Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression.

ABSTRACT:

Background

Gene expression is regulated mainly by transcription factors (TFs) that interact with regulatory cis-elements on DNA sequences. To identify functional regulatory elements, computer searching can predict TF binding sites (TFBS) using position weight matrices (PWMs) that represent positional base frequencies of collected experimentally determined TFBS. A disadvantage of this approach is the large output of results for genomic DNA. One strategy to identify genuine TFBS is to utilize local concentrations of predicted TFBS. It is unclear whether there is a general tendency for TFBS to cluster at promoter regions, although this is the case for certain TFBS. Also unclear is the identification of TFs that have TFBS concentrated in promoters and to what level this occurs. This st

SUBMITTER: Murakami K 

PROVIDER: S-EPMC375527 | biostudies-literature | 2004 Feb

REPOSITORIES: biostudies-literature