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Author, Editor(s)

Author(s):

Alexa, Adrian
Rahnenführer, Jörg
Lengauer, Thomas

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BibTeX cite key*:

Alexa2006a

Title

Title*:

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

Journal

Journal Title*:

Bioinformatics

Journal's URL:

http://bioinformatics.oxfordjournals.org/

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Language:

English

Publisher

Publisher's
Name:


Publisher's URL:


Publisher's
Address:


ISSN:


Vol, No, pp, Date

Volume*:

22

Number:

13

Publishing Date:

2006

Pages*:

1600-1607

Number of
VG Pages:


Page Start:


Page End:


Sequence Number:


DOI:


Note, Abstract, ©

Note:


(LaTeX) 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}

URL for the Abstract:

http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btl140?ijkey=eiQBvvr1FcdzQ0w&keytype=ref

Categories,
Keywords:

Gene Ontology, functional groups, graph structure, Fisher's exact test

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Access Level:

Intranet

Correlation

MPG Unit:

Max-Planck-Institut für Informatik



MPG Subunit:

Computational Biology and Applied Algorithmics

Appearance:

MPII WWW Server, MPII FTP Server, MPG publications list, university publications list, working group publication list, Fachbeirat, VG Wort


BibTeX Entry:

@ARTICLE{Alexa2006a,
AUTHOR = {Alexa, Adrian and Rahnenf{\"u}hrer, J{\"o}rg and Lengauer, Thomas},
TITLE = {Improved Scoring of Functional Groups from Gene Expression Data by Decorrelating {GO} Graph Structure},
JOURNAL = {Bioinformatics},
YEAR = {2006},
NUMBER = {13},
VOLUME = {22},
PAGES = {1600--1607},
}


Entry last modified by Christine Kiesel, 02/20/2007
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Editor(s)
Adrian Alexa
Created
04/13/2006 04:58:49 PM
Revisions
2.
1.
0.

Editor(s)
Christine Kiesel
Jörg Rahnenführer
Adrian Alexa

Edit Dates
20.02.2007 15:02:07
11/29/2006 11:18:33 AM
04/13/2006 04:58:50 PM