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




CYP96A12 (At4g39510) 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







C-compound and carbohydrate metabolism FunCat 208 32







chlorophyll biosynthesis TAIR-GO 189 23







chlorophyll biosynthesis AraCyc 188 24







chlorophyll biosynthesis LitPath 183 22
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.








photosynthesis FunCat 114 16




























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 12 annotation points)
CYP96A12 (At4g39510)







max. difference between log2-ratios: 5.0











max. difference between log2-ratios excluding lowest and highest 5%: 4.1











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






Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone) BioPath 45 0.000 7 0.002










Miscellaneous acyl lipid metabolism AcylLipid 44 0.000 11 0.000


C-compound and carbohydrate metabolism FunCat 42 0.001 6 0.080

Photosystems BioPath 38 0.000 5 0.081

Gluconeogenesis from lipids in seeds BioPath 32 0.000 4 0.043

additional photosystem II components BioPath 26 0.000 3 0.024

Chlorophyll biosynthesis and breakdown BioPath 23 0.000 4 0.002

Flavonoid and anthocyanin metabolism BioPath 23 0.000 4 0.019

flavonoid biosynthesis AraCyc 22 0.000 3 0.001

Pentose phosphate pathway KEGG 22 0.000 3 0.001

Flavonoid biosynthesis KEGG 21 0.000 3 0.000

flavonoid biosynthesis TAIR-GO 20 0.000 2 0.001

pentose-phosphate shunt TAIR-GO 20 0.000 2 0.003

fatty acid oxidation pathway AraCyc 20 0.000 2 0.003

octane oxidation AraCyc 20 0.000 2 0.000










biosynthesis of phenylpropanoids FunCat 20 0.000 2 0.012










biosynthesis of secondary products derived from L-phenylalanine and L-tyrosine FunCat 20 0.000 2 0.012










energy FunCat 20 0.000 2 0.000










metabolism of energy reserves (e.g. glycogen, trehalose) FunCat 20 0.000 2 0.000










pentose-phosphate pathway FunCat 20 0.000 2 0.003










flavonoid, anthocyanin, and proanthocyanidin biosynthesis LitPath 20 0.000 2 0.002










proanthocyanidin biosynthesis LitPath 20 0.000 2 0.002










secondary metabolism FunCat 19 0.000 2 0.054










glycolysis and gluconeogenesis FunCat 18 0.048 3 0.086










Photosynthesis KEGG 18 0.000 2 0.004










chloroplast thylakoid membrane protein import TAIR-GO 17 0.000 2 0.000










Porphyrin and chlorophyll metabolism KEGG 17 0.000 3 0.000










chlorophyll and phytochromobilin metabolism LitPath 17 0.000 3 0.007










Chlorophyll a/b binding proteins BioPath 16 0.000 2 0.016










photosystem II type II chlorophyll a /b binding protein BioPath 16 0.000 2 0.000










fatty acid biosynthesis TAIR-GO 16 0.000 2 0.006










photosynthesis FunCat 16 0.000 2 0.025










chlorophyll biosynthesis TAIR-GO 15 0.000 2 0.005










acetate fermentation AraCyc 14 0.000 3 0.023










chlorophyll biosynthesis AraCyc 14 0.000 3 0.009












































Pathways co-expressed in the Stress data set ( with more than 18 annotation points)
CYP96A12 (At4g39510)







max. difference between log2-ratios: 3.8











max. difference between log2-ratios excluding lowest and highest 5%: 2.0











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






Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone) BioPath 77 0.000 10 0.000










C-compound and carbohydrate metabolism FunCat 76 0.000 13 0.003










Intermediary Carbon Metabolism BioPath 46 0.000 6 0.209
Biosynthesis of steroids KEGG 34 0.000 4 0.001
Carotenoid and abscisic acid metabolism LitPath 32 0.000 4 0.001
Photosystems BioPath 30 0.017 5 0.107
Glycolysis / Gluconeogenesis KEGG 30 0.000 4 0.008
chlorophyll biosynthesis TAIR-GO 29 0.000 3 0.000
chlorophyll biosynthesis LitPath 29 0.000 3 0.000
Carotenoid biosynthesis BioPath 28 0.000 3 0.000
carotenoid biosynthesis AraCyc 28 0.000 3 0.000
glycolysis and gluconeogenesis FunCat 28 0.000 5 0.057
photosynthesis FunCat 28 0.000 4 0.003
carotenid biosynthesis LitPath 28 0.000 3 0.001
regulation of transcription TAIR-GO 27 0.000 3 0.000
energy FunCat 26 0.000 3 0.000










