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  Detection of interacting transcription factors in human tissues using predicted DNA binding affinity

Mysickova, A., & Vingron, M. (2012). Detection of interacting transcription factors in human tissues using predicted DNA binding affinity. BMC Genomics, 13 Suppl 1, S2-S2. doi:10.1186/1471-2164-13-S1-S2.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-000E-E876-8 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-000E-E877-6
Genre: Journal Article

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© 2012 Myšičková and Vingron; licensee BioMed Central Ltd.
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 Creators:
Mysickova, Alena1, Author              
Vingron, Martin2, Author              
Affiliations:
1Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433547              
2Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              

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Free keywords: Computational Biology/ methods DNA/ metabolism Gene Expression Regulation Humans Protein Binding/genetics/physiology Transcription Factors/chemistry/genetics/ metabolism
 Abstract: BACKGROUND: Tissue-specific gene expression is generally regulated by combinatorial interactions among transcription factors (TFs) which bind to the DNA. Despite this known fact, previous discoveries of the mechanism that controls gene expression usually consider only a single TF. RESULTS: We provide a prediction of interacting TFs in 22 human tissues based on their DNA-binding affinity in promoter regions. We analyze all possible pairs of 130 vertebrate TFs from the JASPAR database. First, all human promoter regions are scanned for single TF-DNA binding affinities with TRAP and for each TF a ranked list of all promoters ordered by the binding affinity is created. We then study the similarity of the ranked lists and detect candidates for TF-TF interaction by applying a partial independence test for multiway contingency tables. Our candidates are validated by both known protein-protein interactions (PPIs) and known gene regulation mechanisms in the selected tissue. We find that the known PPIs are significantly enriched in the groups of our predicted TF-TF interactions (2 and 7 times more common than expected by chance). In addition, the predicted interacting TFs for studied tissues (liver, muscle, hematopoietic stem cell) are supported in literature to be active regulators or to be expressed in the corresponding tissue. CONCLUSIONS: The findings from this study indicate that tissue-specific gene expression is regulated by one or two central regulators and a large number of TFs interacting with these central hubs. Our results are in agreement with recent experimental studies.

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Language(s): eng - English
 Dates: 2012-01-17
 Publication Status: Published online
 Pages: -
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 Rev. Type: Peer
 Identifiers: DOI: 10.1186/1471-2164-13-S1-S2
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Title: BMC Genomics
Source Genre: Journal
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Publ. Info: BioMed Central
Pages: - Volume / Issue: 13 Suppl 1 Sequence Number: - Start / End Page: S2 - S2 Identifier: ISSN: 1471-2164
CoNE: https://pure.mpg.de/cone/journals/resource/111000136905010