Systematic identification of conserved motif modules in the human genome

BMC Genomics

Table 1 Functional evidence used.

Source	Number of gene sets	Number of significant motif modules
		FDR = 0.05	FDR = 0.01
BioCarta	155	0	0
KEGG	168	122,279	10,378
Genmapp	88	5486	14
GO	1141	1,296,621	460,973
PicTar	162	2,645,699	1,647,433
Cancer Module	380	485,850	67,135
Total	2094	2,871,863	1,855,459

The first column lists the different sources of functional evidence. The second column is the number of all gene sets. The third and fourth columns are the number of motif modules whose target genes significantly overlap with the gene sets. All of them except KEGG pathways are downloaded from MSigDB. For KEGG pathways, we directly downloaded from the KEGG ftp site. Only the gene sets with at least ten genes are used.

ISSN: 1471-2164