggedArray.transpose |> Array.map Seq.mean
- let mu = mutTraces |> JaggedArray.transpose |> Array.map Seq.mean
- let wtStd = wtTraces |> JaggedArray.transpose |> Array.map Seq.stDev
- let muStd = mutTraces |> JaggedArray.transpose |> Array.map Seq.stDev
-
- let meanChart =
- [
- Chart.Line(wt |> Seq.mapi (fun i x-> i+1,x),Color=colors.[0],Name="wt mean")|> Chart.withYErrorStyle(wtStd)
- Chart.Line(mu |> Seq.mapi (fun i x-> i+1,x),Color=colors.[5],Name="mut mean")|> Chart.withYErrorStyle(muStd)
- ]
- |> Chart.Combine
- //|> Chart.withAxisAnchor(Y=1)
-
- //let dTW = DTW.distanceDefault wt mu
- let euc = ML.DistanceMetrics.euclidean wt mu
- let dfi = getDTWeuc wt mu
-
- ///Testing
- let wtSums = wtTraces |> Array.map Seq.sum |> vector
- let mutSums = mutTraces |> Array.map Seq.sum |> vector
- let sumFoldChange = Seq.map2 (fun w m -> m/w) wtSums mutSums |> Seq.mean
-
- let ttest =
- if Seq.mean wtSums = 0. then
- if Seq.mean mutSums = 0. then nan
- else (Testing.TTest.twoSample false mutSums wtSums).PValue
- else (Testing.TTest.twoSample false wtSums mutSums).PValue
-
- let ttestPval = ttest
- //contasts
- let wtSlices = (wtTraces |> JaggedArray.transpose)
- let mutSlices = (mutTraces |> JaggedArray.transpose)
- let appendedSlices = Array.append wtSlices mutSlices
- //let contrasts =
- // Array.init 36 (fun testIndex ->
- // let tmpContrast :float [] = Array.zeroCreate (36*2)
- // tmpContrast.[testIndex] <- 1.
- // tmpContrast.[testIndex+36] <- 1.
- // tmpContrast
- // )
- //let contrastResults =
- // Testing.PostHoc.fishersLSD contrasts appendedSlices //auf gar keinen fall einen post hoc test nehmen!! wegen variance estimation!
- let contrastResults =
- Array.mapi2 (fun i w m ->
- if Seq.mean w = 0. (*|| Seq.mean m = 0.*) then
- if Seq.mean m <> 0. then
- i+1,(Testing.TTest.twoSample false (vector m) (vector w)).PValue
- else i+1,nan
- else
- i+1,(Testing.TTest.twoSample false (vector w) (vector m)).PValue
- )
- wtSlices
- mutSlices
- //let contrastResults = Testing.PostHoc.fishersLSD contrasts appendedSlices //auf gar keinen fall einen post hoc test nehmen!! wegen variance estimation!
- let contrastResultStrings =
- contrastResults
- |> Array.map (fun (i,x) -> $"{i}\t\t%.2f{x}")
- |> Array.chunkBySize 9
- |> fun chunks ->
- chunks.[0]
- |> Array.mapi (fun j chunk9 ->
- sprintf "%s\t\t%s\t\t%s\t\t%s" chunk9 chunks.[1].[j] chunks.[2].[j] chunks.[3].[j]
- )
- |> String.concat "<br>"
- let pValues =
- contrastResults
- |> Array.partition (fun (i,x) -> x < 0.05)
- |> fun (pos,neg) ->
- [Chart.Column(pos|> Array.map (fun (i,x) -> i,- log10 x),Color="green");Chart.Column(neg|> Array.map (fun (i,x) -> i,- log10 x),Color="grey")]
- |> Chart.Combine
- |> Chart.withTraceName "pVals Welch"
-
- let intMeasureStr =
- match intmeasure with
- | IntMeasurement.LFQ -> "LFQ"
- | IntMeasurement.Intensity -> "Intensities"
- | IntMeasurement.IBAQ -> "IBaq"
-
- let annotation =
- Annotation.jgi55ToDesStr ((cre.Split '.').[0..1] |> String.concat ".")
-
- [
- //[pValues |> styleChartwR "" "-log10 pValue"(1.,36.)]
- [meanChart |> styleChartwR "" "means" (1.,36.)]
- [normedChart |> styleChartwR "" (intMeasureStr + " normed") (1.,36.)]
- [originalChart |> styleChartwR "" (intMeasureStr + " raw") (1.,36.)]
- ]
- |> fun t -> Chart.Grid(t,true,rowOrder=LayoutGridRowOrder.BottomToTop)
- |> Chart.withTitle (cre + " " + synonym)
- |> Chart.withSize (1100.,800.)
- |> fun t ->
- if not save then
- t
- //|> Chart.ShowWithDescription {Heading="";Text= $"dwt_distance: %.2f{dTW}<br>euclidean: %.2f{euc}<br>meanInt: %.2f{max (Seq.mean wt) (Seq.mean mu)}<br>myDist: %.2f{dfi}<br><br>MapMan: {annotation}<br><br>H0_distances: {h0Distances}<br><br>TTest LFQSums: %.4f{ttestPval}<br><br>TestSingleContrasts:<br>{contrastResultStrings}"}
- |> Chart.ShowWithDescription {Heading="";Text= $"Trivial name: {synonym}<br><br>Euclidean distance: %.2f{euc}<br>Mean Intensity (WT): %.2f{Seq.mean wt}<br>Mean Intensity (Mut): %.2f{Seq.mean mu}<br>Distance: %.2f{dfi}<br><br>MapMan: {annotation}<br><br>p value of intensity sums Welch test: %.4f{ttestPval}"}
- else
- let path =
- if weight then (@"C:\Users\bvenn\OneDrive - tukl\Projects\Benni\results\plots\distance\" + sprintf "%03.0f_%s_%s" dfi synonym cre + ".html" )
- else (@"C:\Users\bvenn\OneDrive - tukl\Projects\Benni\results\plots\" + sprintf "%s_%s" synonym cre + ".html" )
- t
- |> Chart.SaveHtmlWithDescriptionAs
- path
- //{Heading="";Text= $"dwt_distance: %.2f{dTW}<br>euclidean: %.2f{euc}<br>meanInt: %.2f{max (Seq.mean wt) (Seq.mean mu)}<br>myDist: %.2f{dfi}<br><br>H0_distances: {h0Distances}<br><br>TTest LFQSums: %.4f{ttestPval}<br><br>TestSingleContrasts:<br>{contrastResultStrings}"}
- //{Heading="";Text= $"dwt_distance: %.2f{dTW}<br>euclidean: %.2f{euc}<br>meanInt: %.2f{max (Seq.mean wt) (Seq.mean mu)}<br>myDist: %.2f{dfi}<br><br>MapMan: {annotation}<br><br>H0_distances: {h0Distances}<br><br>TestSingleContrasts:<br>{contrastResultStrings}"}
- {Heading="";Text= $"Trivial name: {synonym}<br><br>Euclidean distance: %.2f{euc}<br>Mean Intensity (WT): %.2f{Seq.mean wt}<br>Mean Intensity (Mut): %.2f{Seq.mean mu}<br>Distance: %.2f{dfi}<br><br>MapMan: {annotation}<br><br>p value of intensity sums Welch test: %.4f{ttestPval}"}
-
-
- //printfn "diff_adj %f" (getDTWeuc wt mu)
- //printfn "euc %f" (ML.DistanceMetrics.euclidean wt mu)
- //printfn "dtw %f" (DTW.distanceDefault wt mu)
-
-
-plotSignals false false "Cre12.g493250" IntMeasurement.Intensity
-
-
-datasets
-|> Array.map (fun x ->
- x
- |> Array.map (fun protein ->
- protein.ID
- )
- )
-|> Array.concat
-|> Array.distinct
-|> Array.filter (fun x -> not (x.Contains ";"))
-|> Array.mapi (fun i x ->
- printfn "%i" i
- plotSignals true false ((x.Split '.').[0..1] |> String.concat ".") IntMeasurement.Intensity
- )
-
-
-
-
-//check cases with unique (PSHB4...)
-datasets
-|> Array.map (fun x ->
- x
- |> Array.map (fun protein ->
- protein.ID
- )
- )
-|> Array.concat
-|> Array.distinct
-|> Array.filter (fun x -> not (x.Contains ";"))
-|> Array.mapi (fun i cre ->
- let vorher =
- datasets
- |> Array.mapi (fun laneIndex x ->
- x
- |> Array.map (fun x -> x)
- |> Array.filter (fun (x) -> x.ID.StartsWith cre)
- )
- |> Array.mapi (fun i x -> i,x)
-
-
- let nachher =
- datasets |> Array.map (Array.filter (fun x -> (x.ID |> String.filter (fun s -> s = 'C') |> fun c -> c.Length = 1))) //new
- |> Array.mapi (fun laneIndex x ->
- x
- |> Array.map (fun x -> x)
- |> Array.filter (fun (x) -> x.ID.StartsWith cre)
- )
- |> Array.mapi (fun i x -> i,x)
- (cre,vorher=nachher),(vorher |> Array.map (fun (i,x) -> sprintf "%i" x.Length),nachher |> Array.map (fun (i,x) -> sprintf "%i" x.Length))
- )
-|> Array.filter (fun (a,b) -> not (snd a))
-|> Array.iteri (fun i (a,b) -> printfn "%i\t%s\t%s\t%s\t%s" i (Annotation.jgi55ToSynStr (fst a)) (fst a) ((fst b) |> String.concat ";") ((snd b) |> String.concat ";"))
-
-
\ No newline at end of file
diff --git a/workflows/alignData_3_v7_CEDAR2.fsx b/workflows/prepareDataForCedarSubmission.fsx
similarity index 100%
rename from workflows/alignData_3_v7_CEDAR2.fsx
rename to workflows/prepareDataForCedarSubmission.fsx
diff --git a/workflows/proteomics.ipynb b/workflows/proteomics.ipynb
index 5008b8e782b566fbd6bf1606683decb1964a05df..628ff08618ecc81f4969b9e19a94beff7e21bae8 100644
--- a/workflows/proteomics.ipynb
+++ b/workflows/proteomics.ipynb
@@ -22,16 +22,7 @@
{
"data": {
"text/html": [
- "<div><div></div><div></div><div><strong>Installed Packages</strong><ul><li><span>BioFSharp, 2.0.0-preview.3</span></li><li><span>FSharp.Stats, 0.4.7</span></li><li><span>FSharpAux, 1.1.0</span></li><li><span>Plotly.NET, 3.0.0</span></li><li><span>Plotly.NET.Interactive, 3.0.2</span></li></ul></div></div>"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- },
- {
- "data": {
- "text/markdown": [
- "Loading extensions from `Plotly.NET.Interactive.dll`"
+ "<div><div></div><div></div><div><strong>Installed Packages</strong><ul><li><span>BioFSharp, 2.0.0-preview.3</span></li><li><span>BioFSharp.BioDB, 1.2.1</span></li><li><span>FSharp.Stats, 0.4.7</span></li><li><span>FSharpAux, 1.1.0</span></li><li><span>Plotly.NET, 3.0.0</span></li><li><span>Plotly.NET.Interactive, 3.0.2</span></li></ul></div></div>"
]
},
"metadata": {},
