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An integrated software system for analyzing ChIP-chip and ChIP-seq data
Open accessAbstract
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.
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Metadata
- Authors
- Ji, H., Jiang, H., Ma, W., Johnson, D. S., Myers, R. M., & Wong, W. H.
- Venue
- Nature Biotechnology
- Published
- 2008-11
- Volume
- 26
- Issue
- 11
- Pages
- 1293-1300
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W1967656072
- Cited by
- 716
- References
- 6
- FWCI
- 31.64
- Type
- journal article
- Language
- en
- Open access
- green
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