Proteomic patterns of cervical cancer cell lines, a network perspective

BMC Systems Biology

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.

ISSN: 1752-0509