Application of the Simple and Efficient Mpeak Modeling in Binding Peak Identification in ChIP-Chip Studies

Chromatin immunoprecipitation and hybridization of high-density promoter microarray (ChIP-chip) is a powerful strategy to identify target genes for specific transcription factors and other DNA-binding nuclear proteins in a genome-wide manner. Services of core facilities have greatly enhanced the accessibility of these technologies to new investigators to the field. The Mpeak modeling is a simple and efficient computer program, capable of identifying chromatin-binding peaks in ChIP-chip datasets. It utilizes advanced statistical computation, but yet offers a simple procedure with user inputs on parameters in its operation. The Mpeak-fitted signals are tabulation in convenient formats and can be visualized in various genome-display graphic programs, including SignalMap and Genome Browser, and analyzed together with other datasets, such as microarray expression patterns. Several research groups have used the Mpeak program in their respective ChIP-chip studies. The various features of Mpeak will be illustrated with ChIP-chip datasets from a study designed to identify the target genes for the sex-determining factor, SRY, in mouse embryonic gonads at the time of sex determination.