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

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