. 2011 Dec 9;6(12):e28358. doi: 10.1371/journal.pone.0028358

Table 2. Enrichment of functionally related genes in groups of co-expressed genes.

Cluster	Gene Count	Total # Genes	GO Category	Ontology	Description of GO Category	p-value	Enrichment
cluster 1 (44 genes)	4	47	GO:0048704	BP	embryonic skeletal system morphogenesis	0.0002	36.83
	19	682	GO:0003700	MF	sequence-specific DNA binding transcription factor activity	0.0000	12.06
	3	114	GO:0045892	BP	negative regulation of transcription, DNA-dependent	0.0259	11.39
	8	406	GO:0045944	BP	positive regulation of transcription from RNA polymerase II promoter	0.0001	8.53
	4	211	GO:0016564	MF	transcription repressor activity	0.0187	8.20
	18	1499	GO:0003677	MF	DNA binding	0.0000	5.20
cluster 2 (51 genes)	2	6	GO:0070700	MF	BMP receptor binding	0.0056	124.44
	2	6	GO:0060272	BP	embryonic skeletal joint morphogenesis	0.0056	124.44
	4	33	*GO:0001649*	BP	*osteoblast differentiation*	*0.0008*	*45.25*
	3	28	*GO:0030855*	BP	*epithelial cell differentiation*	*0.0033*	*40.00*
	4	42	GO:0030509	BP	BMP signaling pathway	0.0014	35.56
	4	55	GO:0030326	BP	embryonic limb morphogenesis	0.0022	27.15
	5	144	GO:0007507	BP	heart development	0.0029	12.96
	7	211	GO:0016564	MF	transcription repressor activity	0.0008	12.39
	6	406	GO:0045944	BP	positive regulation of transcription from RNA polymerase II promoter	0.0124	5.52
cluster 5 (186 genes)	4	33	GO:0048706	BP	embryonic skeletal system development	0.0425	12.54
	5	47	*GO:0048704*	BP	*embryonic skeletal system morphogenesis*	*0.0194*	*11.01*
	6	99	GO:0004888	MF	transmembrane receptor activity	0.0471	6.27
	6	*101*	*GO:0009952*	BP	*anterior/posterior pattern formation*	*0.0473*	*6.15*
	18	488	GO:0043565	MF	sequence-specific DNA binding	0.0008	3.82
	10	274	GO:0045941	BP	positive regulation of transcription	0.0425	3.78
cluster 6 (475 genes)	4	8	*GO:0048699*	BP	*generation of neurons*	*0.0186*	*20.52*
	5	22	*GO:0035108*	BP	*limb morphogenesis*	*0.0405*	*9.33*
	7	38	*GO:0042733*	BP	*embryonic digit morphogenesis*	*0.0150*	*7.56*
	7	45	GO:0060021	BP	palate development	0.0279	6.38
	11	103	GO:0003735	MF	structural constituent of ribosome	0.0150	4.38
	10	100	GO:0006414	BP	translational elongation	0.0351	4.10
	20	242	GO:0006397	BP	mRNA processing	0.0037	3.39
	17	236	GO:0008380	BP	RNA splicing	0.0186	2.96
cluster 7 (73 genes)	3	18	*GO:0001837*	BP	*epithelial to mesenchymal transition*	*0.0288*	*45.33*
cluster 11 (405 genes)	4	6	GO:0042273	BP	ribosomal large subunit biogenesis	0.0057	31.58
	29	100	GO:0006414	BP	translational elongation	0.0000	13.74
	21	103	GO:0003735	MF	structural constituent of ribosome	0.0000	9.66
	19	214	GO:0006412	BP	translation	0.0001	4.21
cluster 12 (491 genes)	5	17	GO:0070491	MF	repressing transcription factor binding	0.0373	11.43
	8	56	GO:0016566	MF	specific transcriptional repressor activity	0.0373	5.55
	21	261	GO:0000122	BP	negative regulation of transcription from RNA polymerase II promoter	0.0058	3.13
	16	209	GO:0016481	BP	negative regulation of transcription	0.0373	2.97
	16	211	GO:0016564	MF	transcription repressor activity	0.0373	2.95
	18	262	GO:0051301	BP	cell division	0.0437	2.67
	29	468	GO:0015031	BP	protein transport	0.0112	2.41
cluster 14 (151 genes)	5	49	*GO:0051216*	BP	*cartilage development*	*0.0224*	*12.95*

8/15 clusters were identified to contain cohorts of functional related genes (p<0.05; >2-fold enrichment) primarily represented by transcription factors (clustes 1/2/5/12) and genes associated with limb/skeletal morphogenesis (clusters 1/2/5/6). ‘Gene count’ represents the number of genes in the cluster with the specified biological process or molecular function, while ‘total # genes’ represents the total number of genes present on the microarray within the same category. Enrichment is fold over background. Genes corresponding to GO enriched categories highlighted in brown are plotted in Figure 5. BP biological process; MF molecular function.