Bioinformatics. 2008 May 1;24(9):1208-9. Epub 2008 Mar 12.

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

Abascal F, Carmona-Saez P, Carazo JM, Pascual-Montano A.

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BioComputing Unit, National Center of Biotechnology (CSIC), Madrid, Spain.

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

PMID:: 18339638; [PubMed - indexed for MEDLINE]

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