A general co-expression network-based approach to gene expression analysis: comparison and applications

BMC Systems Biology

Table 2 Functional modules in a yeast co-expression network

Cluster	Size	Category¹	Term	Count	Enrichment²	P-value
1	361	BP	protein catabolism	32	4.2	2.0E-12
		BP	protein folding	21	5.9	1.6E-11
2	498	BP	ribosome biogenesis	133	9.2	2.0E-106
3	18	BP	chromatin assembly or disassembly	9	36.4	5.3E-13
		TF	HIR2	6	129.8	2.3E-12
		TF	HIR1	6	62.9	3.0E-10
		TF	HIR3	6	57.7	5.3E-10
4	25	BP	telomerase-independent telomere maintenance	4	82.3	1.1E-07
		BP	biological process unknown	16	2.9	7.6E-06
		TF	GAT3	13	56.8	3.5E-21
		TF	YAP5	15	43.5	5.8E-17
		TF	PDR1	9	25.8	3.1E-11
		TF	MSN4	8	35.0	3.8E-11
5	422	BP	spore wall assembly	16	7.0	1.6E-10
		BP	biological process unknown	138	1.5	1.2E-07
		TF	NRG1	21	4.2	1.4E-08
		TF	SUM1	16	3.9	2.3E-06
		TF	PHD1	15	3.4	3.2E-05
6	99	-	-	-	-	-
7	463	BP	carbohydrate metabolism	41	2.9	4.6E-10
		BP	biological process unknown	178	1.7	9.5E-17
		BP	response to stimulus	62	1.7	2.0E-05
		TF	UME6	25	2.5	2.6E-05
		TF	NRG1	15	2.8	3.6E-04
8	108	BP	nitrogen compound metabolism	25	7.0	5.2E-15
		TF	MET31	4	9.6	8.0E-04
		TF	MET32	5	5.7	2.1E-03
9	192	BP	generation of precursor metabolites and energy	50	8.2	7.5E-33
		TF	HAP4	22	9.2	5.1E-16
10	22	BP	Ty element transposition	17	58.6	6.2E-29
		TF	SUM1	4	18.9	5.8E-05
11	604	BP	carboxylic acid metabolism	76	3.0	2.4E-19
		BP	cell organization and biogenesis	212	1.6	3.7E-15
		TF	SWI6	45	2.9	3.6E-11
		TF	SWI4	44	2.8	2.7E-10
		TF	FKH2	35	3.0	4.7E-09
		TF	MBP1	36	2.8	1.9E-08
		TF	STE12	22	3.6	7.9E-08
		TF	NDD1	30	2.9	1.1E-07
		TF	FKH1	34	2.5	9.6E-07
		TF	MCM1	22	2.9	3.9E-06
12	186	BP	protein biosynthesis	131	6.4	6.4E-85
		TF	FHL1	96	17.1	3.3E-105
		TF	RAP1	58	11.5	2.2E-48

¹ For each cluster, significantly enriched biological process GO terms (BP) or binding of transcription factors (TF) are counted.
²Fold of enrichment is calculated as: .

ISSN: 1752-0509