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

Bioinformatics
Xu ShiJianhua Xuan

Abstract

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. 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.

References

Aug 10, 2002·Bioinformatics·Trey IdekerAndrew F Siegel
Aug 3, 2004·Nature Reviews. Cancer·Samir Hanash
Oct 18, 2007·Molecular Systems Biology·Han-Yu ChuangTrey Ideker
Nov 8, 2008·Nucleic Acids Research·T S Keshava PrasadAkhilesh Pandey
May 19, 2010·Proceedings of the National Academy of Sciences of the United States of America·Sherene LoiChristos Sotiriou
Dec 15, 2010·Bioinformatics·Michael E SmootTrey Ideker

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Citations

Mar 21, 2019·Frontiers in Genetics·Hung NguyenTin Nguyen
May 5, 2020·Briefings in Bioinformatics·Shuting JinXiangrong Liu
Apr 14, 2018·Journal of Proteomics·David Gomez-VarelaManuela Schmidt

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