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An integrated software system for analyzing ChIP-chip and ChIP-seq (2008)
| Citations: | 166 - 5 self |
BibTeX
@MISC{Ji08anintegrated,
author = {Hongkai Ji and Hui Jiang and Wenxiu Ma and David S Johnson and Richard M Myers and Wing H Wong},
title = {An integrated software system for analyzing ChIP-chip and ChIP-seq},
year = {2008}
}
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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. Chromatin immunoprecipitation followed by either genome tiling array analysis (ChIP-chip) 1–3 or massively parallel sequencing (ChIP-seq) 4–10 enables transcriptional regulation to be studied on a genome-wide scale (Supplementary Fig. 1 online). By systematically identifying protein-DNA interactions of interest, studies using these
Keyphrases
software system parallel sequencing batch-mode computation transcription factor nrsf rest modular design gene structure motif information motif analysis supplementary fig basic need genome-wide scale negative control sample graphic user interface data normalization false discovery rate computation comparative analysis peak detection sox2-binding region statistical method chip-seq analysis chip microarray new motif chromatin immunoprecipitation chip data analysis dna sequence enables transcriptional regulation interactive analysis genome tiling array analysis advanced data mining genome-wide chromatin immunoprecipitation array image built-in browser analysis method chip-seq data protein-dna interaction present cisgenome gene-peak association
