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Bioinformatics Advance Access published online on July 14, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl385
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received April 28, 2006
Revised June 26, 2006
Accepted July 6, 2006

Applications note

OrderedList - a bioconductor package for detecting similarity in ordered gene lists

Claudio Lottaz 1 *, Xinan Yang 2, Stefanie Scheid 1, and Rainer Spang 1

1 Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Ihnestrasse 63-73, D-14195 Berlin, Germany
2 Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Ihnestrasse 63-73, D-14195 Berlin, Germany; State Key Laboratory of Bioelectronics, Southeast University, 210096 Nanjing, P.R. China

* To whom correspondence should be addressed.
Claudio Lottaz, E-mail: claudio.lottaz{at}molgen.mpg.de


  Abstract

Summary: OrderedList is a Bioconductor compliant package for meta-analysis based on ordered gene lists like those resulting from differential gene expression analysis. Our package quantifies the similarity between gene lists. The significance of the similarity score is estimated from random scores computed on perturbed data. OrderedList illustrates list similarity in intuitive plots and determines the score-driving genes for further analysis.

Availability: http://www.bioconductor.org.

Supplementary information: Please visit our webpage on http://compdiag.molgen.mpg.de/software.

Associate Editor: Joaquin Dopazo
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