Co-Expression Analysis of: CYPedia Home Institut de Biologie Moléculaire des Plantes (Home)




CYP94D2 (At3g56630) save all data as Tab Delimited Table










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Pathways co-expressed in all 4 data sets (with more than 6 annotation points each)
Find below a list of pathways that are co-expressed with the bait. First a list of pathways is given that are co-expressed in all data sets. Lists for each individual dataset are shown underneath. Depending on the number of co-expressed pathways only the top scoring pathways are given; all data can be saved as text using the link above.







Pathway Source Sum of scores Sum of genes







carotenoid biosynthesis AraCyc 100 11




































To the right of each table a thumbnail of the actual co-expression heatmap is given. Klick on the link to see the heatmap containing all co-expressed genes.









































For more information on how these pathway maps were generated please read the methods page
























































Pathways co-expressed in the Organ and Tissue data set (with more than 6 annotation points)
CYP94D2 (At3g56630)







max. difference between log2-ratios: 4.7











max. difference between log2-ratios excluding lowest and highest 5%: 3.5











Pathway Source Scores of Genes p[Score] No. of Genes p[genes] Link to organ heatmap






Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone) BioPath 60 0.000 8 0.000


Carotenoid and abscisic acid metabolism LitPath 39 0.000 6 0.000

Carotenoid biosynthesis BioPath 28 0.000 3 0.000

carotenoid biosynthesis AraCyc 28 0.000 3 0.000

carotenid biosynthesis LitPath 28 0.000 3 0.000

Biosynthesis of prenyl diphosphates BioPath 20 0.000 3 0.004

Folding, Sorting and Degradation KEGG 19 0.000 2 0.065

Glutathione metabolism KEGG 19 0.000 2 0.006

biogenesis of chloroplast FunCat 18 0.000 3 0.004

C-compound and carbohydrate metabolism FunCat 18 0.037 5 0.062

degradation FunCat 17 0.000 3 0.000

protein degradation FunCat 17 0.000 3 0.000

Aromatic amino acid (Phe, Tyr, Trp) metabolism BioPath 16 0.000 2 0.046

Phenylalanine, tyrosine and tryptophan biosynthesis KEGG 16 0.000 2 0.006










Shikimate pathway LitPath 16 0.017 2 0.193










Biosynthesis of steroids KEGG 14 0.000 2 0.007










amino acid metabolism FunCat 12 0.014 2 0.100










Chlorophyll biosynthesis and breakdown BioPath 10 0.004 1 0.084










Delta-pH pathway BioPath 10 0.000 1 0.001










Pathway for nuclear-encoded, thylakoid-localized proteins BioPath 10 0.000 1 0.015










aromatic amino acid family biosynthesis TAIR-GO 10 0.000 1 0.015










aromatic amino acid family biosynthesis, shikimate pathway TAIR-GO 10 0.000 1 0.011










carotene metabolism TAIR-GO 10 0.000 1 0.000










chlorophyll catabolism TAIR-GO 10 0.000 1 0.001










hypersensitive response TAIR-GO 10 0.000 1 0.003










lipoic acid metabolism TAIR-GO 10 0.000 1 0.000










photosystem I TAIR-GO 10 0.000 1 0.004










photosystem II TAIR-GO 10 0.000 1 0.002










photosystem II (sensu Viridiplantae) TAIR-GO 10 0.000 1 0.001










thylakoid membrane organization and biogenesis TAIR-GO 10 0.000 1 0.000










xanthophyll cycle TAIR-GO 10 0.000 1 0.000










xanthophyll metabolism TAIR-GO 10 0.000 1 0.000










phenylalanine degradation I AraCyc 10 0.000 2 0.011










photorespiration AraCyc 10 0.000 4 0.000










TCA cycle -- aerobic respiration AraCyc 10 0.000 2 0.048










TCA cycle variation IV AraCyc 10 0.000 2 0.043










TCA cycle variation VII AraCyc 10 0.014 2 0.123










TCA cycle variation VIII AraCyc 10 0.001 2 0.054










xanthophyll cycle AraCyc 10 0.000 1 0.000










Carbon fixation KEGG 10 0.000 2 0.018










Protein export KEGG 10 0.000 1 0.026










metabolism of acyl-lipids in mitochondria AcylLipid 10 0.000 1 0.006










abscisic acid biosynthesis LitPath 10 0.000 2 0.002










chlorophyll catabolism LitPath 10 0.000 1 0.004










chorismate biosynthesis LitPath 10 0.001 1 0.097










IPP (isopentenyl diphosphate) and DMAPP (dimethylallyl diphosphat) biosynthesis LitPath 10 0.025 2 0.037










