Duemcke, Sebastian, Seizl, Martin, Etzold, Stefanie, Pirkl, Nicole, Martin, Dietmar E., Cramer, Patrick and Tresch, Achim (2012). One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data. Nucleic Acids Res., 40 (18). S. 8883 - 8893. OXFORD: OXFORD UNIV PRESS. ISSN 1362-4962

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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.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Duemcke, SebastianUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Seizl, MartinUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Etzold, StefanieUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Pirkl, NicoleUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Martin, Dietmar E.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Cramer, PatrickUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Tresch, AchimUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-481481
DOI: 10.1093/nar/gks695
Journal or Publication Title: Nucleic Acids Res.
Volume: 40
Number: 18
Page Range: S. 8883 - 8893
Date: 2012
Publisher: OXFORD UNIV PRESS
Place of Publication: OXFORD
ISSN: 1362-4962
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
SACCHAROMYCES-CEREVISIAE; REGULATORY NETWORKS; RESPONSE REGULATOR; CELL-CYCLE; EXPRESSION; BINDING; COOPERATIVITY; PREDICTION; COMPONENTS; DISCOVERYMultiple languages
Biochemistry & Molecular BiologyMultiple languages
URI: http://kups.ub.uni-koeln.de/id/eprint/48148

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