@@ -41,7 +32,7 @@
"source": [
"\n",
"#r \"nuget: BioFSharp,2.0.0-preview.3\"\n",
- "//#r \"nuget: BioFSharp.BioDB\"\n",
+ "#r \"nuget: BioFSharp.BioDB\"\n",
"\n",
"#r \"nuget: Plotly.NET,3.0.0\"\n",
"#r \"nuget: Plotly.NET.Interactive,3.0.2\"\n",
@@ -82,6 +73,13 @@
" |> Chart.withXAxis (myAxis x) \n",
" |> Chart.withYAxis (myAxis y)\n",
" |> Chart.withConfig svgConfig\n",
+ " \n",
+ " let withAxisTitlesWR x y (min,max) chart = \n",
+ " chart \n",
+ " |> Chart.withTemplate ChartTemplates.lightMirrored\n",
+ " |> Chart.withXAxis (myAxisRange x (min,max))\n",
+ " |> Chart.withYAxis (myAxis y)\n",
+ " |> Chart.withConfig svgConfig\n",
"\n",
"let fst3 (a,b,c) = a\n",
"let snd3 (a,b,c) = b\n",
@@ -207,14 +205,14 @@
"\n",
" let jgi55ToSynStr (str :string) =\n",
" let truncatedStr = (str.Split '.').[0..1] |> String.concat \".\"\n",
- " if jgi55ToSyn.ContainsKey truncatedStr then \n",
- " jgi55ToSyn.[truncatedStr] \n",
- " else \"\"\n",
+ " //if jgi55ToSyn.ContainsKey truncatedStr then \n",
+ " // jgi55ToSyn.[truncatedStr] \n",
+ " //else \"\"\n",
"\n",
- " //let bioDBQuery = BioDB.FaToolDb.Queries.getSynonyms truncatedStr\n",
- " //if bioDBQuery = [] then \n",
- " // \"\" \n",
- " //else bioDBQuery |> List.map snd |> String.concat \";\"\n",
+ " let bioDBQuery = BioDB.FaToolDb.Queries.getSynonyms truncatedStr\n",
+ " if bioDBQuery = [] then \n",
+ " \"\" \n",
+ " else bioDBQuery |> List.map snd |> String.concat \";\"\n",
"\n",
" //Map to translate MapManGmm-Term to MapManDescription for most of MapManBins\n",
" let jgi55ToLoc =\n",
@@ -226,7 +224,50 @@
"\n",
" let jgi55ToLocStr (str:string) =\n",
" let str' = (str.Split '.').[0..1] |> String.concat \".\"\n",
- " if jgi55ToLoc.ContainsKey str' then jgi55ToLoc.[str'] else \"\"\n"
+ " if jgi55ToLoc.ContainsKey str' then jgi55ToLoc.[str'] else \"\"\n",
+ "\n",
+ "\n",
+ " let lpa2Mapping = \n",
+ " System.IO.File.ReadAllLines(@\"C:\\Users\\bvenn\\source\\repos\\LPA2_ComplexomeProfiling_Chlamy\\studies\\Cultivation\\resources\\lpa2_mappingfile.txt\")\n",
+ " |> Array.map (fun x -> \n",
+ " let tmp = x.Split '\\t'\n",
+ " tmp.[0],(tmp.[1],tmp.[2],tmp.[3],tmp.[4],tmp.[5])\n",
+ " )\n",
+ "\n",
+ " let lpa2Syn = \n",
+ " lpa2Mapping\n",
+ " |> Array.map (fun (id,(syn,mm,mmdes,go,loc)) -> \n",
+ " id,syn\n",
+ " )\n",
+ " |> Map.ofArray\n",
+ "\n",
+ " let lpa2MM = \n",
+ " lpa2Mapping\n",
+ " |> Array.map (fun (id,(syn,mm,mmdes,go,loc)) -> \n",
+ " id,mmdes\n",
+ " )\n",
+ " |> Map.ofArray\n",
+ "\n",
+ " let lpa2MMdes = \n",
+ " lpa2Mapping\n",
+ " |> Array.map (fun (id,(syn,mm,mmdes,go,loc)) -> \n",
+ " id,mm\n",
+ " )\n",
+ " |> Map.ofArray\n",
+ "\n",
+ " let lpa2GO = \n",
+ " lpa2Mapping\n",
+ " |> Array.map (fun (id,(syn,mm,mmdes,go,loc)) -> \n",
+ " id,go\n",
+ " )\n",
+ " |> Map.ofArray\n",
+ "\n",
+ " let lpa2loc = \n",
+ " lpa2Mapping\n",
+ " |> Array.map (fun (id,(syn,mm,mmdes,go,loc)) -> \n",
+ " id,loc\n",
+ " )\n",
+ " |> Map.ofArray"
]
},
{
@@ -524,64 +565,10 @@
"languageId": "dotnet-interactive.fsharp"
}
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
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- "2_1000\r\n",
- "3_0\r\n",
- "3_500\r\n",
- "3_1000\r\n",
- "4_0\r\n",
- "4_500\r\n",
- "4_1000\r\n",
- "5_0\r\n",
- "5_500\r\n",
- "5_1000\r\n"
- ]
- },
- {
- "data": {
- "text/html": [
- "<table><thead><tr><th><i>index</i></th><th>value</th></tr></thead><tbody><tr><td>0</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>1</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>2</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>3</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>4</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>5</td><td><div class=\"dni-plaintext\"><null></div></td></tr></tbody></table>"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
+ "outputs": [],
"source": [
- "writeDataFrame datasets @\"C:\\Users\\bvenn\\source\\repos\\LPA2_ComplexomeProfiling_Chlamy\\runs\\data\\intensitiesRaw_\"\n",
- "writeDataFrame correctedIntensities @\"C:\\Users\\bvenn\\source\\repos\\LPA2_ComplexomeProfiling_Chlamy\\runs\\data\\intensitiesNormed_\""
+ "//writeDataFrame datasets @\"C:\\Users\\bvenn\\source\\repos\\LPA2_ComplexomeProfiling_Chlamy\\runs\\data\\intensitiesRaw_\"\n",
+ "//writeDataFrame correctedIntensities @\"C:\\Users\\bvenn\\source\\repos\\LPA2_ComplexomeProfiling_Chlamy\\runs\\data\\intensitiesNormed_\""
]
},
{
@@ -602,46 +589,7 @@
"languageId": "dotnet-interactive.fsharp"
}
},
- "outputs": [
- {
- "data": {
- "text/html": [
- "\n",
- "<div>\n",
- " <div id=\"280174d3-67ea-433c-bdf2-7e9a83d59fbb\"><!-- Plotly chart will be drawn inside this DIV --></div>\r\n",
- "<script type=\"text/javascript\">\r\n",
- "\r\n",
- " var renderPlotly_280174d367ea433cbdf27e9a83d59fbb = function() {\r\n",
- " var fsharpPlotlyRequire = requirejs.config({context:'fsharp-plotly',paths:{plotly:'https://cdn.plot.ly/plotly-2.6.3.min'}}) || require;\r\n",
- " fsharpPlotlyRequire(['plotly'], function(Plotly) {\r\n",
- "\r\n",
- " var data = 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- "metadata": {},
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+ "outputs": [],
"source": [
"correctedIntensities\n",
"|> Array.map (fun x -> x |> Array.map (fun x -> x.Intensities))\n",
@@ -705,46 +653,7 @@
"languageId": "dotnet-interactive.fsharp"
}
},
- "outputs": [
- {
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+ "outputs": [],
"source": [
"\n",
"//plotRelativeIntensity \"Cre01.g042200\"\n",
@@ -767,46 +676,7 @@
"languageId": "dotnet-interactive.fsharp"
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@@ -1010,3804 +841,6 @@
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{
"data": {
"text/html": [
@@ -5121,11 +1154,218 @@
},
"outputs": [
{
- "ename": "Error",
- "evalue": "unknown (1,1)-(1,1) interactive error type '<>f__AnonymousType3517731110`3' not found in assembly '<emitted>'. A possible cause may be a version incompatibility. You may need to explicitly reference the correct version of this assembly to allow all referenced components to use the correct version.",
- "output_type": "error",
- "traceback": [
- "unknown (1,1)-(1,1) interactive error type '<>f__AnonymousType3517731110`3' not found in assembly '<emitted>'. A possible cause may be a version incompatibility. You may need to explicitly reference the correct version of this assembly to allow all referenced components to use the correct version."
+ "name": "stdout",
+ "output_type": "stream",
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+ "4\t18\t16\t\r\n",
+ "4\t19\t15\t\r\n",
+ "4\t20\t6\t\r\n",
+ "4\t21\t30\t\r\n",
+ "4\t22\t8\t\r\n",
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+ "4\t33\t2\t\r\n",
+ "4\t34\t3\t\r\n",
+ "4\t35\t2\t\r\n",
+ "5\t0\t73\t\r\n",
+ "5\t1\t48\t\r\n",
+ "5\t2\t10\t\r\n",
+ "5\t3\t20\t\r\n",
+ "5\t4\t1\t\r\n",
+ "5\t6\t6\t\r\n",
+ "5\t7\t1\t\r\n",
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+ "5\t10\t5\t\r\n",
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+ "5\t13\t5\t\r\n",
+ "5\t14\t16\t\r\n",
+ "5\t15\t5\t\r\n",
+ "5\t16\t18\t\r\n",
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+ "5\t18\t14\t\r\n",
+ "5\t19\t14\t\r\n",
+ "5\t20\t14\t\r\n",
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+ "5\t22\t20\t\r\n",
+ "5\t23\t35\t\r\n",
+ "5\t24\t21\t\r\n",
+ "5\t25\t34\t\r\n",
+ "5\t26\t32\t\r\n",
+ "5\t27\t28\t\r\n",
+ "5\t28\t37\t\r\n",
+ "5\t29\t59\t\r\n",
+ "5\t30\t30\t\r\n",
+ "5\t31\t14\t\r\n",
+ "5\t32\t6\t\r\n",
+ "5\t33\t1\t\r\n",
+ "5\t34\t3\t\r\n",
+ "5\t35\t2\t\r\n"
]
}
],
@@ -5184,7 +1424,7 @@
" |> Array.sortBy fst\n",
" |> Array.map (fun (sliceID,items) -> \n",
" let offsets = items |> Array.map (fun x -> x.SliceOffset)\n",
- " printfn \"%i\\t%i\\t%i\\t\" laneID sliceID items.Length\n",
+ " //printfn \"%i\\t%i\\t%i\\t\" laneID sliceID items.Length\n",
" Chart.BoxPlot(Y=offsets,Name=\"sI \" + string sliceID,FillColor=Color.fromString (colors.[laneID]))//|> Chart.withTraceName (sprintf \"%i\" items.Length)\n",
" )\n",
" )\n",
@@ -5199,6 +1439,15 @@
"\n"
]
},
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Peak coverage analysis\n",
+ "\n",
+ "How many values within a signal are higher than 20% of its own max intensity?"