MEP (methylerythritol P) pathway, plastids LitPath 10 0.000 2 0.004










polyprenyl diphosphate biosynthesis LitPath 10 0.000 1 0.034










Protein folding and associated processing KEGG 9 0.000 1 0.021










Chloroplastic protein turnover BioPath 8 0.000 2 0.001










ClpP protease complex BioPath 8 0.000 2 0.000












































Pathways co-expressed in the Stress data set ( with more than 6 annotation points)
CYP94D2 (At3g56630)







max. difference between log2-ratios: 3.7











max. difference between log2-ratios excluding lowest and highest 5%: 1.5











Pathway Source Scores of Genes p[Score] No. of Genes p[genes] Link to stress heatmap






transport FunCat 19 0.000 2 0.000
Transcription (chloroplast) BioPath 18 0.000 2 0.000
transcription initiation TAIR-GO 18 0.000 2 0.000
Folding, Sorting and Degradation KEGG 17 0.000 3 0.000
Chloroplastic protein import via envelope membrane BioPath 13 0.000 2 0.000
Chloroplastic protein turnover BioPath 10 0.000 1 0.002
FtsH protease (many homologues / subcellular localization ambiguous) BioPath 10 0.000 1 0.000
Thylakoid biogenesis and photosystem assembly BioPath 10 0.000 1 0.001










cytochrome b6f complex TAIR-GO 10 0.000 1 0.000










cytochrome b6f complex assembly TAIR-GO 10 0.000 1 0.000










photosynthesis TAIR-GO 10 0.000 1 0.005










photosynthesis, dark reaction TAIR-GO 10 0.000 1 0.000










electron transport and membrane-associated energy conservation FunCat 10 0.000 1 0.001










energy FunCat 10 0.000 1 0.000










mRNA synthesis FunCat 10 0.000 1 0.008










RNA synthesis FunCat 10 0.000 1 0.008










transcription FunCat 10 0.000 1 0.002










transcriptional control FunCat 10 0.000 1 0.002










RNA polymerase KEGG 10 0.000 1 0.005










Transcription KEGG 10 0.000 1 0.019










Toc apparatus BioPath 9 0.000 1 0.002










protein-chloroplast targeting TAIR-GO 9 0.000 1 0.000










chloroplast transport FunCat 9 0.000 1 0.001










degradation FunCat 9 0.000 1 0.007










protein degradation FunCat 9 0.000 1 0.004










protein targeting, sorting and translocation FunCat 9 0.000 1 0.001










transport routes FunCat 9 0.000 1 0.004










Protein folding and associated processing KEGG 9 0.000 1 0.002










additional photosystem II components BioPath 8 0.000 1 0.022










Early light-inducible proteins BioPath 8 0.000 1 0.001










Protein export KEGG 8 0.000 2 0.000












































Pathways co-expressed in the Hormone etc. data set (with more than 6 annotation points)
CYP94D2 (At3g56630)







max. difference between log2-ratios: 2.8











max. difference between log2-ratios excluding lowest and highest 5%: 0.9











Pathway Source Scores of Genes p[Score] No. of Genes p[genes] Link to hormones etc. heatmap






proteasome regulatory particle, base subcomplex (sensu Eukaryota) TAIR-GO 14 0.000 2 0.000





protein catabolism TAIR-GO 14 0.000 2 0.000




ubiquitin-dependent protein catabolism TAIR-GO 14 0.000 2 0.000




Folding, Sorting and Degradation KEGG 14 0.000 2 0.001










Proteasome KEGG 14 0.000 2 0.000










Carotenoid biosynthesis BioPath 10 0.000 1 0.000










Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone) BioPath 10 0.000 1 0.018










carotene metabolism TAIR-GO 10 0.000 1 0.000










carotenoid biosynthesis AraCyc 10 0.000 1 0.000










biosynthesis of derivatives of homoisopentenyl pyrophosphate FunCat 10 0.000 1 0.000










