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          Institute: MPI für molekulare Genetik     Collection: Department of Computational Molecular Biology     Display Documents



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ID: 175671.0, MPI für molekulare Genetik / Department of Computational Molecular Biology
Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites
Authors:Dieterich, Christoph; Herwig, Ralf; Vingron, Martin
Language:English
Date of Publication (YYYY-MM-DD):2003-06-09
Title of Journal:Bioinformatics
Journal Abbrev.:Bioinformatics
Volume:19
Issue / Number:Suppl. 2
Start Page:ii50
End Page:ii56
Copyright:© 2003 Oxford University Press
Review Status:not specified
Audience:Experts Only
Abstract / Description:Many cellular signaling pathways induce gene expression by activating specific transcription factor complexes. Conventional approaches to the prediction of transcription factor binding sites lead to a notoriously high number of false discoveries. To alleviate this problem, we consider only binding sites that are conserved in man-mouse genomic sequence comparisons. We employ two alternative methods for predicting binding sites: exact matches to validated binding site sequences and weight matrix scans. We then ask the question whether there is a characteristic association between a transcription factor or set thereof to a particular group of genes. Our approach is tested on genes, which are induced in dendritic cells in response to the cells’ exposure to LPS. We chose this example because the underlying signaling pathways are well understood. We demonstrate the benefit of conserved predicted binding sites in interpreting the LPS experiment. Additionally, we find that both methods for the prediction of conserved binding sites complement one another. Finally, our results suggest a distinct role for SRF in the context of LPS-induced gene expression.
External Publication Status:published
Document Type:Article
Communicated by:Martin Vingron
Affiliations:MPI für molekulare Genetik
External Affiliations:Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics
Vertebrate Genomics - Bioinformatics group, Max-Planck-Institute for Molecular Genetics, Ihnestraße 63–73, 14195 Berlin, Germany
Identifiers:ISSN:1367-4803 [ID No:1]
ISSN:1460-2059 [ID No:2]
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