UNIT 2.13 Using CisGenome to Analyze ChIP-chip and ChIP-seq Data

  1. Hongkai Ji1,
  2. Hui Jiang2,
  3. Wenxiu Ma2,
  4. Wing Hung Wong2

Published Online: 1 MAR 2011

DOI: 10.1002/0471250953.bi0213s33

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Ji, H., Jiang, H., Ma, W. and Wong, W. H. 2011. Using CisGenome to Analyze ChIP-chip and ChIP-seq Data. Current Protocols in Bioinformatics. 33:2.13:2.13.1–2.13.45.

Author Information

  1. 1

    The Johns Hopkins University, Baltimore, Maryland

  2. 2

    Stanford University, Stanford, California

Publication History

  1. Published Online: 1 MAR 2011
  2. Published Print: MAR 2011


Chromatin immunoprecipitation (ChIP) coupled with genome tiling array hybridization (ChIP-chip) and ChIP followed by massively parallel sequencing (ChIP-seq) are high-throughput 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.Curr. Protoc. Bioinform. 33:2.13.1-2.13.45. © 2011 by John Wiley & Sons, Inc.


  • transcription factor;
  • chromatin immunoprecipitation;
  • tiling array;
  • next generation sequencing;
  • motif;
  • gene regulation