Identification of Potential E2F Target Genes Through cis-regulatory Modules Derived From Chromatin Immunoprecipitation Microarray Data

In the postgenome era, employment of high-throughput data via the integrated use of resources from various domains will lead to the generation of new knowledge and testable hypothesis. In this bioinformatic research, we utilized published chromatin immunoprecipitation microarray (ChIP-chip) results for the promoter binding by E2F1 or E2F4 proteins observed in the primary human WI-38 cells to infer the potential transcription factor binding sites (TFBS). We have compiled “gene vs. motif” and “motif vs. gene” tables from more than 2,700,000 computational predicted transcriptional regulatory motifs representing the regulatory potential for 230 transcription factors families within the proximal promoter sequence (1,200 nucleotides) of human genome. From this approach, for the first time, the transcription of 23 genes is predicted to be under the control of a cis-regulatory module containing four TFBS motifs (CREB, E2F, NF-Y and Nrf-1).