Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors.

ABSTRACT:

Background

Evolutionary conservation has been used successfully to help identify cis-acting DNA regions that are important in regulating tissue-specific gene expression. Motivated by increasing evidence that some DNA regulatory regions are not evolutionary conserved, we have developed an approach for cis-regulatory region identification that does not rely upon evolutionary sequence conservation.

Results

The conservation-independent approach is based on an empirical potential energy between interacting transcription factors (TFs). In this analysis, the potential energy is defined as a function of the number of TF interactions in a genomic region and the strength of the interactions. By identifying sets of interacting TFs, the analysis locates regions enriched with the binding

SUBMITTER: Yu X 

PROVIDER: S-EPMC2194798 | biostudies-literature | 2007 Nov

REPOSITORIES: biostudies-literature