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Table 3 Significantly enriched pathway terms in AGCN modules (I = 1.8).

From: Arabidopsis gene co-expression network and its functional modules

module # pathway genes1 Pathway term2 GO term3 genes in pathway term4 p value
1 192 photosynthesis, light reaction Photosynthesis 27/27 4.69E-15
3 22 de novo biosynthesis of purine nucleotides purine nucleoside monophosphate biosynthesis 7/10 2.84E-09
4 5 de novo biosynthesis of pyrimidine deoxyribonucleotides DNA metabolism 3/6 5.02E-06
11 11 homogalacturonan degradation cell wall modification 10/34 6.47E-13
45 6 acetyl-CoA biosynthesis (from citrate) acetyl-CoA biosynthesis 2/2 7.82E-05
67 6 starch degradation starch metabolism 5/11 3.66E-09
79 8 glucosinolate biosynthesis from tryptophan indoleacetic acid metabolism 5/5 7.45E-11
80 6 flavonoid biosynthesis phenylpropanoid metabolism 4/6 3.67E-08
140 3 tryptophan biosynthesis nitrogen compound metabolism 3/5 2.53E-07
273 3 salicylic acid biosynthesis aromatic compound biosynthesis 2/3 4.69E-05
  1. 1. The number of genes which were annotated as pathways genes in a module.
  2. 2. Only the most over-represented pathway term was listed for each module.
  3. 3. The column lists the over-represented GO term that matches or relates to the pathway term for each module.
  4. 4. The two values listed in this column refer to the number of genes annotated to the over-represented pathway in the module and the number of genes annotated to the same pathway in the network.