+ ]
+ },
{
"cell_type": "code",
"execution_count": null,
@@ -5210,21 +1459,53 @@
"languageId": "dotnet-interactive.fsharp"
}
},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div>\n",
+ " <div id=\"3397f1ab-2653-4f16-8b20-05a86df120cc\"><!-- Plotly chart will be drawn inside this DIV --></div>\r\n",
+ "<script type=\"text/javascript\">\r\n",
+ "\r\n",
+ " var renderPlotly_3397f1ab26534f168b2005a86df120cc = function() {\r\n",
+ " var fsharpPlotlyRequire = requirejs.config({context:'fsharp-plotly',paths:{plotly:'https://cdn.plot.ly/plotly-2.6.3.min'}}) || require;\r\n",
+ " fsharpPlotlyRequire(['plotly'], function(Plotly) {\r\n",
+ "\r\n",
+ " var data = 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+ " };\r\n",
+ " if ((typeof(requirejs) !== typeof(Function)) || (typeof(requirejs.config) !== typeof(Function))) {\r\n",
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+ " renderPlotly_3397f1ab26534f168b2005a86df120cc();\r\n",
+ " };\r\n",
+ " document.getElementsByTagName(\"head\")[0].appendChild(script);\r\n",
+ " }\r\n",
+ " else {\r\n",
+ " renderPlotly_3397f1ab26534f168b2005a86df120cc();\r\n",
+ " }\r\n",
+ "</script>\r\n",
+ "\n",
+ " \n",
+ "</div> \n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
- "\n",
- "\n",
- "//////////////////////////////////\n",
- "////////////////////////////////// plot peak coverage\n",
- "//////////////////////////////////\n",
- "//////////////////////////////////\n",
- "\n",
"correctedIntensities\n",
"|> Array.mapi (fun i lane -> \n",
" lane\n",
" |> Array.map (fun protein -> \n",
- " let maxIntens = protein.LFQ |> Array.max\n",
- " protein.LFQ |> Array.filter (fun x -> x > 0.2*maxIntens)\n",
+ " let maxIntens = protein.Intensities |> Array.max\n",
+ " protein.Intensities |> Array.filter (fun x -> x > 0.2*maxIntens)\n",
" |> Array.length\n",
" |> fun x -> float x \n",
" )\n",
@@ -5232,27 +1513,87 @@
" Chart.BoxPlot(Y=j,Jitter=0.2,BoxPoints=BoxPoints.All,BoxMean=BoxMean.True,FillColor=Color.fromString(colors.[i]))\n",
" )\n",
"|> Chart.combine\n",
- "|> Chart.withAxisTitles \"\" \"signal / lane\"\n",
- "|> Chart.show\n",
- "\n",
- "\n",
- "let getPeakWidths signal percentageForMinIntensity =\n",
- " let minSig = signal |> Array.max |> fun x -> x * percentageForMinIntensity\n",
- " let rec loop i acc current =\n",
- " if i = signal.Length-1 then \n",
- " if signal.[i] > minSig then \n",
- " if current = 0 then \n",
- " 1::acc \n",
- " else (current+1)::acc\n",
- " else \n",
- " if current = 0 then acc else (current)::acc\n",
- " else \n",
- " if current <> 0 then \n",
- " if signal.[i] < minSig then \n",
- " loop (i+1) (current::acc) 0\n",
- " else loop (i+1) acc (current+1)\n",
- " else \n",
- " if signal.[i] > minSig then\n",
+ "|> Chart.withAxisTitles \"\" \"signal / lane\""
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "How many peaks are there per lane? Is it the same for all samples?\n",
+ "What is the average signal width of all profiles? Thresholds of 5, 10, and 20% max signal intensity were applied. "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "dotnet_interactive": {
+ "language": "fsharp"
+ },
+ "vscode": {
+ "languageId": "dotnet-interactive.fsharp"
+ }
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div>\n",
+ " <div id=\"87b87522-9e1a-4aa5-9e66-e50a725398a0\"><!-- Plotly chart will be drawn inside this DIV --></div>\r\n",
+ "<script type=\"text/javascript\">\r\n",
+ "\r\n",
+ " var renderPlotly_87b875229e1a4aa59e66e50a725398a0 = function() {\r\n",
+ " var fsharpPlotlyRequire = requirejs.config({context:'fsharp-plotly',paths:{plotly:'https://cdn.plot.ly/plotly-2.6.3.min'}}) || require;\r\n",
+ " fsharpPlotlyRequire(['plotly'], function(Plotly) {\r\n",
+ "\r\n",
+ " var data = 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y6\"}];\r\n",
+ " var layout = {\"width\":1500,\"height\":1000,\"template\":{\"layout\":{\"paper_bgcolor\":\"white\",\"plot_bgcolor\":\"white\",\"xaxis\":{\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"zeroline\":true},\"yaxis\":{\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"zeroline\":true}},\"data\":{}},\"xaxis\":{\"title\":{\"text\":\"\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"yaxis\":{\"title\":{\"text\":\"peaks / lane\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"title\":{\"text\":\"5% (left), 10% (middle) and 20% (right) threshold\"},\"xaxis2\":{\"title\":{\"text\":\"\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"yaxis2\":{\"title\":{\"text\":\"peaks / lane\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"xaxis3\":{\"title\":{\"text\":\"\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"yaxis3\":{\"title\":{\"text\":\"peaks / lane\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"xaxis4\":{\"title\":{\"text\":\"\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"yaxis4\":{\"title\":{\"text\":\"peakwidth / lane\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"xaxis5\":{\"title\":{\"text\":\"\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"yaxis5\":{\"title\":{\"text\":\"peakwidth / lane\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"xaxis6\":{\"title\":{\"text\":\"\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"yaxis6\":{\"title\":{\"text\":\"peakwidth / lane\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"grid\":{\"rows\":2,\"columns\":3,\"pattern\":\"independent\"}};\r\n",
+ " var config = {\"responsive\":true,\"toImageButtonOptions\":{\"format\":\"svg\"}};\r\n",
+ " Plotly.newPlot('87b87522-9e1a-4aa5-9e66-e50a725398a0', data, layout, config);\r\n",
+ "});\r\n",
+ " };\r\n",
+ " if ((typeof(requirejs) !== typeof(Function)) || (typeof(requirejs.config) !== typeof(Function))) {\r\n",
+ " var script = document.createElement(\"script\");\r\n",
+ " script.setAttribute(\"src\", \"https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js\");\r\n",
+ " script.onload = function(){\r\n",
+ " renderPlotly_87b875229e1a4aa59e66e50a725398a0();\r\n",
+ " };\r\n",
+ " document.getElementsByTagName(\"head\")[0].appendChild(script);\r\n",
+ " }\r\n",
+ " else {\r\n",
+ " renderPlotly_87b875229e1a4aa59e66e50a725398a0();\r\n",
+ " }\r\n",
+ "</script>\r\n",
+ "\n",
+ " \n",
+ "</div> \n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "\n",
+ "let getPeakWidths signal percentageForMinIntensity =\n",
+ " let minSig = signal |> Array.max |> fun x -> x * percentageForMinIntensity\n",
+ " let rec loop i acc current =\n",
+ " if i = signal.Length-1 then \n",
+ " if signal.[i] > minSig then \n",
+ " if current = 0 then \n",
+ " 1::acc \n",
+ " else (current+1)::acc\n",
+ " else \n",
+ " if current = 0 then acc else (current)::acc\n",
+ " else \n",
+ " if current <> 0 then \n",
+ " if signal.[i] < minSig then \n",
+ " loop (i+1) (current::acc) 0\n",
+ " else loop (i+1) acc (current+1)\n",
+ " else \n",
+ " if signal.[i] > minSig then\n",
" loop (i+1) acc 1\n",
" else loop (i+1) acc 0\n",
" loop 0 [] 0\n",
@@ -5262,7 +1603,7 @@
" |> Array.mapi (fun i lane -> \n",
" lane\n",
" |> Array.map (fun protein -> \n",
- " getPeakWidths protein.LFQ percentageForMinIntensity\n",
+ " getPeakWidths protein.Intensities percentageForMinIntensity\n",
" |> Seq.length\n",
" )\n",
" |> fun j -> Chart.BoxPlot(Y=j,Name=laneHeader.[i],Jitter=0.2,BoxPoints=BoxPoints.All,BoxMean=BoxMean.True,FillColor=Color.fromString colors.[i])\n",
@@ -5276,7 +1617,7 @@
" |> Array.mapi (fun i lane -> \n",
" lane\n",
" |> Array.map (fun protein -> \n",
- " getPeakWidths protein.LFQ percentageForMinIntensity\n",
+ " getPeakWidths protein.Intensities percentageForMinIntensity\n",
" |> Seq.length\n",
" )\n",
" )\n",
@@ -5292,7 +1633,7 @@
" |> Array.mapi (fun i lane -> \n",
" lane\n",
" |> Array.map (fun protein -> \n",
- " getPeakWidths protein.LFQ percentageForMinIntensity\n",
+ " getPeakWidths protein.Intensities percentageForMinIntensity\n",
" )\n",
" |> Seq.concat\n",
" |> fun j -> Chart.BoxPlot(Y=j,Name=laneHeader.[i],Jitter=0.2,BoxPoints=BoxPoints.All,BoxMean=BoxMean.True,FillColor=Color.fromString colors.[i])\n",
