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

Research output: Contribution to journalA1: Web of Science-article

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.

Original languageEnglish
Article number37
JournalGenome Biology and Evolution
Volume7
Issue number5
Number of pages14
ISSN1474-760X
DOIs
Publication statusPublished - 2006
Externally publishedYes

Keywords

  • NITROGEN CATABOLITE REPRESSION
  • ZINC-FINGER PROTEINS
  • SACCHAROMYCES-CEREVISIAE
  • GENE-EXPRESSION
  • CELL-CYCLE
  • SIGNAL-TRANSDUCTION
  • BINDING PROTEIN
  • HYPOXIC GENES
  • YEAST
  • STRESS

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