Arabidopsis gene co-expression network and its functional modules

BMC Bioinformatics

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

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. The number of genes which were annotated as pathways genes in a module.
2. Only the most over-represented pathway term was listed for each module.
3. The column lists the over-represented GO term that matches or relates to the pathway term for each module.
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.

ISSN: 1471-2105