BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method: Fig. 1

Xu Shi, Robert O. Barnes, Li Chen, Ayesha N. Shajahan-Haq, Leena Hilakivi-Clarke, Robert Clarke, Yue Wang, Jianhua Xuan
2015 Bioinformatics  
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 Cþþ, 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
more » ... e 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 The package is tested under Ubuntu 12.04 (64-bit), Java 7, glibc 2.15 and Cytoscape 3.1.0.
doi:10.1093/bioinformatics/btv137 pmid:25755273 pmcid:PMC4495295 fatcat:x45x6p6nnjcnflyzf4bngogizi