Expression-guided in silico evaluation of candidate cis regulatory codes for Drosophila muscle founder cells.

ABSTRACT: While combinatorial models of transcriptional regulation can be inferred for metazoan systems from a priori biological knowledge, validation requires extensive and time-consuming experimental work. Thus, there is a need for computational methods that can evaluate hypothesized cis regulatory codes before the difficult task of experimental verification is undertaken. We have developed a novel computational framework (termed "CodeFinder") that integrates transcription factor binding site and gene expression information to evaluate whether a hypothesized transcriptional regulatory model (TRM; i.e., a set of co-regulating transcription factors) is likely to target a given set of co-expressed genes. Our basic approach is to simultaneously predict cis regulatory modules (CRMs) associated with a g

SUBMITTER: Philippakis AA 

PROVIDER: S-EPMC1464814 | biostudies-literature | 2006 May

REPOSITORIES: biostudies-literature