carotenid biosynthesis LitPath 10 0.000 1 0.001










Carotenoid and abscisic acid metabolism LitPath 10 0.000 1 0.005










additional photosystem II components BioPath 8 0.000 1 0.004










Early light-inducible proteins BioPath 8 0.000 1 0.000










Photosystems BioPath 8 0.000 1 0.029





























































Pathways co-expressed in the Mutant data set (with more than 30 annotation points)
CYP94D2 (At3g56630)







max. difference between log2-ratios: 8.2











max. difference between log2-ratios excluding lowest and highest 5%: 1.4











Pathway Source Scores of Genes p[Score] No. of Genes p[genes] Link to mutants heatmap






C-compound and carbohydrate metabolism FunCat 176 0.000 33 0.052



Biosynthesis of Amino Acids and Derivatives BioPath 146 0.007 19 0.307


Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone) BioPath 143 0.000 18 0.001


transport FunCat 111 0.000 20 0.000


Pyruvate metabolism KEGG 94 0.000 14 0.031


Oxidative phosphorylation KEGG 85 0.000 21 0.000


transport facilitation FunCat 69 0.000 12 0.000


development TAIR-GO 59 0.000 7 0.082


Sulfur metabolism KEGG 59 0.000 8 0.001


Selenoamino acid metabolism KEGG 58 0.000 7 0.028


Methionin/SAM/ethylene metabolism from cysteine and aspartate BioPath 56 0.000 6 0.034


biogenesis of chloroplast FunCat 56 0.006 11 0.014


Carotenoid and abscisic acid metabolism LitPath 55 0.000 8 0.000


Valine, leucine and isoleucine degradation KEGG 53 0.000 8 0.025










Cysteine metabolism KEGG 51 0.000 7 0.015










Glycine, serine and threonine metabolism KEGG 47 0.000 8 0.030










leucine degradation I AraCyc 46 0.000 6 0.008










leucine degradation II AraCyc 46 0.000 6 0.000










Citrate cycle (TCA cycle) KEGG 46 0.004 7 0.134










Carotenoid biosynthesis BioPath 44 0.000 5 0.000










carotenoid biosynthesis AraCyc 44 0.000 5 0.000










sulfate assimilation III AraCyc 44 0.000 6 0.043










carotenid biosynthesis LitPath 44 0.000 5 0.000










Ascorbate and aldarate metabolism KEGG 43 0.000 6 0.030










metabolism of acyl-lipids in mitochondria AcylLipid 43 0.000 5 0.017










TCA cycle -- aerobic respiration AraCyc 42 0.000 8 0.042










TCA cycle variation VIII AraCyc 42 0.001 8 0.053










chlorophyll biosynthesis TAIR-GO 40 0.000 4 0.026










photorespiration AraCyc 40 0.000 7 0.017










Methionine metabolism KEGG 40 0.000 4 0.096










chlorophyll and phytochromobilin metabolism LitPath 40 0.030 4 0.306










Synthesis of membrane lipids in endomembrane system AcylLipid 39 0.007 6 0.147










ATP-dependent proteolysis TAIR-GO 38 0.000 8 0.000










Synthesis of fatty acids in plastids AcylLipid 38 0.001 6 0.056










sterol biosynthesis BioPath 36 0.007 4 0.135










transported compounds (substrates) FunCat 35 0.000 5 0.000










Protein folding and associated processing KEGG 35 0.000 6 0.037










Chloroplastic protein turnover BioPath 34 0.000 7 0.000










Protein folding / chaperonins (chloroplast) BioPath 34 0.000 5 0.002










leucine biosynthesis AraCyc 34 0.000 6 0.001










serine-isocitrate lyase pathway AraCyc 34 0.022 6 0.163










Propanoate metabolism KEGG 34 0.005 5 0.166










Bile acid biosynthesis KEGG 33 0.000 5 0.010










Tryptophan metabolism KEGG 33 0.004 6 0.126










ascorbic acid biosynthesis BioPath 32 0.000 4 0.064










growth TAIR-GO 32 0.024 4 0.188










electron transport TAIR-GO 31 0.001 5 0.035










threonine degradation AraCyc 31 0.000 9 0.000










stress response FunCat 31 0.000 4 0.000












































page created by Vincent Sauveplane 04/13/06