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                                             BIOINFORMATICS COLLOQUIUM
						College of Science
                                              George Mason University
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                      CisGenome: an integrated system for analyzing ChIP-chip and ChIP-seq data

						 
                                                   Hongkai Ji

                                                 Johns Hopkins

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.