BMRF-Net
Computational Tool
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General Information
DescriptionA software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method
Homepagehttp://sourceforge.net/projects/bmrfcjava/
Publications
BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method
Xu Shi; Robert O. Barnes; Li Chen; Ayesha N. Shajahan-Haq; Leena Hilakivi-Clarke; Robert Clarke; Yue Wang; Jianhua Xuan
Summary: Identification of protein interaction subnetworks is an important step to help us understand complex molecular mechanisms in cancer. In this paper, we develop a BMRF-Net package, implemented in Java and C++, to identify protein interaction subnetworks based on a bagging Markov random field (BMRF) framework. By integrating gene expression data and protein–protein interaction data, this software tool can be used to identify biologically meaningful subnetworks. A user friendly graphic user interface is developed as a Cytoscape plugin for the BMRF-Net software to deal with the input/output interface. The detailed structure of the identified networks can be visualized in Cytoscape conveniently. The BMRF-Net package has been applied to breast cancer data to identify significant subnetworks related to breast cancer recurrence.
Availability and implementation : The BMRF-Net package is available at http://sourceforge.net/projects/bmrfcjava/. The package is tested under Ubuntu 12.04 (64-bit), Java 7, glibc 2.15 and Cytoscape 3.1.0.
Contact: xuan@vt.edu
Supplementary information : Supplementary data are available at Bioinformatics online.
DOI: https://doi.org/10.1093/bioinformatics/btv137
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