@@ -5306,7 +1647,7 @@
" |> Array.mapi (fun i lane -> \n",
" lane\n",
" |> Array.map (fun protein -> \n",
- " getPeakWidths protein.LFQ percentageForMinIntensity\n",
+ " getPeakWidths protein.Intensities percentageForMinIntensity\n",
" )\n",
" |> Seq.concat\n",
" )\n",
@@ -5325,8 +1666,76 @@
"]\n",
"|> Chart.Grid(2,3)\n",
"|> Chart.withSize (1500.,1000.)\n",
- "|> Chart.withTitle (\"5% (left), 10% (middle) and 20% (right) threshold\" )\n",
- "|> Chart.show\n",
+ "|> Chart.withTitle (\"5% (left), 10% (middle) and 20% (right) threshold\" )\n"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "As seen above the peak count and peak width looks good and is very homogeneous throughout the samples"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Plot the same figure as histogram."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "dotnet_interactive": {
+ "language": "fsharp"
+ },
+ "vscode": {
+ "languageId": "dotnet-interactive.fsharp"
+ }
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div>\n",
+ " <div id=\"debd6b3e-9f09-4c5e-ac26-0a8cb7dea6f2\"><!-- Plotly chart will be drawn inside this DIV --></div>\r\n",
+ "<script type=\"text/javascript\">\r\n",
+ "\r\n",
+ " var renderPlotly_debd6b3e9f094c5eac260a8cb7dea6f2 = function() {\r\n",
+ " var fsharpPlotlyRequire = requirejs.config({context:'fsharp-plotly',paths:{plotly:'https://cdn.plot.ly/plotly-2.6.3.min'}}) || require;\r\n",
+ " fsharpPlotlyRequire(['plotly'], function(Plotly) {\r\n",
+ "\r\n",
+ " var data = 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4,1,5,1,2,1,1,2,4,1,1,2,2,1,2,2,1,1,1,1,1,1,1,3,3,1,1,1,4,5,1,3,4,5,5,1,1,1,4,2,2,5,2,1,1,2,1,1,4,1,4,8,1,3,4,1,3,2,3,1,5,1,3,7,2,1,1,2,1,3,1,2,1,3,1,1,1,2,3,4,1,2,4,1,1,1,2,1,2,6,6,1,5,1,2,1,2,1,2,2,2,1,1,1,1,4,1,4,1,1,1,3,1,1,4,2,1,4,1,1,2,1,4,1,4,1,1,3,2,2,1,4,1,2,1,4,2,1,5,2,3,1,1,5,1,2,1,4,3,2,1,3,1,2,5,1,3,1,1,1,3,1,4,4,1,4,1,1,1,5,1,1,2,2,2,4,4,2,1,2,1,1,2,2,1,2,1,2,2,2,5,1,1,4,2,4,1,3,1,5,2,1,1,1,2,1,3,1,4,3,1,2,1,1,2,1,2,1,1,1,4,1,1,1,1,1,1,1,1,1,1,3,4,3,2,4,1,1,1,1,2,8,1,2,1,1,1,1,4,2,2,3,1,3,1,1,3,2,4,1,4,1,5,1,4,1,1,2,1,3,1,1,2,1,1,4,2,2,1,1,2,1,2,1,1,2,2,3,2,3,2,1,1,1,1,1,1,1,1,1,1,1,1,2,7,1,2,4,1,1,4,2,2,1,2,2,7,5,1,1,2,1,1,2,4,9,1,3,1,1,5,1,1,2,2,3,5,2,2,7,3,4,1,2,4,1,2,3,4,13,1,2,1,1,4,2,4,2,4,6,2,3,1,2,3,3,2,2,1,2,1,2,4,1,1,2,11,1,1,2,1,2,1,3,2,3,1,2,2,1,2,2,1,4,3,1,3,3,2,1,4,2,1,3,2,1,3,1,1,2,1,3,7,1,10,1,2,2,13,1,1,1,1,1,1,1,1,1,2,3,3,1,1,2,6,1,6,1,2,3,4,6,1,1,1,3,2,2,4,2,1,2,1,2,1,1,2,1,3,1,1,2,2,3,1,1,1,1,1,1,1,2,2,1,2,5,1,1,8,2,2,1,1,1,9,2,4,5,2,1,1,1,2,7,1,3,2,3,1,2,1,1,2,1,1,2,1,2,1,3,1,2,2,2,1,4,6,1,1,2,1,6,1,1,4,1,6,1,1,2,7,1,2,1,2,1,1,4,1,3,2,4,4,1,1,2,1,1,1,7,1,2,1,1,1,1,1,5,1,1,1,1,7,1,4,1,6,1,2,5,1,2,2,1,1,8,1,1,2,2,3,1,1,1,1,2,7,3,2,4,1,3,3,4,1,1,8,2,1,2,3,2,3,2,1,3,1,4,1,1,1,1,1,1,3,3,2,2,1,4,1,2,2,1,1,1,5,9,1,2,1,3,2,2,5,1,2,1,2,1,1,3,2,2,2,2,1,1,1,1,1,2,1,1,3,4,3,2,1,1,6,1,2,4,4,1,1,1,1,3,1,2,1,2,1,1,3,1,1,4,3,6,1,1,2,1,1,1,2,2,2,3,1,1,4,1,4,2,1,2,2,4,2,1,6,1,4,4,13,2,1,1,1,5,3,5,1,1,1,2,1,2,1,3,1,2,2,4,4,1,2,7,2,2,2,2,1,2,6,4,1,5,1,2,2,1,4,1,1,5,8,8,6,1,1,1,1,1,1,2,1,1,3,1,1,2,1,4,2,1,1,1,3,1,3,4,4,1,1,7,4,1,1,2,1,3,5,1,3,1,5,1,1,1,7,1,1,3,1,2,4,3,1,1,1,1,4,1,1,1,2,1,2,1,1,1,2,1,1,2,1,2,1,2,4,1,1,1,6,1,1,1,2,3,1,1,3,3,1,1,1,1,4,1,3,1,3,2,1,1,1,1,1,5,3,11,4,1,4,2,1,5,1,1,3,1,1,1,1,1,8,1,1,1,2,1,3,1,4,1,5,1,2,2,1,2,1,2,1,1,2,1,1,3,1,1,2,1,1,2,3,4,1,2,2,1,1,1,2,1,2,1,1,3,3,1,2,3,4,2,1,1,1,4,1,2,1,2,4,1,3,1,4,5,1,1,2,3,2,33,1,2,2,1,1,3,2,2,2,4,1,2,1,2,1,2,3,3,4,1,4,1,1,1,2,1,1,3,6,1,4,2,2,3,1,3,1,2,1,1,6,1,5,2,5,2,5,3,3,1,1,3,2,2,3,5,4,3,1,5,1,5,1,2,1,1,2,2,2,1,1,2,1,1,1,4,3,1,1,2,2,2,1,4,2,3,1,3,2,3,3,1,2,2,1,1,1,2,1,1,2,1,5,2,1,3,2,2,2,3,1,1,1,3,1,4,1,2,5,3,4,4,9,3,1,6,1,3,1,2,6,3,1,1,3,2,4,3,2,1,7,3,5,1,2,1,2,2,1,1,5,2,1,2,1,1,1,3,6,2,4,4,1,1,2,3,2,3,1,1,5,4,1,2,2,1,1,1,2,3,3,2,1,2,1,4,2,1,2,1,1,1,1,1,1,13,1,1,1,4,4,6,1,1,4,6,2,2,4,2,1,1,8,3,2,3,1,1,2,2,1,1,1,2,1,3,3,2,2,1,3,1,2,2,2,3,3,2,3,1,2,1,1,1,1,1,1,1,9,1,3,7,6,5,1,1,2,1,4,3,1,1,4,1,2,2,2,2,6,3,7,1,1,2,2,1,1,2,1,2,1,1,5,3,2,1,1,2,1,2,2,3,1,4,2,1,2,4,1,2,2,9,1,1,3,1,2,4,3,1,1,2,1,2,1,1,1,1,7,1,1,2,3,4,4,1,2,2,3,2,3,5,1,1,3,2,3,1,1,1,1,1,3,2,13,4,2,1,1,2,1,4,2,4,3,2,3,1,2,1,1,3,3,1,3,3,3,1,2,2,2,1,3,2,3,1,1,2,1,1,1,5,1,1,1,5,1,1,1,2,2,2,4,2,2,5,2,2,1,2,1,2,2,6,3,2,1,5,1,3,2,1,2,6,1,2,3,1,1,3,2,1,1,1,3,1,1,2,2,2,1,1,1,2,5,3,3,3,3,2,2,1,2,1,1,1,4,2,1,1,1,1,4,2,2,1,4,3,11,2,1,1,3,3,2,1,1,1,1,2,3,1,1,1,12,4,3,3,3,6,4,1,5,1,3,7,1,3,1,4,2,4,2,2,3,2,1,4,1,2,7,6,1,8,2,1,2,1,3,4,4,2,4,1,3,1,1,1,1,1,1,2,1,1,1,1,2,1,2,4,1,3,3,2,4,2,3,1,4,1,1,2,1,1,1,1,1,1,1,5,1,1,4,2,1,1,2,2,3,4,1,1,3,2,3,1,3,1,2,2,1,1,1,3,2,1,1,1,1,1,2,1,2,1,3,2,2,3,1,3,2,2,1,2,1,1,1,2,1,3,1,3,3,4,5,2,4,1,4,2,2,2,1,5,2,3,1,1,3,1,1,2,1,6,4,2,1,4,1,1,2,2,4,2,2,4,1,3,1,6,1,1,2,2,2,2,1,1,1,3,3,1,1,1,1,2,1,2,2,2,4,4,2,2,2,6,1,1,1,1,3,1,1,3,7,4,3,5,2,4,2,1,1,1,1,4,3,1,1,1,2,1,1,3,2,3,13,1,3,3,2,5,1,6,2,2,1,1,1,2,1,1,2,1,1,1,5,1,1,1,3,2,2,1,2,1,3,2,1,1,2,1,1,4,1,1,5,2,2,1,1,1,2,1,5,2,2,2,2,1,3,8,1,2,1,2,1,2,1,2,2,1,1,1,5,1,1,3,2,3,1,4,3,3,1,1,1,2,3,2,1,3,2,1,1,1,6,2,1,3,2,1,1,2,3,1,3,1,2,3,1,3,2,3,2,3,1,3,2,2,1,1,2,1,2,3,1,2,1,1,3,2,1,2,1,2,1,1,3,2,3,4,4,2,2,1,2,2,1,2,2,2,1,2,2,5,3,2,4,10,2,2,3,2,2,1,3,2,2,3,1,3,2,1,1,1,2,2,1,1,3,3,4,1,1,1,2,2,1,2,4,1,1,2,2,3,4,12,1,1,1,1,4,1,5,1,1,5,1,1,1,5,1,1,1,3,2,2,3,2,1,1,1,1,2,1,1,3,4,2,1,1,2,2,2,2,1,1,1,1,3,6,1,1,2,4,3,1,2,2,1,2,2,1,2,1,1,5,2,1,3,1,1,3,1,3,1,3,4,3,1,3,2,1,1,2,1,3,2,3,1,4,2,1,4,1,3,3,1,1,2,1,2,4,1,1,4,2,4,1,1,1,2,2,1,1,1,1,1,3,4,2,3,3,1,1,1,1,2,1,6,2,2,1,1,2,3,1,1,1,2,2,2,5,1,1,3,1,2,2,5,1,1,2,4,1,2,3,1,3,1,1,1,2,2,1,4,1,2,2,5,3,2,2,1,1,2,3,6,2,4,1,5,6,1,2,1,1,4,2,1,5,2,3,1,1,1,5,1,3,8,1,1,1,1,3,1,1,1,1,3,2,1,2,2,2,4,3,5,2,2,2,2,1,3,2,2,3,1,1,2,1,1,1,3,1,3,2,3,4,3,5,1,1,1,2,1,1,6,2,6,1,5,1,2,2,1,2,3,2,1,1,1,3,1,1,1,1,4,1,2,1,3,1,1,4,1,2,3,4,1,2,2,3,4,1,1,1,2,1,2,1,1,2,1,1,5,1,1,2,3,1,2,2,4,2,3,4,4,1,3,4,2,1,1,5,1,1,3,4,1,1,3,1,3,1,3,1,2,1,1,3,4,7,3,4,1,1,1,6,1,1,1,1,2,1,5,1,1,2,2,1,1,1,5,2,1,5,1,2,1,1,2,1,2,1,1,1,1,2,1,3,2,3,8,2,1,1,1,4,1,1,2,2,3,1,1,1,1,1,1,3,1,1,1,3,4,4,4,2,3,2,3,2,4,3,1,1,1,3,1,2,2,4,3,1,2,1,3,2,4,3,1,1,2,1,3,1,1,1,4,1,1,1,4,2,3,1,4,3,1,3,1,8,2,1,1,2,2,1,1,2,1,1,4,1,2,1,4,1,4,1,2,1,1,2,2,4,1,3,3,1,2,1,1,1,6,2,2,1,1,1,3,1,1,1,1,1,1,4,1,2,5,1,1,1,3,1,3,3,2,3,2,2,4,1,1,1,2,4,6,6,1,1,1,2,2,4,1,2,1,2,2,1,3,1,9,6,1,2,1,2,5,2,1,3,7,1,1,3,8,1,1,3,1,2,1,2,4,6,1,7,5,1,1,4,1,1,4,1,1,5,4,5,11,2,1,1,1,1,5,1,3,1,2,6,5,2,4,1,1,2,1,3,2,1,3,3,1,1,1,3,2,4,1,1,12,1,3,1,1,4,4,1,1,3,1,1,2,2,2,1,2,3,1,1,2,4,1,1,1,2,1,2,1,4,12,2,2,3,2,1,2,1,1,1,2,1,3,5,3,1,1,1,2,2,6,2,2,5,3,2,3,1,3,1,1,1,2,2,1,4,5,1,2,2,1,2,5,5,1,1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,2,2,1,3,3,1,3,4,4,1,2,2,2,1,1,1,1,7,3,1,2,1,2,2,3,2,2,2,2,3,1,1,2,1,2,1,2,3,1,1,2,2,1,4,1,3,1,1,1,2,2,2,1,1,3,3,1,1,3,1,2,1,2,1,2,1,2,2,2,2,1,2,1,1,2,2,3,2,1,1,2,1,2,1,1,2,2,4,1,2,1,1,2,2,3,1,1,1,2,1,5,3,1,2,2,2,1,2,2,1,2,1,2,1,1,1,1,7,1,3,1,2,1,3,3,1,1,1,3,1,3,6,2,2,1,3,2,2,1,2,4,1,1,2,1,2,2,1,1,2,1,2,2,1,2,2,1,4,1,2,1,2,1,1,2,1,4,1,1,2,4,2,2,1,2,1,1,1,2,1,3,2,1,1,1,2,1,1,1,3,1,1,1,2,7,3,1,1,1,1,2,1,2,1,1,1,1,1,1,1,1,1,1,3,1,2,2,2,1,2,6,1,1,3,1,5,1,1,3,2,1,1,2,2,1,2,1,2,3,1,2,3,1,3,2,1,1,2,2,2,2,2,2,1,1,2,2,3,3,1,2,1,1,1,2,2,3,1,1,1,3,3,5,2,3,1,2,2,2,2,1,1,1,1,2,2,2,4,1,1,1,1,3,1,3,2,1,1,1,1,1,1,2,1,2,1,3,1,2,2,1,2,1,5,6,1,2,1,1,1,2,1,1,3,1,2,2,1,1,3,1,1,1,1,1,3,1,4,1,1,1,4,1,1,3,3,1,1,2,2,3,2,3,2,1,2,2,3,4,2,1,1,1,1,1,2,1,1,1,2,1,1,1,2,1,3,1,3,1,4,1,1,1,1,2,1,1,1,1,1,1,4,2,2,1,1,1,1,1,1,1,1,1,5,1,2,1,1,2,2,1,3,1,11,2,1,2,4,1,1,1,2,1,2,1,4,1,2,1,2,2,1,2,2,1,1,1,3,3,1,1,2,1,1,1,2,2,1,2,1,2,1,2,1,2,1,1,1,1,1,2,2,3,1,2,3,1,1,2,1,2,1,2,1,1,2,1,2,1,3,2,4,2,3,3,1,2,36,2,2,2,2,2,2,1,2,2,4,1,1,2,1,1,1,1,1,1,1,4,1,1,3,1,2,2,1,1,4,1,4,2,2,2,1,2,1,1,1,2,1,3,1,2,1,1,2,1,1,1,1,2,3,1,2,2,2,1,1,2,1,2,3,1,1,1,1,1,1,1,5,2,1,2,2,2,2,5,1,3,3,1,1,1,4,2,3,2,2,1,6,3,4,1,1,1,3,2,1,2,2,2,3,2,1,1,2,1,1,1,3,2,1,2,1,1,7,3,3,1,5,1,4,2,1,1,1,2,1,2,1,1,9,1,1,2,3,2,1,1,9,2,4,3,3,2,4,2,1,3,1