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Updated: Jul 6, 2026

Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation
Published on: June 21, 2016
ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene
Peter Van Loo1, Stein Aerts, Bernard Thienpont
1Department 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.
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