ArticleBioinformatics (Oxford, England)2015
BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- A Comprehensive Survey of Tools and Software for Active Subnetwork Identification.Frontiers in genetics · 2019Review
- Region-Resolved Quantitative Proteome Profiling Reveals Molecular Dynamics Associated With Chronic Pain in the PNS and Spinal Cord.Frontiers in molecular neuroscience · 2018Article
- CyNetSVM: A Cytoscape App for Cancer Biomarker Identification Using Network Constrained Support Vector Machines.PloS one · 2017Article
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Authors and funding
8 authors.
Funding
Abstract
unlabelledIdentification 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.
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Registered trials
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