,1,1,1,2,2,1,2,1,2,1,1,7,4,1,2,2,2,1,2,1,2,2,2,4,1,2,3,2,1,1,2,1,1,4,1,1,3,1,1,2,3,1,1,3,1,1,1,2,1,1,2,2,2,1,1,1,3,1,1,2,5,1,1,2,4,4,1,1,2,1,1,1,3,1,2,3,1,1,2,2,1,2,2,3,2,1,1,3,1,2,4,2,2,1,2,3,2,1,3,2,1,1,2,1,1,1,1,2,1,1,1,1,1,2,1,1,1,1,2,2,1,7,1,1,3,2,3,1,2,2,1,5,4,2,1,1,1,2,1,1,1,1,1,1,1,1,1,4,1,1,1,1,2,1,4,1,1,2,2,3,2,1,2,3,2,1,1,2,3,2,1,1,1,3,2,1,1,2,5,2,2,1,1,1,1,2,2,2,1,1,1,3,4,2,1,3,2,1,1,2,1,1,4,1,5,1,1,4,1,5,1,1,1,4,2,3,2,3,3,1,1,1,2,1,1,1,3,3,1,1,1,3,2,2,3,2,1,2,1,2,2,1,2,1,1,2,1,1,1,1,1,1,2,2,3,2,1,1,1,2,2,1,1,1,1,2,2,2,2,2,2,6,1,2,1,2,1,2,1,1,1,1,2,2,4,1,1,2,2,2,1,2,1,3,1,1,1,2,1,1,4,4,1,1,1,2,1,1,2,2,1,4,1,1,1,3,1,4,2,1,2,2,1,1,1,1,2,2,2,4,1,1,1,1,2,5,2,6,4,2,3,2,2,3,1,1,2,1,6,5,1,1,1,2,2,4,1,3,3,1,2,2,1,3,5,1,1,1,1,3,1,6,2,1,2,1,2,1,1,2,1,4,2,1,2,1,2,1,2,1,1,1,5,2,2,1,2,5,1,3,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,3,2,2,2,4,1,6,2,1,1,1,7,1,1,7,1,1,4,2,1,6,1,1,2,1,1,2,2,4,1,2,2,2,1,2,4,2,2,1,2,1,1,1,1,4,4,1,1,2,2,2,1,1,1,1,2,2,8,1,1,1,1,1,2,1,7,1,1,1,2,1,2,2,2,2,1,3,1,1,1,1,1,3,1,1,1,3,1,1,2,1,1,1,1,2,4,1,1,3,1,1,2,1,1,1,2,1,2,4,1,1,1,1,1,2,1,2,2,1,3,2,1,1,4,1,1,3,2,1,1,2,1,2,2,3,2,2,2,2,1,1,1,1,1,2,1,1,2,2,2,1,1,2,3,1,1,1,3,1,3,4,1,1,1,1,1,1,1,1,1,1,2,2,1,2,1,2,1,3,1,1,2,1,1,2,3,1,1,2,2,1,3,2,1,1,1,2,1,1,2,2,1,1,4,2,2,5,4,1,1,2,1,2,3,4,4,2,1,4,2,2,3,1,1,1,3,7,1,1,3,2,1,4,2,1,1,1,1,1,2,1,2,3,1,1,1,4,1,1,2,1,5,2,2,1,2,7,7,2,1,1,1,1,2,1,2,1,3,1,2,1,1,3,1,1,2,1,1,2,1,2,2,4,1,2,1,1,1,1,1,1,1,3,1,1,1,2,1,2,1,1,1,1,2,3,2,1,1,1,3,2,2,1,3,4,1,2,1,1,1,1,4,1,3,1,2,1,1,1,1,1,1,2,2,2,1,4,1,1,1,1,2,1,1,3,1,2,4,2,2,1,2,2,2,1,2,2,1,3,2,2,2,2,2,2,1,1,1,1,1,1,1,1,2,1,2,1,1,1,2,3,1,1,2,1,2,1,3,1,1,6,1,1,1,2,2,2,1,1,1,1,1,3,1,2,2,2,1,1,1,4,2,3,1,4,1,1,2,1,1,1,1,1,1,1,3,2,1,1,2,1,1,1,2,1,3,1,1,2,2,3,2,2,1,2,2,2,1,2,1,4,2,2,4,1,1,4,2,1,1,2,2,6,3,1,2,3,3,5,1,2,1,3,2,3,1,1,2,2,1,1,1,3,1,1,2,2,4,8,1,1,1,4,1,2,1,1,1,6,17,4,2,2,1,1,2,4,1,1,1,3,1,2,2,1,3,2,1,1,2,1,1,2,1,1,2,2,2,2,2,2,3,1,2,2,2,1,1,2,2,1,4,1,2,1,1,1,2,3,2,2,2,2,1,2,1,1,4,3,1,4,2,3,7,1,1,1,1,3,1,1,2,2,1,1,1,1,3,2,1,3,1,2,2,4,2,1,3,1,1,1,2,1,2,1,2,1,1,4,2,2,1,1,1,2,1,4,1,1,4,3,1,1,1,7,2,3,2,1,2,1,1,2,5,1,2,1,2,2,1,1,2,2,2,2,2,1,1,1,2,1,2,3,3,2,2,5,2,3,1,2,5,3,2,2,2,3,1,2,1,1,2,4,2,1,1,1,1,3,3,1,2,2,1,1,3,3,1,1,1,3,1,3,2,1,2,2,1,2,1,2,1,1,2,3,1,1,3,4,2,1,1,1,2,4,2,1,4,1,1,1,2,1,2,4,1,4,1,1,2,1,1,2,1,3,1,1,1,3,1,3,6,1,1,1,2,3,1,1,1,1,2,2,1,1,1,1,1,1,1,1,2,2,2,1,2,5,3,2,1,1,1,1,1,2,2,1,3,1,2,1,1,2,3,2,1,1,2,3,2,1,1,1,2,2,2,3,2,2,1,1,2,1,1,1,1,2,1,1,6,2,4,3,2,2,3,1,2,1,1,1,2,4,1,1,3,4,2,2,1,1,2,1,2,3,2,1,3,1,5,4,4,3,1,1,1,1,2,2,1,1,1,1,1,3,1,1,1,1,1,1,3,3,1,1,2,1,1,3,3,1,1,5,7,2,1,3,1,2,3,4,3,1,1,1,4,1,1,2,1,2,2,1,1,1,2,1,1,1,1,1,4,2,3,1,1,1,1,3,1,1,1,1,2,1,2,1,1,3,8,1,2,1,2,2,3,1,1,2,2,1,1,1,1,2,1,2,1,1,2,2,1,2,2,2,2,2,1,1,1,2,2,1,1,1,1,2,1,2,1,2,1,2,1,2,1,1,1,1,3,2,2,1,1,1,2,1,1,1,3,1,2,2,2,5,1,1,1,36],\"histnorm\":\"probability\",\"marker\":{\"color\":\"grey\"},\"xaxis\":\"x6\",\"yaxis\":\"y6\"}];\r\n",
+ " var layout = {\"width\":1500,\"height\":1000,\"template\":{\"layout\":{\"paper_bgcolor\":\"white\",\"plot_bgcolor\":\"white\",\"xaxis\":{\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"zeroline\":true},\"yaxis\":{\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"zeroline\":true}},\"data\":{}},\"xaxis\":{\"title\":{\"text\":\"\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"yaxis\":{\"title\":{\"text\":\"peaks / lane\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"title\":{\"text\":\"5% (left), 10% (middle) and 20% (right) threshold\"},\"xaxis2\":{\"title\":{\"text\":\"\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"yaxis2\":{\"title\":{\"text\":\"peaks / lane\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"xaxis3\":{\"title\":{\"text\":\"\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"yaxis3\":{\"title\":{\"text\":\"peaks / lane\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"xaxis4\":{\"title\":{\"text\":\"\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"yaxis4\":{\"title\":{\"text\":\"peakwidth / lane\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"xaxis5\":{\"title\":{\"text\":\"\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"yaxis5\":{\"title\":{\"text\":\"peakwidth / lane\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"xaxis6\":{\"title\":{\"text\":\"\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"yaxis6\":{\"title\":{\"text\":\"peakwidth / lane\"},\"ticks\":\"inside\",\"mirror\":\"all\",\"showline\":true,\"showgrid\":false},\"grid\":{\"rows\":2,\"columns\":3,\"pattern\":\"independent\"}};\r\n",
+ " var config = {\"responsive\":true,\"toImageButtonOptions\":{\"format\":\"svg\"}};\r\n",
+ " Plotly.newPlot('debd6b3e-9f09-4c5e-ac26-0a8cb7dea6f2', data, layout, config);\r\n",
+ "});\r\n",
+ " };\r\n",
+ " if ((typeof(requirejs) !== typeof(Function)) || (typeof(requirejs.config) !== typeof(Function))) {\r\n",
+ " var script = document.createElement(\"script\");\r\n",
+ " script.setAttribute(\"src\", \"https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js\");\r\n",
+ " script.onload = function(){\r\n",
+ " renderPlotly_debd6b3e9f094c5eac260a8cb7dea6f2();\r\n",
+ " };\r\n",
+ " document.getElementsByTagName(\"head\")[0].appendChild(script);\r\n",
+ " }\r\n",
+ " else {\r\n",
+ " renderPlotly_debd6b3e9f094c5eac260a8cb7dea6f2();\r\n",
+ " }\r\n",
+ "</script>\r\n",
+ "\n",
+ " \n",
+ "</div> \n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "\n",
"\n",
"[\n",
" plotPeaksPerLaneHisto 0.05\n",
@@ -5339,9 +1748,1072 @@
"|> Chart.Grid(2,3)\n",
"|> Chart.withSize (1500.,1000.)\n",
"|> Chart.withTitle (\"5% (left), 10% (middle) and 20% (right) threshold\" )\n",
- "|> Chart.show\n",
"\n"
]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Distance measurements\n",
+ "\n",
+ "In the following a module is defined that enables DTWarping "
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Writing the transformed, normalized data with their respective distances between wt and lpa2\n",
+ "\n",
+ "The following function does all calculations, adds hyperlinks to plots, and in the end writes the data into a file. The file can be copied into an xlsx excel file to resolve the hyperlinks."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "dotnet_interactive": {
+ "language": "fsharp"
+ },
+ "vscode": {
+ "languageId": "dotnet-interactive.fsharp"
+ }
+ },
+ "outputs": [],
+ "source": [
+ "correctedIntensities"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "dotnet_interactive": {
+ "language": "fsharp"
+ },
+ "vscode": {
+ "languageId": "dotnet-interactive.fsharp"
+ }
+ },
+ "outputs": [],
+ "source": [
+ "\n",
+ "let combinedFunction intMeasurement= \n",
+ " let getPeaks signal (percentageForMinIntensity :float) =\n",
+ " let minSig = signal |> Array.max |> fun x -> x * percentageForMinIntensity\n",
+ " let sigLength = signal.Length\n",
+ " [for i=1 to signal.Length - 2 do \n",
+ " let currSignal = signal.[i]\n",
+ " if currSignal > signal.[i-1] && currSignal > signal.[i+1] && currSignal > minSig then yield (i+1)]\n",
+ " |> fun acc -> if signal.[0] > signal.[1] && signal.[0] > minSig then 1::acc else acc\n",
+ " |> fun acc -> if signal.[sigLength-1] > signal.[sigLength-2] && signal.[sigLength-1]> minSig then sigLength::acc else acc\n",
+ "\n",
+ " let dataset = \n",
+ " match intMeasurement with\n",
+ " | IntMeasurement.LFQ -> correctedLFQs |> Array.map (fun lane -> lane |> Array.filter (fun x -> not (x.ID.Contains \";\") && not (x.ID.Contains \"iRT\")))\n",
+ " | IntMeasurement.IBAQ -> correctedIBAQss |> Array.map (fun lane -> lane |> Array.filter (fun x -> not (x.ID.Contains \";\") && not (x.ID.Contains \"iRT\")))\n",
+ " | IntMeasurement.Intensity -> correctedIntensities |> Array.map (fun lane -> lane |> Array.filter (fun x -> not (x.ID.Contains \";\") && not (x.ID.Contains \"iRT\")))\n",
+ "\n",
+ " dataset\n",
+ " |> Array.mapi (fun laneIndex lane -> \n",
+ " lane\n",
+ " //|> Array.filter (fun protein -> Normalization.intersUniqueMin2.Contains protein.ID)\n",
