UNIT 2.13 Using CisGenome to Analyze ChIP-chip and ChIP-seq Data
Published Online: 1 MAR 2011
Copyright © 2011 by John Wiley & Sons, Inc.
Lab Protocol Title
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.
- Published Online: 1 MAR 2011
- 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;
- gene regulation