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


BACKGROUND
http://chipcodis.dacya.ucm.es
Abascal
Federico
F
BioComputing Unit, National Center of Biotechnology (CSIC), Madrid, Spain.
Carmona-Saez
Pedro
P
Carazo
Jose-Maria
JM
Pascual-Montano
Alberto
A
D047369:Chromatin Immunoprecipitation / Q000379:methods; D003628:Database Management Systems; D030541:Databases, Genetic; D016247:Information Storage and Retrieval / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D014157:Transcription Factors / Q000235:genetics*
D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors