Using CisGenome to analyze ChIP-chip and ChIP-seq data

Hongkai Ji, Hui Jiang, Wenxiu Ma, Wing Hung Wong

Research output: Contribution to journalArticlepeer-review

27 Scopus citations


Chromatin immunoprecipitation (ChIP) coupled with genome tiling array hybridization (ChIP-chip) and ChIP followed by massively parallel sequencing (ChIP-seq) are highthroughput approaches to profiling genome-wide protein-DNA interactions. Both technologies are increasingly used to study transcription-factor binding sites and chromatin modifications. CisGenome is an integrated software system for analyzing ChIP-chip and ChIP-seq data. This unit describes basic functions of CisGenome and how to use them to find genomic regions with protein-DNA interactions, visualize binding signals, associate binding regions with nearby genes, search for novel transcription-factor binding motifs, and map existing DNA sequence motifs to user-supplied genomic regions to define their exact locations.

Original languageEnglish (US)
Pages (from-to)1-45
Number of pages45
JournalCurrent Protocols in Bioinformatics
Issue numberSUPP.33
StatePublished - Mar 2011


  • Chromatin immunoprecipitation
  • Gene regulation
  • Motif
  • Next generation sequencing
  • Tiling array
  • Transcription factor

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry


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