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

Bioinformatics. 2008 May 1;24(9):1208-9. doi: 10.1093/bioinformatics/btn094. Epub 2008 Mar 12.


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.


Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatin Immunoprecipitation / methods
  • Database Management Systems
  • Databases, Genetic*
  • Information Storage and Retrieval / methods*
  • Oligonucleotide Array Sequence Analysis / methods*
  • Regulatory Sequences, Nucleic Acid / genetics*
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Sequence Analysis, DNA / methods
  • Software*
  • Transcription Factors / genetics*


  • Saccharomyces cerevisiae Proteins
  • Transcription Factors