Abstract

CisGenome is a software system for analyzing genome-wide chromatin immunoprecipitation (ChIP) data. It is designed to meet all basic needs of ChIP data analyses, including visualization, data normalization, peak detection, false discovery rate (FDR) computation, gene-peak association, and sequence and motif analysis. In addition to implementing previously published ChIP-chip analysis methods, the software contains new statistical methods designed specifically for ChIP-seq data. CisGenome has a modular design so that it supports 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 illustrate 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 without negative control sample, and an analysis of a novel motif in Nanog- and Sox2-binding regions.

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