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Bioinformatics Advance Access published online on March 12, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn094
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

ChIPCodis: Mining complex regulatory systems in yeast by concurrent enrichment analysis of Chip-on-chip data

Federico Abascal 1, Pedro Carmona-Saez 2, Jose-Maria Carazo 1 and Alberto Pascual-Montano 1,*

1BioComputing Unit, National Center of Biotechnology (CSIC), Madrid, Spain; 2Integromics SL, Madrid, Spain; 3Computer Architecture Department. Facultad de CC Físicas. Universidad Complutense de Madrid, Spain.

*To whom correspondence should be addressed. Alberto Pascual-Montano, E-mail: pascual{at}fis.ucm.es


  Abstract

Motivation: Eukaryotic genes are often regulated by multiple transcription factors (TFs). Depending on the interactions among different TFs the expression of a gene can be tuned to respond to diverse environmental conditions. Chip-on-chip experiments provide a snapshot of which TF are in vivo bound to which genes in a particular condition, and have been applied to characterize the regulatory code of yeast under several experimental settings. ChIPCodis mines this data to provide new insights about how the expression of a particular group of genes is regulated. For a given list of yeast genes ChIPCodis determines which combinations of TFs are significantly overrepresented in a series of environmental conditions.

Availability: http://chipcodis.dacya.ucm.es

Supplementary material: http://chipcodis.dacya.ucm.es/sm.html

Contact: pascual{at}fis.ucm.es

Associate Editor: Prof. Martin Bishop

Received on October 29, 2007; revised on March 6, 2008; accepted on March 6, 2008

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