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Bioinformatics Advance Access originally published online on March 12, 2008
Bioinformatics 2008 24(9):1208-1209; 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 3,*

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

*To whom correspondence should be addressed.


  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 over-represented in a series of environmental conditions.

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

Contact: pascual{at}fis.ucm.es

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

Associate Editor: Martin Bishop

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

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