Computational discovery of regulatory elements in a continuous expression space.
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ABSTRACT:
SUBMITTER: Lajoie M
PROVIDER: S-EPMC4053739 | biostudies-literature | 2012 Nov
REPOSITORIES: biostudies-literature
Publications
Computational discovery of regulatory elements in a continuous expression space.
Lajoie Mathieu M Gascuel Olivier O Lefort Vincent V Bréhélin Laurent L
Genome biology 20121127 11
Approaches for regulatory element discovery from gene expression data usually rely on clustering algorithms to partition the data into clusters of co-expressed genes. Gene regulatory sequences are then mined to find overrepresented motifs in each cluster. However, this ad hoc partition rarely fits the biological reality. We propose a novel method called RED2 that avoids data clustering by estimating motif densities locally around each gene. We show that RED2 detects numerous motifs not detected ...[more]
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