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TurboID-Based Proximity Labeling for In Planta Identification of Protein-Protein Interaction Networks
Published on: May 17, 2020
BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random
Xu Shi1, Robert O Barnes1, Li Chen2
1Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA 22203, USA.
Unlabelled:
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.
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