ModuleMiner - Improved computational detection of cis-regulatory modules: Are there different modes of gene regulation in embryonic development and adult tissues?

Abstract

We present ModuleMiner, a novel algorithm for computationally detecting cis-regulatory modules (CRMs) in a set of co-expressed genes. ModuleMiner outperforms other methods for CRM detection on benchmark data, and successfully detects CRMs in tissue-specific microarray clusters and in embryonic development gene sets. Interestingly, CRM predictions for differentiated tissues exhibit strong enrichment close to the transcription start site, whereas CRM predictions for embryonic development gene sets are depleted in this region. © 2008 Van Loo et al.; licensee BioMed Central Ltd.