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  One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data

Dümcke, S., Seizl, M., Etzold, S., Pirkl, N., Martin, D. E., Cramer, P., et al. (2012). One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data. Nucleic Acids Research, 40(18), 8883-8892. doi:10.1093/nar/gks695.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0015-3DAE-2 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-C51A-6
Genre: Journal Article

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 Creators:
Dümcke, S., Author
Seizl, M., Author
Etzold, S., Author
Pirkl, N., Author
Martin, D. E., Author
Cramer, P.1, Author              
Tresch, A., Author
Affiliations:
1Department of Molecular Biology, MPI for Biophysical Chemistry, Max Planck Society, ou_1863498              

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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.

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Language(s): eng - English
 Dates: 2012-07-25
 Publication Status: Published online
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 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.1093/nar/gks695
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Title: Nucleic Acids Research
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Source Genre: Journal
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Pages: - Volume / Issue: 40 (18) Sequence Number: - Start / End Page: 8883 - 8892 Identifier: ISSN: 0301-5610
CoNE: /journals/resource/1000000000262810