Data and Software

Mpeak: A model-based peak detection software for ChIP-Chip data

Ming Zheng, Ph.D. Stanford University

Mpeak is a simple and efficient computer program, developed in Microsoft Visual C++ 2008 in Win7/WinXP environment, for detection of 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. Mpeak development and uses have been described in the following articles:

Zheng M, Barrera LO, Ren B and Wu YN (2007). ChIP-chip: Data, Model and Analysis. Biometrics, 63:787-796.

Kim TH, Barrera LO, Zheng M, Qu C, Singer MA, Richmand TA, Wu YN, Green RD and Ren B (2005). A high-resolution map of active promoters in the human genome. Nature 436:876-880.

Zheng M, Li YM and Lau Y-FC (2013). Application of the simple and efficient Mpeak modeling in binding peak identification in ChIP-Chip studies. Methods in Molecular Biology, 1067:186-202.

Mpeak download here: Mpeak Program

Mpeak instructions download here: Mpeak Instructions


Data from Cell Reports Article

Yunmin Li, Ming Zheng and Yun-Fai Chris Lau (2014). The Sex-Determining Factors SRY and SOX9 Regulate Similar Target Genes and Promote Testis Cord Formation during Testicular Differentiation. Cell Reports 8:723-733.

The following files can be downloaded from Folder S1 Genome Browser WIG Files in the Supplemental Information section of the article:

1. SRY-ChIP-Exp1.txt

2. SRY-ChIP-Exp2.txt

3. SOX9-ChIP-Exp1.txt

4. SOX9-ChIP-Exp2.txt

5. T11-T12-T13-MvF.txt

6. T11vT11-T12-T13-M.txt

7. Mouse-MM8-promoters.txt

8. Readme.doc