Table 5

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

Transcription Factor

cell line

tissue of origin

peaks near TSS of the genes of the extended network

peaks near TSS reported on SwitchGear

p-value


Pol2

HeLa-S3

cervical

608

7766

2.15E-067

TCF4

HCT-116

colorectal

455

5543

1.93E-050

E2F6

k562

Leukemia

488

6343

1.12E-046

Max

HeLa-S3

cervical

313

3375

2.90E-042

c-Myc

HeLa-S3

cervical

250

2395

1.88E-041

NFKB

GM12878

Lymphoblastoid

195

1802

6.78E-034

E2F1-HA

HeLa-S3

cervical

315

4272

7.57E-024


ChIP-Seq peaks mapped to regions corresponding to the promoter sequences as considered for this study (-700, 300 bp), based upon transcription start sites (TSS) annotated by SwitchGear. Peaks near TSS of the genes of the extended network and reported on SwitchGear refers to the amount of peaks found in the corresponding promoter regions. 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 reported TSS reported on SwitchGear with a score greater than 20.

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

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