Genome-wide discovery of functional transcription factor binding sites by comparative genomics: the case of Stat3.

ABSTRACT: The identification of direct targets of transcription factors is a key problem in the study of gene regulatory networks. However, the use of high throughput experimental methods, such as ChIP-chip and ChIP-sequencing, is limited by their high cost and strong dependence on cellular type and context. We developed a computational method for the genome-wide identification of functional transcription factor binding sites based on positional weight matrices, comparative genomics, and gene expression profiling. The method was applied to Stat3, a transcription factor playing crucial roles in inflammation, immunity and oncogenesis, and able to induce distinct subsets of target genes in different cell types or conditions. A newly generated positional weight matrix enabled us to assign affinity score

SUBMITTER: Vallania F 

PROVIDER: S-EPMC2664024 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature