Inferring transcriptional modules from ChIP-chip, motif and microarray data.

Karen Lemmens; Thomas Dhollander; Tijl De Bie; Pieter Monsieurs; Kristof Engelen; Bart Smets; Joris Winderickx; Bart De Moor; Kathleen Marchal

doi:10.1186/gb-2006-7-5-r37

PubMed · 16677396

Inferring transcriptional modules from ChIP-chip, motif and microarray data.

Karen Lemmens·Thomas Dhollander·Tijl De Bie·Pieter Monsieurs·Kristof Engelen·Bart Smets·Joris Winderickx·Bart De Moor·Kathleen Marchal

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Abstract

'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.

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Algorithms Amino Acids Cell Cycle Chromatin Immunoprecipitation Galactose Gene Expression Profiling Gene Expression Regulation Oligonucleotide Array Sequence Analysis Regulatory Elements, Transcriptional Ribosomes Software Transcription Factors Yeasts Evaluation Study Journal Article Research Support, Non-U.S. Gov't

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BibTeX RIS

Karen Lemmens, Thomas Dhollander, Tijl De Bie, Pieter Monsieurs, Kristof Engelen, Bart Smets, Joris Winderickx, Bart De Moor, Kathleen Marchal. 2006-05-05. Inferring transcriptional modules from ChIP-chip, motif and microarray data.. https://doi.org/10.1186/gb-2006-7-5-r37

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