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  Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites

Dieterich, C., Herwig, R., & Vingron, M. (2003). Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites. Bioinformatics, 19(Suppl. 2), ii50-ii56.

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Genre: Journal Article
Alternative Title : Bioinformatics

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 Creators:
Dieterich, Christoph1, Author
Herwig, Ralf2, Author              
Vingron, Martin3, Author              
Affiliations:
1Max Planck Society, ou_persistent13              
2Bioinformatics (Ralf Herwig), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479648              
3Gene 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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 Abstract: 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.

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Language(s): eng - English
 Dates: 2003-06-09
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: eDoc: 175671
 Degree: -

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Title: Bioinformatics
  Alternative Title : Bioinformatics
Source Genre: Journal
 Creator(s):
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Publ. Info: -
Pages: - Volume / Issue: 19 (Suppl. 2) Sequence Number: - Start / End Page: ii50 - ii56 Identifier: ISSN: 1367-4803
ISSN: 1460-2059