+ " //|> Array.filter (fun protein -> Normalization.intersUnique.Contains protein.ID)\n",
+ " |> Array.map (fun x -> \n",
+ " let intensities = \n",
+ " match intMeasurement with\n",
+ " | IntMeasurement.LFQ -> x.LFQ\n",
+ " | IntMeasurement.IBAQ -> x.IBaq\n",
+ " | IntMeasurement.Intensity -> x.Intensities\n",
+ " laneIndex,x.ID,intensities)\n",
+ " )\n",
+ " |> Array.concat\n",
+ " |> Array.groupBy snd3\n",
+ " //|> Array.sortByDescending (fun (id,it) -> it|> Array.map snd|> JaggedArray.transpose |> Array.map Seq.mean |> Seq.indexed |> Seq.maxBy snd |> fst)\n",
+ " |> Array.map (fun (id,x) -> \n",
+ " let id' = (id.Split '.').[0..1] |> String.concat \".\"\n",
+ " let (wt,wtCount) = \n",
+ " let empty :float [] []= Array.init 3 (fun _ -> Array.zeroCreate 36)\n",
+ " let intensities = x |> Array.filter (fun (lI,id,lfq) -> lI <=2) \n",
+ " for elem in intensities do empty.[fst3 elem] <- trd3 elem\n",
+ " //for i=0 to intensities.Length-1 do empty.[i] <- intensities.[i]\n",
+ " empty,(intensities |> Array.map trd3 |> Array.filter (fun x -> (Array.exists (fun t -> t>0.) x))).Length\n",
+ " let wtMeans = wt |> JaggedArray.transpose |> Array.map Seq.mean\n",
+ " let (mut,mutCount) =\n",
+ " let empty :float [] []= Array.init 3 (fun _ -> Array.zeroCreate 36)\n",
+ " let intensities = x |> Array.filter (fun (lI,id,lfq) -> lI >=3)\n",
+ " for elem in intensities do empty.[fst3 elem - 3] <- trd3 elem\n",
+ " //for i=0 to intensities.Length-1 do empty.[i] <- intensities.[i]\n",
+ " empty,(intensities |> Array.map trd3 |> Array.filter (fun x -> (Array.exists (fun t -> t>0.) x))).Length\n",
+ " let mutMeans = mut |> JaggedArray.transpose |> Array.map Seq.mean\n",
+ " let ttestSums = \n",
+ " let wtSums = (wt |> Array.map Seq.sum |> vector)\n",
+ " let mutSums = (mut |> Array.map Seq.sum |> vector)\n",
+ " //printfn \"%A %A\" wtSums mutSums\n",
+ " if Seq.mean wtSums = 0. then\n",
+ " if Seq.mean mutSums = 0. then nan\n",
+ " else (Testing.TTest.twoSample false mutSums wtSums).PValue\n",
+ " else (Testing.TTest.twoSample false wtSums mutSums).PValue\n",
+ " \n",
+ " let dH0_wt = getWarpDistancesOfSignals wt\n",
+ " let dH0_mut = getWarpDistancesOfSignals mut\n",
+ " let combinedH0Distances = Array.append dH0_wt dH0_mut\n",
+ " [id' + \" wt\";id' + \" mu\"],[wtMeans;mutMeans;(*x.[0..2] |> Array.map snd |> JaggedArray.transpose |> Array.map Seq.mean*)],(combinedH0Distances,ttestSums,(wtCount,mutCount))\n",
+ " )\n",
+ " |> Array.unzip3\n",
+ " |> fun (rowNames,heatmapdata,h0andTests) -> \n",
+ " //log of distance + euclidean\n",
+ " let (h0Distances,pVal,replicates) = \n",
+ " Array.unzip3 h0andTests\n",
+ "\n",
+ " let (listString,distances) =\n",
+ " heatmapdata\n",
+ " |> Array.mapi (fun i x -> \n",
+ " let d = getDTWeuc x.[0] x.[1]\n",
+ " let string = sprintf \"%s\\t%f\" ((rowNames.[i].[0].Split ' ').[0]) d \n",
+ " string,d)\n",
+ " |> Array.unzip\n",
+ " \n",
+ " let sortedIndices = \n",
+ " distances \n",
+ " |> Array.indexed\n",
+ " |> Array.sortBy snd\n",
+ " |> Array.map fst\n",
+ " \n",
+ " let sortedRownames =\n",
+ " sortedIndices \n",
+ " |> Array.map (fun i -> rowNames.[i])\n",
+ "\n",
+ " let pValSorted = \n",
+ " sortedIndices \n",
+ " |> Array.map (fun i -> pVal.[i])\n",
+ "\n",
+ " let replicateSorted = \n",
+ " sortedIndices \n",
+ " |> Array.map (fun i -> replicates.[i])\n",
+ "\n",
+ "\n",
+ " let distanceHeatmap =\n",
+ " distances\n",
+ " |> Array.sort\n",
+ " |> Array.map (fun x -> [|[|x|];[|x|]|])\n",
+ " |> Seq.concat\n",
+ " |> fun x -> \n",
+ " Chart.Heatmap(x,MultiText=(sortedRownames|> Seq.concat))\n",
+ " |> Chart.withXAxis(LinearAxis.init(ShowTickLabels=false,TickFont=Font.init(Color=Color.fromString \"white\"),Ticks=TickOptions.Empty))\n",
+ " \n",
+ " let traces = \n",
+ " sortedIndices\n",
+ " |> Array.map (fun i -> heatmapdata.[i])\n",
+ " |> Array.map (fun x -> [| DTW.zNorm x.[0];DTW.zNorm x.[1]|])\n",
+ " //DTW.zNorm [|0.;0.;0.;|]\n",
+ "\n",
+ " let peaks =\n",
+ " sortedIndices\n",
+ " |> Array.map (fun i -> heatmapdata.[i])\n",
+ " |> Array.map (fun x -> \n",
+ " \"[\" + (getPeaks x.[0] 0.1 |> List.map string |> String.concat \";\") + \";]\",\n",
+ " \"[\" + (getPeaks x.[1] 0.1 |> List.map string |> String.concat \";\") + \";]\"\n",
+ " )\n",
+ "\n",
+ " //let rplicateCount = \n",
+ " // sortedIndices\n",
+ " // |> Array.map (fun i -> heatmapdata.[i])\n",
+ " // |> Array.map (fun x -> x.[0] x.[1]|])\n",
+ "\n",
+ " let tracesOrig = \n",
+ " sortedIndices\n",
+ " |> Array.map (fun i -> heatmapdata.[i])\n",
+ " |> Array.map (fun x -> [|x.[0];x.[1]|])\n",
+ "\n",
+ " let traceHeatmap = \n",
+ " Chart.Heatmap((traces|> Array.concat),X=[1..36],Y=(sortedRownames|> Seq.concat),ShowLegend=false)\n",
+ " |> Chart.withColorBarStyle(\"int\",XAnchor=HorizontalAlign.Left)\n",
+ " |> Chart.withXAxisStyle \"Slice index\"\n",
+ "\n",
+ " let h0Distances = h0Distances |> Array.concat\n",
+ " let h0Size = h0Distances.Length\n",
+ " let cutOffIndex =0.95 * (float h0Size)\n",
+ " let cutOffThreshold = (h0Distances |> Array.sort).[int cutOffIndex]\n",
+ " \n",
+ " //distances\n",
+ " //|> Array.sort\n",
+ " //|> Array.iteri (fun i difference -> \n",
+ " // if difference > cutOffThreshold then \n",
+ " // printfn \"%s\\t%f\\t%s\\t%s\\t%s\" sortedRownames.[i].[0] difference (Annotation.jgi55ToSynStr sortedRownames.[i].[0]) (traces.[i].[0] |> Array.map string |> String.concat \"\\t\") (traces.[i].[1]|> Array.map string |> String.concat \"\\t\")\n",
+ " // )\n",
+ " \n",
+ " let lines =\n",
+ " distances\n",
+ " |> Array.sort\n",
+ " |> Array.mapi (fun i difference -> \n",
+ " if i%100=0 then printfn \"%i\" i\n",
+ " let name = (sortedRownames.[i].[0].Split ' ').[0]\n",
+ " //printfn \"%s\" name\n",
+ " let synonym = Annotation.lpa2Syn.[name]\n",
+ " let wtmeans = tracesOrig.[i].[0]\n",
+ " let mutmeans = tracesOrig.[i].[1] \n",
+ " let wtMeanSum = Seq.sum wtmeans\n",
+ " let mutMeanSum = Seq.sum mutmeans\n",
+ " let wtMeansStr= wtmeans |> Array.map string |> String.concat \"\\t\"\n",
+ " let mutMeansStr= mutmeans |> Array.map string |> String.concat \"\\t\"\n",
+ " let pValSums = pValSorted.[i]\n",
+ " let dtweucAdj = getDTWeuc wtmeans mutmeans\n",
+ " let euc = DistanceMetrics.euclidean wtmeans mutmeans\n",
+ " let maxMean = max (Seq.mean wtmeans) (Seq.mean mutmeans)\n",
+ " //printfn \"%s\\t%f\\t%s\\t%s\\t%s\" sortedRownames.[i].[0] difference (Annotation.jgi55ToSynStr sortedRownames.[i].[0]) (traces.[i].[0] |> Array.map string |> String.concat \"\\t\") \n",
+ " let (mapMan,mapManDes) = \n",
+ " Annotation.lpa2MM.[name],Annotation.lpa2MMdes.[name]//\n",
+ " //(BioFSharp.BioDB.FaToolDb.Queries.getOntologyterms BioDB.FaToolDb.MapManOntology name).OntologyGroups |> List.unzip |> fun (a,b) -> (a |> String.concat \";\").Replace(\"GMM:\",\"\"),b |> String.concat \";\" \n",
+ " let annotationGO = \n",
+ " Annotation.lpa2GO.[name]\n",
+ " //(BioFSharp.BioDB.FaToolDb.Queries.getOntologyterms BioDB.FaToolDb.GeneOntology name).OntologyGroups |> List.map snd |> String.concat \";\" \n",
+ " let annotationLoc = \n",
+ " Annotation.lpa2loc.[name]\n",
+ " //(BioFSharp.BioDB.FaToolDb.Queries.getOntologyterms BioDB.FaToolDb.SubCellularLocalisationOntology name).OntologyGroups |> List.map snd |> String.concat \";\" \n",
+ " //sprintf $\"{name}\\t{synonym}\\t{annotation}\\t{pValSums}\\t{difference}\\t{dtw}\\t{euc}\\t{maxMean}\\t{wtMeansStr}\\t{mutMeansStr}\"\n",
+ " \n",
+ " //let linkToFile = \"=HYPERLINK(LEFT(CELL(\\\"filename\\\", $A$1), FIND(\\\"[\\\",CELL(\\\"filename\\\",$A$1))-1) & \\\"plots\\LFQ\\\\\" + synonym + \"_\" + name + \".html\\\",\\\"\" + name + \"\\\")\"\n",
+ " let linkToFile = \n",
+ " match intMeasurement with\n",
+ " | IntMeasurement.LFQ -> \"=HYPERLINK(LEFT(CELL(\\\"filename\\\", $A$1), FIND(\\\"[\\\",CELL(\\\"filename\\\",$A$1))-1) & \\\"plots\\LFQ\\\\\" + synonym + \"_\" + name + \".html\\\",\\\"\" + name + \"\\\")\"\n",
