Table 4

Significantly overrepresented transcription factors identified by ENCODE ChIP-Seq peaks based on the GENCODE Database

Transcription Factor

cell line

tissue of origin

peaks near TSS of the gene of the extended network

peaks near TSS of all the

GENCODE genes

p-value


E2F1

HeLa-S3

cervical

187

1445

4.81E-013

TCF4

HCT-116

colorectal

244

2059

1.46E-012

Pol2

HeLa-S3

cervical

312

2878

3.93E-011

c-Myc

HeLa-S3

cervical

123

880

5.52E-011

Max

HeLa-S3

cervical

161

1266

9.77E-011

E2F6

k562

Leukemia

265

2379

1.17E-010

NFKB

GM12878

Lymphoblastoid

111

794

5.02E-010


The peaks were mapped to regions corresponding to the promoter sequences as considered for this study (-700, 300 bp), based upon transcription start sites (TSS) annotated by GENCODE. Peaks near TSS of the genes of the extended network and all GENCODE genes refers to the amount of peaks found in the promoter region. P-values were calculated by a hypergeometric test. Sample size was considered as the amount of genes that corresponded to the proteins of the extended network. Population size was the number of annotated GENCODE entries that had a complete status and were separated by a distance of up to 500 base pairs.

Higareda-Almaraz et al. BMC Systems Biology 2011 5:96   doi:10.1186/1752-0509-5-96

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