Proteomic patterns of cervical cancer cell lines, a network perspective

BMC Systems Biology

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.

ISSN: 1752-0509