Method
Inferring transcriptional modules from ChIP-chip, motif and microarray data
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* Corresponding author: Kathleen Marchal kathleen.marchal@biw.kuleuven.be
1 BIOI@SCD, Department of Electrical Engineering, KU Leuven, Kasteelpark Arenberg, B-3001 Heverlee, Belgium
2 Research Group on Quantitative Psychology, Department of Psychology, KU Leuven, Tiensestraat, B-3000 Leuven, Belgium
3 Molecular Physiology of Plants and Micro-organisms Section, Biology Department, KU Leuven, Kasteelpark Arenberg, B-3001 Heverlee, Belgium
4 CMPG, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg, B-3001 Heverlee, Belgium
Genome Biology 2006, 7:R37 doi:10.1186/gb-2006-7-5-r37
Published: 5 May 2006Abstract
'ReMoDiscovery' is an intuitive algorithm to correlate regulatory programs with regulators and corresponding motifs to a set of co-expressed genes. It exploits in a concurrent way three independent data sources: ChIP-chip data, motif information and gene expression profiles. When compared to published module discovery algorithms, ReMoDiscovery is fast and easily tunable. We evaluated our method on yeast data, where it was shown to generate biologically meaningful findings and allowed the prediction of potential novel roles of transcriptional regulators.