Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks

Nucleic Acids Res. 2019 Jul 2;47(W1):W206-W211. doi: 10.1093/nar/gkz332.


Characterizing the ontologies of genes directly regulated by a transcription factor (TF), can help to elucidate the TF's biological role. Previously, we developed a widely used method, BETA, to integrate TF ChIP-seq peaks with differential gene expression (DGE) data to infer direct target genes. Here, we provide Cistrome-GO, a website implementation of this method with enhanced features to conduct ontology analyses of gene regulation by TFs in human and mouse. Cistrome-GO has two working modes: solo mode for ChIP-seq peak analysis; and ensemble mode, which integrates ChIP-seq peaks with DGE data. Cistrome-GO is freely available at

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin Immunoprecipitation Sequencing / methods
  • Computational Biology / methods*
  • Databases, Genetic*
  • Gene Expression Regulation*
  • Humans
  • Mice
  • Software*
  • Transcription Factors / physiology*


  • Transcription Factors