metabolism of energy reserves (e.g. glycogen, trehalose) FunCat 26 0.000 3 0.000










pentose-phosphate pathway FunCat 26 0.000 3 0.001










Pentose phosphate pathway KEGG 26 0.000 3 0.004










mRNA processing in chloroplast BioPath 24 0.000 5 0.000










Transcriptional regulators (chloroplast) BioPath 20 0.000 2 0.000










carotene biosynthesis TAIR-GO 20 0.000 2 0.000










pentose-phosphate shunt TAIR-GO 20 0.000 2 0.003










positive regulation of transcription TAIR-GO 20 0.000 2 0.000










secondary metabolism FunCat 20 0.000 3 0.053










Carbon fixation KEGG 20 0.000 3 0.021










Chlorophyll biosynthesis and breakdown BioPath 19 0.000 2 0.080










lipid, fatty acid and isoprenoid metabolism FunCat 19 0.000 2 0.072










chlorophyll and phytochromobilin metabolism LitPath 19 0.011 2 0.162












































Pathways co-expressed in the Hormone etc. data set (with more than 29 annotation points)
CYP96A12 (At4g39510)







max. difference between log2-ratios: 3.4











max. difference between log2-ratios excluding lowest and highest 5%: 1.7











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






Photosystems BioPath 109 0.000 18 0.000





C-compound and carbohydrate metabolism FunCat 82 0.000 12 0.066




Plastidial Isoprenoids (Chlorophylls, Carotenoids, Tocopherols, Plastoquinone, Phylloquinone) BioPath 71 0.000 10 0.005




Intermediary Carbon Metabolism BioPath 62 0.008 10 0.236




additional photosystem II components BioPath 56 0.000 8 0.000




Photosynthesis KEGG 53 0.000 11 0.000




Carbon fixation KEGG 52 0.000 7 0.001




photosynthesis FunCat 50 0.000 7 0.000




biogenesis of chloroplast FunCat 47 0.000 7 0.001




Leaf Glycerolipid Biosynthesis in Plastid BioPath 45 0.000 6 0.034




Chlorophyll biosynthesis and breakdown BioPath 43 0.000 6 0.002




chlorophyll biosynthesis AraCyc 42 0.000 7 0.001




glycosylglyceride desaturation pathway AraCyc 37 0.000 4 0.000




Nucleotide Metabolism KEGG 37 0.000 6 0.010










Porphyrin and chlorophyll metabolism KEGG 37 0.000 5 0.000










Synthesis of membrane lipids in plastids AcylLipid 37 0.000 4 0.000










chlorophyll and phytochromobilin metabolism LitPath 37 0.000 5 0.001










Photosystem I BioPath 35 0.001 6 0.034










chlorophyll biosynthesis TAIR-GO 35 0.000 4 0.000










tricarboxylic-acid pathway (citrate cycle, Krebs cycle, TCA cycle) FunCat 32 0.001 4 0.210










glycolysis and gluconeogenesis FunCat 31 0.009 5 0.160










Purine metabolism KEGG 31 0.000 5 0.011










phospholipid desaturation pathway AraCyc 30 0.000 3 0.000










1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradatio KEGG 30 0.000 3 0.000










1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation KEGG 30 0.000 3 0.000










Androgen and estrogen metabolism KEGG 30 0.000 3 0.000










Benzoate degradation via hydroxylation KEGG 30 0.000 3 0.000










Glycolysis / Gluconeogenesis KEGG 30 0.001 4 0.095





























































Pathways co-expressed in the Mutant data set (with more than 10 annotation points)
CYP96A12 (At4g39510)







max. difference between log2-ratios: 3.1











max. difference between log2-ratios excluding lowest and highest 5%: 1.8











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






Cell Wall Carbohydrate Metabolism BioPath 12 0.000 2 0.030



pectin metabolism BioPath 12 0.000 2 0.003


core phenylpropanoid metabolism BioPath 10 0.000 1 0.004


Phenylpropanoid Metabolism BioPath 10 0.000 1 0.053


biogenesis of cell wall FunCat 10 0.000 1 0.006










biosynthesis of phenylpropanoids FunCat 10 0.000 1 0.002










biosynthesis of secondary products derived from L-phenylalanine and L-tyrosine FunCat 10 0.000 1 0.002










Phenylpropanoid pathway LitPath 10 0.000 1 0.000










C-compound and carbohydrate metabolism FunCat 8 0.010 1 0.085










Ribosome KEGG 8 0.000 2 0.000



























page created by Alexandre OLRY 05/02/06