+ " | IntMeasurement.Intensity -> \"=HYPERLINK(LEFT(CELL(\\\"filename\\\", $A$1), FIND(\\\"[\\\",CELL(\\\"filename\\\",$A$1))-1) & \\\"plots\\\\\" + synonym + \"_\" + name + \".html\\\",\\\"\" + name + \"\\\")\"\n",
+ " sprintf $\"{linkToFile}\\t{synonym}\\t{mapManDes}\\t{mapMan}\\t{annotationGO}\\t{annotationLoc}\\t{fst replicateSorted.[i]}\\t{snd replicateSorted.[i]}\\t{pValSums}\\t{difference}\\t{euc}\\t{maxMean}\\t{fst peaks.[i]}\\t{snd peaks.[i]}\\t{wtMeansStr}\\t{mutMeansStr}\"\n",
+ " )\n",
+ " |> fun x -> \n",
+ " [| \n",
+ " yield sprintf \"Name\\tSynonym\\tMapMan\\tMapManTerm\\tGO\\tSubLoc\\treplicatesWT\\treplicatesMut\\tpValSum\\tdiff_adj\\teuc\\tmaxMean\\tpeaksWT\\tpeaksMut\\twtMean1\\twtMean2\\twtMean3\\twtMean4\\twtMean5\\twtMean6\\twtMean7\\twtMean8\\twtMean9\\twtMean10\\twtMean11\\twtMean12\\twtMean13\\twtMean14\\twtMean15\\twtMean16\\twtMean17\\twtMean18\\twtMean19\\twtMean20\\twtMean21\\twtMean22\\twtMean23\\twtMean24\\twtMean25\\twtMean26\\twtMean27\\twtMean28\\twtMean29\\twtMean30\\twtMean31\\twtMean32\\twtMean33\\twtMean34\\twtMean35\\twtMean36\\tmutMean1\\tmutMean2\\tmutMean3\\tmutMean4\\tmutMean5\\tmutMean6\\tmutMean7\\tmutMean8\\tmutMean9\\tmutMean10\\tmutMean11\\tmutMean12\\tmutMean13\\tmutMean14\\tmutMean15\\tmutMean16\\tmutMean17\\tmutMean18\\tmutMean19\\tmutMean20\\tmutMean21\\tmutMean22\\tmutMean23\\tmutMean24\\tmutMean25\\tmutMean26\\tmutMean27\\tmutMean28\\tmutMean29\\tmutMean30\\tmutMean31\\tmutMean32\\tmutMean33\\tmutMean34\\tmutMean35\\tmutMean36\"\n",
+ " yield! x\n",
+ " |]\n",
+ " //x |> Array.iter (printfn \"%s\")\n",
+ " \n",
+ " let shape() = Shape.init(ShapeType.Line,cutOffThreshold,cutOffThreshold,0.,0.05)\n",
+ " \n",
+ " [\n",
+ " h0Distances\n",
+ " |> fun x -> Chart.Histogram(x,HistNorm=HistNorm.Probability)\n",
+ " |> Chart.withShape (shape())\n",
+ " |> Chart.withTraceInfo \"h0_distances\"\n",
+ " |> Chart.withAxisTitlesWR \"\" \"count\" (0.,100.)\n",
+ " distances\n",
+ " |> fun x -> Chart.Histogram(x,HistNorm=HistNorm.Probability)\n",
+ " //|> Chart.withShape (shape())\n",
+ " |> Chart.withTraceInfo \"vs distances\"\n",
+ " |> Chart.withAxisTitlesWR \"DWTeuc_adj\" \"count\" (0.,100.)\n",
+ " ]\n",
+ " |> Chart.Grid(2,1)\n",
+ " //|> Chart.show\n",
+ "\n",
+ " [\n",
+ " traceHeatmap\n",
+ " distanceHeatmap\n",
+ " ]\n",
+ " |> Chart.Grid(1,2)\n",
+ " |> Chart.withSize (900.,900.)\n",
+ " |> Chart.withMarginSize (150.)\n",
+ " |> Chart.withTitle \"Migration distances of WT vs Mut\"\n",
+ " |> Chart.withDescription({Heading =\"Interactive chart of migration distances\";Text=\"(left) zNormed intensities of wild type and mutant.<br>(right) Adjusted euclidean distance of each protein pair.<br><br>Note: Distance is 36 if signal of WT or Mut is missing. Click and zoom vertically for more details\"})\n",
+ " //|> Chart.show \n",
+ " \n",
+ " \n",
+ " listString\n",
+ " lines\n",
+ "\n",
+ "\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "dotnet_interactive": {
+ "language": "fsharp"
+ },
+ "vscode": {
+ "languageId": "dotnet-interactive.fsharp"
+ }
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "0\r\n",
+ "100\r\n",
+ "200\r\n",
+ "300\r\n",
+ "400\r\n",
+ "500\r\n",
+ "600\r\n",
+ "700\r\n",
+ "800\r\n",
+ "900\r\n",
+ "1000\r\n",
+ "1100\r\n",
+ "1200\r\n",
+ "1300\r\n",
+ "1400\r\n",
+ "1500\r\n",
+ "1600\r\n",
+ "1700\r\n"
+ ]
+ }
+ ],
+ "source": [
+ "let lines = combinedFunction IntMeasurement.Intensity\n",
+ "\n",
+ "//uncomment and copy the lines into an excel file at the same storage folder\n",
+ "System.IO.File.WriteAllLines(@\"C:\\Users\\bvenn\\source\\repos\\LPA2_ComplexomeProfiling_Chlamy\\runs\\proteinDistances.txt\",lines)\n",
+ "\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "dotnet_interactive": {
+ "language": "fsharp"
+ },
+ "vscode": {
+ "languageId": "dotnet-interactive.fsharp"
+ }
+ },
+ "outputs": [],
+ "source": [
+ "let plotSignals save weight (cre:string) intmeasure =\n",
+ " \n",
+ " let synonym = Annotation.lpa2Syn.[cre]\n",
+ " let original = \n",
+ " datasets\n",
+ " |> Array.map (Array.filter (fun x -> (x.ID |> String.filter (fun s -> s = 'C') |> fun c -> c.Length = 1))) //new\n",
+ " |> Array.mapi (fun laneIndex x -> \n",
+ " x \n",
+ " |> Array.map (fun x -> x)\n",
+ " |> Array.filter (fun (x) -> x.ID.StartsWith cre)\n",
+ " |> fun x -> \n",
+ " if x = [||] then \n",
+ " laneIndex,Array.init 36 (fun _ -> 0.)\n",
+ " else \n",
+ " if x.Length > 2 then printfn \"WARNING: %A\" x\n",
+ " match intmeasure with\n",
+ " | IntMeasurement.LFQ -> laneIndex,x.[0].LFQ\n",
+ " | IntMeasurement.Intensity -> laneIndex,x.[0].Intensities\n",
+ " | IntMeasurement.IBAQ -> laneIndex,x.[0].IBaq\n",
+ " )\n",
+ "\n",
+ " let originalChart = \n",
+ " original\n",
+ " |> Array.map (fun (j,x) -> x |> Seq.mapi (fun i x-> i+1,x) |> fun x -> Chart.Line(x,Name=laneHeader.[j] + \" raw\",LineColor=Color.fromString colors.[j]))\n",
+ " |> Chart.combine\n",
+ " \n",
+ " let normed = \n",
+ " let normedData = \n",
+ " match intmeasure with\n",
+ " | IntMeasurement.LFQ -> correctedLFQs\n",
+ " | IntMeasurement.Intensity -> correctedIntensities\n",
+ " | IntMeasurement.IBAQ -> correctedIBAQss\n",
+ " \n",
+ " normedData\n",
+ " |> Array.map (Array.filter (fun x -> (x.ID |> String.filter (fun s -> s = 'C') |> fun c -> c.Length = 1))) //new\n",
+ " |> Array.mapi (fun laneIndex x -> \n",
+ " x \n",
+ " |> Array.map (fun x -> x)\n",
+ " |> Array.filter (fun (x) -> x.ID.StartsWith cre)\n",
+ " |> fun x -> \n",
+ " if x = [||] then \n",
+ " laneIndex,Array.init 36 (fun _ -> 0.)\n",
+ " else \n",
+ " if x.Length > 2 then printfn \"WARNING: %A\" x\n",
+ " match intmeasure with\n",
+ " | IntMeasurement.LFQ -> laneIndex,x.[0].LFQ\n",
+ " | IntMeasurement.Intensity -> laneIndex,x.[0].Intensities\n",
+ " | IntMeasurement.IBAQ -> laneIndex,x.[0].IBaq\n",
+ " )\n",
+ " //|> Array.concat\n",
+ " //|> Array.mapi (fun j (laneIndex,x) -> laneIndex,x.LFQ)\n",
+ " \n",
+ " let normedChart = \n",
+ " normed\n",
+ " |> Array.map (fun (j,x) -> x |> Seq.mapi (fun i x-> i+1,x) |> fun x -> Chart.Line(x,Name=laneHeader.[j] + \" norm\",LineColor=Color.fromString colors.[j]) )\n",
+ " |> Chart.combine\n",
+ "\n",
+ " let wtTraces = (normed |> Array.filter (fun (i,x) -> i <= 2) |> Array.map snd)\n",
+ " let mutTraces = (normed |> Array.filter (fun (i,x) -> i >= 3) |> Array.map snd)\n",
+ " //let h0Distances = \n",
+ " // Array.append \n",
+ " // (getWarpDistancesOfSignals wtTraces)\n",
+ " // (getWarpDistancesOfSignals mutTraces )\n",
+ " // |> Array.map (sprintf \"%.2f\") |> String.concat \", \"\n",
+ "\n",
+ " let wt = wtTraces |> JaggedArray.transpose |> Array.map Seq.mean\n",
+ " let mu = mutTraces |> JaggedArray.transpose |> Array.map Seq.mean\n",
+ " let wtStd = wtTraces |> JaggedArray.transpose |> Array.map Seq.stDev\n",
+ " let muStd = mutTraces |> JaggedArray.transpose |> Array.map Seq.stDev\n",
+ "\n",
+ " let meanChart = \n",
+ " [\n",
+ " Chart.Line(wt |> Seq.mapi (fun i x-> i+1,x),LineColor=Color.fromString colors.[0],Name=\"wt mean\")|> Chart.withYErrorStyle(Array=wtStd)\n",
+ " Chart.Line(mu |> Seq.mapi (fun i x-> i+1,x),LineColor=Color.fromString colors.[5],Name=\"mut mean\")|> Chart.withYErrorStyle(Array=muStd)\n",
+ " ]\n",
+ " |> Chart.combine\n",
+ " //|> Chart.withAxisAnchor(Y=1)\n",
+ "\n",
+ " //let dTW = DTW.distanceDefault wt mu\n",
+ " let euc = ML.DistanceMetrics.euclidean wt mu\n",
+ " let dfi = getDTWeuc wt mu\n",
+ "\n",
+ " ///Testing\n",
+ " let wtSums = wtTraces |> Array.map Seq.sum |> vector\n",
+ " let mutSums = mutTraces |> Array.map Seq.sum |> vector\n",
+ " let sumFoldChange = Seq.map2 (fun w m -> m/w) wtSums mutSums |> Seq.mean\n",
+ "\n",
+ " let ttest = \n",
+ " if Seq.mean wtSums = 0. then\n",
+ " if Seq.mean mutSums = 0. then nan\n",
+ " else (Testing.TTest.twoSample false mutSums wtSums).PValue\n",
+ " else (Testing.TTest.twoSample false wtSums mutSums).PValue\n",
+ " \n",
+ " let ttestPval = ttest\n",
+ " //contasts\n",
+ " let wtSlices = (wtTraces |> JaggedArray.transpose)\n",
