title: One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data.
abstract: We present One Hand Clapping (OHC), a method for the detection of condition-specific interactions between transcription factors (TFs) from genome-wide gene activity measurements. OHC is based on a mapping between transcription factors and their target genes. Given a single case-control experiment, it uses a linear regression model to assess whether the common targets of two arbitrary TFs behave differently than expected from the genes targeted by only one of the TFs. When applied to osmotic stress data in S. cerevisiae, OHC produces consistent results across three types of expression measurements: gene expression microarray data, RNA Polymerase II ChIP-chip binding data and messenger RNA synthesis rates. Among the eight novel, condition-specific TF pairs, we validate the interaction between Gcn4p and Arr1p experimentally. We apply OHC to a large gene activity dataset in S. cerevisiae and provide a compendium of condition-specific TF interactions.
authors: Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany.
authors: Sebastian
authors: S
authors: Dümcke
authors: Martin
authors: M
authors: Seizl
authors: Stefanie
authors: S
authors: Etzold
authors: Nicole
authors: N
authors: Pirkl
authors: Dietmar E
authors: DE
authors: Martin
authors: Patrick
authors: P
authors: Cramer
authors: Achim
authors: A
authors: Tresch
mesh_terms: D050976:Basic-Leucine Zipper Transcription Factors / Q000378:metabolism; D001665:Binding Sites; D001667:Binding, Competitive; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D023281:Genomics / Q000379:methods*; D016014:Linear Models; D010641:Phenotype; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: C494591:ARR1 protein, S cerevisiae; D050976:Basic-Leucine Zipper Transcription Factors; C501391:GCN4 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors