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

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, i...

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Autores principales: Dümcke, Sebastian, Seizl, Martin, Etzold, Stefanie, Pirkl, Nicole, Martin, Dietmar E., Cramer, Patrick, Tresch, Achim
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467085/
https://www.ncbi.nlm.nih.gov/pubmed/22844089
http://dx.doi.org/10.1093/nar/gks695
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author Dümcke, Sebastian
Seizl, Martin
Etzold, Stefanie
Pirkl, Nicole
Martin, Dietmar E.
Cramer, Patrick
Tresch, Achim
author_facet Dümcke, Sebastian
Seizl, Martin
Etzold, Stefanie
Pirkl, Nicole
Martin, Dietmar E.
Cramer, Patrick
Tresch, Achim
author_sort Dümcke, Sebastian
collection PubMed
description 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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spelling pubmed-34670852012-10-10 One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data Dümcke, Sebastian Seizl, Martin Etzold, Stefanie Pirkl, Nicole Martin, Dietmar E. Cramer, Patrick Tresch, Achim Nucleic Acids Res Computational Biology 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. Oxford University Press 2012-10 2012-07-25 /pmc/articles/PMC3467085/ /pubmed/22844089 http://dx.doi.org/10.1093/nar/gks695 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Computational Biology
Dümcke, Sebastian
Seizl, Martin
Etzold, Stefanie
Pirkl, Nicole
Martin, Dietmar E.
Cramer, Patrick
Tresch, Achim
One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data
title One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data
title_full One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data
title_fullStr One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data
title_full_unstemmed One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data
title_short One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data
title_sort one hand clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data
topic Computational Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467085/
https://www.ncbi.nlm.nih.gov/pubmed/22844089
http://dx.doi.org/10.1093/nar/gks695
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