An integrated software system for analyzing ChIP-chip and ChIP-seq data

Hongkai Ji, Hui Jiang, Wenxiu Ma, David S. Johnson, Richard M. Myers, Wing H. Wong

Research output: Contribution to journalArticle

Abstract

We present CisGenome, a software system for analyzing genome-wide chromatin immunoprecipitation (ChIP) data. CisGenome is designed to meet all basic needs of ChIP data analyses, including visualization, data normalization, peak detection, false discovery rate computation, gene-peak association, and sequence and motif analysis. In addition to implementing previously published ChIP-microarray (ChIP-chip) analysis methods, the software contains statistical methods designed specifically for ChlP sequencing (ChIP-seq) data obtained by coupling ChIP with massively parallel sequencing. The modular design of CisGenome enables it to support interactive analyses through a graphic user interface as well as customized batch-mode computation for advanced data mining. A built-in browser allows visualization of array images, signals, gene structure, conservation, and DNA sequence and motif information. We demonstrate the use of these tools by a comparative analysis of ChIP-chip and ChIP-seq data for the transcription factor NRSF/REST, a study of ChIP-seq analysis with or without a negative control sample, and an analysis of a new motif in Nanog- and Sox2-binding regions.

Original languageEnglish (US)
Pages (from-to)1293-1300
Number of pages8
JournalNature biotechnology
Volume26
Issue number11
DOIs
StatePublished - Nov 1 2008

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ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology
  • Molecular Medicine
  • Biomedical Engineering

Cite this

Ji, H., Jiang, H., Ma, W., Johnson, D. S., Myers, R. M., & Wong, W. H. (2008). An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nature biotechnology, 26(11), 1293-1300. https://doi.org/10.1038/nbt.1505