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Table 4 Significantly overrepresented transcription factors identified by ENCODE ChIP-Seq peaks based on the GENCODE Database

From: Proteomic patterns of cervical cancer cell lines, a network perspective

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
  1. 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.