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  Improved Scoring of Functional Groups from Gene Expression Data by Decorrelating GO Graph Structure

Alexa, A., Rahnenführer, J., & Lengauer, T. (2006). Improved Scoring of Functional Groups from Gene Expression Data by Decorrelating GO Graph Structure. Bioinformatics, 22, 1600-1607.

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Item Permalink: https://hdl.handle.net/11858/00-001M-0000-000F-232C-1 Version Permalink: https://hdl.handle.net/11858/00-001M-0000-000F-232D-0
Genre: Journal Article

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GOscoring.pdf (Publisher version), 244KB
 
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Alexa, Adrian1, 2, Author           
Rahnenführer, Jörg1, Author           
Lengauer, Thomas1, Author           
Affiliations:
1Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society, ou_40046              
2International Max Planck Research School, MPI for Informatics, Max Planck Society, ou_1116551              

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 Abstract: \begin{abstract} \section{Motivation:} The result of a typical microarray experiment is a long list of genes with corresponding expression measurements. This list is only the starting point for a meaningful biological interpretation. Modern methods identify relevant biological processes or functions from gene expression data by scoring the statistical significance of predefined functional gene groups, for example based on \emph{Gene Ontology} (GO). We develop methods that increase the explanatory power of this approach by integrating knowledge about relationships between the GO terms into the calculation of the statistical significance. \section{Results:} We present two novel algorithms that improve GO group scoring using the underlying GO graph topology. The algorithms are evaluated on real and on simulated gene expression data. We show that both methods eliminate local dependencies between GO terms and point to relevant areas in the GO graph that remain undetected with state-of-the-art algorithms for scoring functional terms. A simulation study demonstrates that the new methods exhibit a higher level of detecting relevant biological terms than competing methods. \section{Availability:} \href{http://topgo.bioinf.mpi-inf.mpg.de}{topgo.bioinf.mpi-inf.mpg.de} \section{Contact:} \href{alexa@mpi-sb.mpg.de}{alexa@mpi-sb.mpg.de} \end{abstract}

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Language(s): eng - English
 Dates: 2007-02-202006
 Publication Status: Issued
 Pages: -
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 Table of Contents: -
 Rev. Type: Peer
 Identifiers: eDoc: 314665
Other: Local-ID: C125673F004B2D7B-FBB39D7F605386EBC125714F00524A67-Alexa2006a
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Title: Bioinformatics
Source Genre: Journal
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Pages: - Volume / Issue: 22 Sequence Number: - Start / End Page: 1600 - 1607 Identifier: -