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  Non-transcriptional pathway features reconstructed from secondary effects of RNA interference

Markowetz, F., Bloch, J., & Spang, R. (2005). Non-transcriptional pathway features reconstructed from secondary effects of RNA interference. Bioinformatics, 21, 4026-4032. doi:10.1093/bioinformatics/bti662.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-8563-9 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-8564-7
Genre: Journal Article
Alternative Title : Bioinformatics

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4026.pdf (Any fulltext), 212KB
 
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 Creators:
Markowetz, Florian1, Author
Bloch, Jacques1, Author
Spang, Rainer2, Author              
Affiliations:
1Max Planck Society, ou_persistent13              
2Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433547              

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 Abstract: Motivation: Cellular signaling pathways, which are not modulated on a transcriptional level, cannot be directly deduced from expression profiling experiments. The situation changes, when external interventions such as RNA interference or gene knock-outs come into play. Even if the expression of the signaling genes is not changed, secondary effects in downstream genes shed light on the pathway, and allow partial reconstruction of its topology. Results: We introduce an algorithm to infer non-transcriptional pathway features based on differential gene expression in silencing assays. We demonstrate the power of our algorithm in the controlled setting of simulation studies, and explain its practical use in the context of an RNA interference dataset investigating the response to microbial challenge in Drosophila melanogaster.

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Language(s): eng - English
 Dates: 2005-11-13
 Publication Status: Published in print
 Pages: -
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 Identifiers: eDoc: 267398
DOI: 10.1093/bioinformatics/bti662
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Title: Bioinformatics
  Alternative Title : Bioinformatics
Source Genre: Journal
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Pages: - Volume / Issue: 21 Sequence Number: - Start / End Page: 4026 - 4032 Identifier: ISSN: 1367-4803