+ " let mutSlices = (mutTraces |> JaggedArray.transpose)\n",
+ " let appendedSlices = Array.append wtSlices mutSlices\n",
+ " //let contrasts = \n",
+ " // Array.init 36 (fun testIndex -> \n",
+ " // let tmpContrast :float [] = Array.zeroCreate (36*2)\n",
+ " // tmpContrast.[testIndex] <- 1.\n",
+ " // tmpContrast.[testIndex+36] <- 1.\n",
+ " // tmpContrast\n",
+ " // )\n",
+ " //let contrastResults = \n",
+ " // Testing.PostHoc.fishersLSD contrasts appendedSlices //auf gar keinen fall einen post hoc test nehmen!! wegen variance estimation!\n",
+ " let contrastResults = \n",
+ " Array.mapi2 (fun i w m -> \n",
+ " if Seq.mean w = 0. (*|| Seq.mean m = 0.*) then \n",
+ " if Seq.mean m <> 0. then \n",
+ " i+1,(Testing.TTest.twoSample false (vector m) (vector w)).PValue\n",
+ " else i+1,nan\n",
+ " else \n",
+ " i+1,(Testing.TTest.twoSample false (vector w) (vector m)).PValue\n",
+ " ) \n",
+ " wtSlices \n",
+ " mutSlices\n",
+ " //let contrastResults = Testing.PostHoc.fishersLSD contrasts appendedSlices //auf gar keinen fall einen post hoc test nehmen!! wegen variance estimation!\n",
+ " let contrastResultStrings = \n",
+ " contrastResults \n",
+ " |> Array.map (fun (i,x) -> $\"{i}\\t\\t%.2f{x}\")\n",
+ " |> Array.chunkBySize 9\n",
+ " |> fun chunks -> \n",
+ " chunks.[0]\n",
+ " |> Array.mapi (fun j chunk9 -> \n",
+ " sprintf \"%s\\t\\t%s\\t\\t%s\\t\\t%s\" chunk9 chunks.[1].[j] chunks.[2].[j] chunks.[3].[j]\n",
+ " )\n",
+ " |> String.concat \"<br>\"\n",
+ " let pValues =\n",
+ " contrastResults \n",
+ " |> Array.partition (fun (i,x) -> x < 0.05)\n",
+ " |> fun (pos,neg) -> \n",
+ " [Chart.Column(pos|> Array.map (fun (i,x) -> i,- log10 x),MarkerColor=Color.fromString \"green\");Chart.Column(neg|> Array.map (fun (i,x) -> i,- log10 x),MarkerColor=Color.fromString \"grey\")] \n",
+ " |> Chart.combine\n",
+ " |> Chart.withTraceInfo \"pVals Welch\"\n",
+ " \n",
+ " let intMeasureStr =\n",
+ " match intmeasure with\n",
+ " | IntMeasurement.LFQ -> \"LFQ\"\n",
+ " | IntMeasurement.Intensity -> \"Intensities\"\n",
+ " | IntMeasurement.IBAQ -> \"IBaq\"\n",
+ "\n",
+ " let annotation = \n",
+ " //Annotation.jgi55ToDesStr ((cre.Split '.').[0..1] |> String.concat \".\")\n",
+ " Annotation.lpa2MMdes.[cre]\n",
+ " Annotation.lpa2MMdes.[cre]\n",
+ "\n",
+ " [\n",
+ " //[pValues |> styleChartwR \"\" \"-log10 pValue\"(1.,36.)]\n",
+ " originalChart |> Chart.withAxisTitlesWR \"\" (intMeasureStr + \" raw\") (1.,36.)\n",
+ " normedChart |> Chart.withAxisTitlesWR \"\" (intMeasureStr + \" normed\") (1.,36.)\n",
+ " meanChart |> Chart.withAxisTitlesWR \"\" \"means\" (1.,36.)\n",
+ " ]\n",
+ " |> Chart.Grid(3,1,Pattern=StyleParam.LayoutGridPattern.Coupled)\n",
+ " //Chart.Grid(t,true,rowOrder=LayoutGridRowOrder.BottomToTop)\n",
+ " |> Chart.withTitle (Title.init (cre + \" \" + synonym))\n",
+ " |> Chart.withSize (1100.,800.)\n",
+ " |> fun t -> \n",
+ " if not save then \n",
+ " t\n",
+ " //|> Chart.ShowWithDescription {Heading=\"\";Text= $\"dwt_distance: %.2f{dTW}<br>euclidean: %.2f{euc}<br>meanInt: %.2f{max (Seq.mean wt) (Seq.mean mu)}<br>myDist: %.2f{dfi}<br><br>MapMan: {annotation}<br><br>H0_distances: {h0Distances}<br><br>TTest LFQSums: %.4f{ttestPval}<br><br>TestSingleContrasts:<br>{contrastResultStrings}\"}\n",
+ " |> Chart.withDescription({Heading=\"\";Text= $\"Trivial name: {synonym}<br><br>Euclidean distance: %.2f{euc}<br>Mean Intensity (WT): %.2f{Seq.mean wt}<br>Mean Intensity (Mut): %.2f{Seq.mean mu}<br>Distance: %.2f{dfi}<br><br>MapMan: {annotation}<br><br>p value of intensity sums Welch test: %.4f{ttestPval}\"})\n",
+ " |> Chart.show \n",
+ " else \n",
+ " let path = (@\"C:\\Users\\bvenn\\source\\repos\\LPA2_ComplexomeProfiling_Chlamy\\runs\\plots\\\" + sprintf \"%s_%s\" synonym cre + \".html\" ) \n",
+ " \n",
+ " t \n",
+ " |> Chart.withDescription(\n",
+ " {Heading=\"\";Text= $\"Trivial name: {synonym}<br><br>Euclidean distance: %.2f{euc}<br>Mean Intensity (WT): %.2f{Seq.mean wt}<br>Mean Intensity (Mut): %.2f{Seq.mean mu}<br>Distance: %.2f{dfi}<br><br>MapMan: {annotation}<br><br>p value of intensity sums Welch test: %.4f{ttestPval}\"}\n",
+ " )\n",
+ " |> Chart.saveHtml path\n",
+ " //{Heading=\"\";Text= $\"dwt_distance: %.2f{dTW}<br>euclidean: %.2f{euc}<br>meanInt: %.2f{max (Seq.mean wt) (Seq.mean mu)}<br>myDist: %.2f{dfi}<br><br>H0_distances: {h0Distances}<br><br>TTest LFQSums: %.4f{ttestPval}<br><br>TestSingleContrasts:<br>{contrastResultStrings}\"}\n",
+ " //{Heading=\"\";Text= $\"dwt_distance: %.2f{dTW}<br>euclidean: %.2f{euc}<br>meanInt: %.2f{max (Seq.mean wt) (Seq.mean mu)}<br>myDist: %.2f{dfi}<br><br>MapMan: {annotation}<br><br>H0_distances: {h0Distances}<br><br>TestSingleContrasts:<br>{contrastResultStrings}\"}\n",
+ "\n",
+ "\n",
+ " //printfn \"diff_adj %f\" (getDTWeuc wt mu)\n",
+ " //printfn \"euc %f\" (ML.DistanceMetrics.euclidean wt mu)\n",
+ " //printfn \"dtw %f\" (DTW.distanceDefault wt mu)\n",
+ " \n",
+ "\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "dotnet_interactive": {
+ "language": "fsharp"
+ },
+ "vscode": {
+ "languageId": "dotnet-interactive.fsharp"
+ }
+ },
+ "outputs": [],
+ "source": [
+ "\n",
+ "plotSignals true false \"Cre12.g493250\" IntMeasurement.Intensity"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "iterate over total dataset and save plots as html"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "dotnet_interactive": {
+ "language": "fsharp"
+ },
+ "vscode": {
+ "languageId": "dotnet-interactive.fsharp"
+ }
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "1301\r\n",
+ "1302\r\n",
+ "1303\r\n",
+ "1304\r\n",
+ "1305\r\n",
+ "1306\r\n",
+ "1307\r\n",
+ "1308\r\n",
+ "1309\r\n",
+ "1310\r\n",
+ "1311\r\n",
+ "1312\r\n",
+ "1313\r\n",
+ "1314\r\n",
+ "1315\r\n",
+ "1316\r\n",
+ "1317\r\n",
+ "1318\r\n",
+ "1319\r\n",
+ "1320\r\n",
+ "1321\r\n",
+ "1322\r\n",
+ "1323\r\n",
+ "1324\r\n",
+ "1325\r\n",
+ "1326\r\n",
+ "1327\r\n",
+ "1328\r\n",
+ "1329\r\n",
+ "1330\r\n",
+ "1331\r\n",
+ "1332\r\n",
+ "1333\r\n",
+ "1334\r\n",
+ "1335\r\n",
+ "1336\r\n",
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+ },
+ {
+ "data": {
+ "text/html": [
+ "<table><thead><tr><th><i>index</i></th><th>value</th></tr></thead><tbody><tr><td>0</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>1</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>2</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>3</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>4</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>5</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>6</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>7</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>8</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>9</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>10</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>11</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>12</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>13</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>14</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>15</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>16</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>17</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>18</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td>19</td><td><div class=\"dni-plaintext\"><null></div></td></tr><tr><td colspan=\"2\"><i>(1762 more)</i></td></tr></tbody></table>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "\n",
+ "datasets\n",
+ "|> Array.map (fun x -> \n",
+ " x \n",
+ " |> Array.map (fun protein -> \n",
+ " protein.ID\n",
+ " )\n",
+ " )\n",
+ "|> Array.concat\n",
+ "|> Array.distinct\n",
+ "|> Array.filter (fun x -> not (x.Contains \";\") && not (x.StartsWith \"i\"))\n",
+ "|> Array.mapi (fun i x ->\n",
+ " //if i > 1300 then printfn \"%i\" i\n",
+ " plotSignals true false ((x.Split '.').[0..1] |> String.concat \".\") IntMeasurement.Intensity\n",
+ " )"
+ ]
}
],
"metadata": {