ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?
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.
Van Loo
Peter
P
Department of Molecular and Developmental Genetics, VIB, Herestraat 49, B-3000 Leuven, Belgium. Peter.VanLoo@med.kuleuven.be
Aerts
Stein
S
Thienpont
Bernard
B
De Moor
Bart
B
Moreau
Yves
Y
Marynen
Peter
P
D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D047108:Embryonic Development; D004742:Enhancer Elements, Genetic; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental / Q000235:genetics*; D053263:Gene Regulatory Networks; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D050436:Regulatory Elements, Transcriptional / Q000235:genetics*