TY - JOUR
T1 - An integrated software system for analyzing ChIP-chip and ChIP-seq data
AU - Ji, Hongkai
AU - Jiang, Hui
AU - Ma, Wenxiu
AU - Johnson, David S.
AU - Myers, Richard M.
AU - Wong, Wing H.
N1 - Funding Information:
We thank W. Li for assistance with analyzing the ChIP-chip spike-in data. This research was supported by National Institutes of Health grant HG003903 (to W.H.W.) and the National Human Genome Research Institute’s ENCODE project (to R.M.M.). H. Ji is partially supported by the Johns Hopkins Bloomberg School of Public Health Richard L. Gelb Cancer Research Fund.
PY - 2008/11
Y1 - 2008/11
N2 - 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.
AB - 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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U2 - 10.1038/nbt.1505
DO - 10.1038/nbt.1505
M3 - Article
C2 - 18978777
AN - SCOPUS:55749094855
SN - 1087-0156
VL - 26
SP - 1293
EP - 1300
JO - Nature biotechnology
JF - Nature biotechnology
IS - 11
ER -