ModuleMiner is a tool to detect similar cis-regulatory modules (CRMs) in a set of co-regulated or co-expressed genes. The algorithm takes as input a set of genes thought to have similar regulatory elements in their upstream regions (under the form of Ensembl gene IDs), and detects these similar CRMs. Apart from the CRMs near the given genes, the algorithm also creates a model of these similar CRMs and uses this model to find new target genes in the whole genome.
Bioinformatics Research Group, Belgium
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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?
Van Loo P1, Aerts S, Thienpont B, De Moor B, Moreau Y, Marynen P.