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

Peter Van Loo1,2,3*, Stein Aerts1,2, Bernard Thienpont2, Bart De Moor3, Yves Moreau3 and Peter Marynen1,2

Author Affiliations

1 Department of Molecular and Developmental Genetics, VIB, Herestraat 49, B-3000 Leuven, Belgium

2 Department of Human Genetics, University of Leuven, Herestraat 49, B-3000 Leuven, Belgium

3 Bioinformatics group, Department of Electrical Engineering (ESAT-SCD), University of Leuven, Kasteelpark Arenberg, B-3001 Heverlee, Belgium

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Genome Biology 2008, 9:R66 doi:10.1186/gb-2008-9-4-r66

Published: 7 April 2008

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.