CisGenome

CisGenome is a software system that comprehensively analyzes genome-wide chromatin immunoprecipitation (ChIP) data. The software is equipped with diverse features specifically developed to meet all the basic needs of ChIP data analysis. These features include peak detection, false discovery rate computation, gene-peak association, and sequence and motif analysis.

One of the key strengths of CisGenome is that it has been specifically designed to support ChIP-sequencing (ChIP-seq) data analysis, which is achieved by coupling ChIP with massively parallel sequencing. This means that the software contains statistical methods that have been tailored to meet the unique challenges that are associated with ChIP-seq data analysis.

CisGenome has a modular design that enables it to support interactive analyses through a graphic user interface and customized batch-mode computation for advanced data mining. This means that users can choose the mode of analysis that best suits their needs, depending on the complexity of the data they are working with.

Another key feature of CisGenome is the built-in browser that enables users to visualize array images, signals, gene structure, conservation, and DNA sequence and motif information. This makes it easier for users to explore and interpret their data in an intuitive and informative way.

The power and versatility of CisGenome are demonstrated by the software's ability to perform a wide range of complex analyses. For example, it can be used for comparative analysis of ChIP-chip and ChIP-seq data for the transcription factor NRSF/REST and for the analysis of a new motif in Nanog- and Sox2-binding regions.