Format

Send to

Choose Destination
Genome Biol. 2008 Apr 7;9(4):R66. doi: 10.1186/gb-2008-9-4-r66.

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

Author information

1
Department of Molecular and Developmental Genetics, VIB, Herestraat 49, B-3000 Leuven, Belgium. Peter.VanLoo@med.kuleuven.be

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.

PMID:
18394174
PMCID:
PMC2643937
DOI:
10.1186/gb-2008-9-4-r66
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center