Computational Methods to Identify Transcription Factor Binding Sites Using CAGE Information

Abstract

This chapter presents a methodology for generating prioritized list of links of the type transcription factors (TF) →transcription factors binding sites (TFBS) → transcription start site (TSS)/promoter→gene, where TF is expected to bind to the TFBS on the gene's promoter determined by the utilized TSS and affect the transcription of the gene in the experiment. It shows how one can prioritize putative links between TFs and the genes they potentially control and use this to enhance predictions of TFBSs and to partly reconstruct transcriptional regulatory networks (TRN) of genes affected in the experiment. The methodology is rather general and results in a significant reduction of false positive associations between TFs and their target genes tch11f01-hrough more accurate association of TFBSs and the genes, thus resulting in much more accurate TRNs. The association of a TF and a gene can be done, for example, by considering the correlation between the expression of the TF and other genes.