title: BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method.
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.
  
  
  METHODS
  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.
authors.affiliation: Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA 22203, USA.
authors.forename: Xu
authors.initials: X
authors.lastname: Shi
authors.affiliation: Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA 22203, USA.
authors.forename: Robert O
authors.initials: RO
authors.lastname: Barnes
authors.affiliation: Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA and.
authors.forename: Li
authors.initials: L
authors.lastname: Chen
authors.affiliation: Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University, Washington, DC 20057, USA.
authors.forename: Ayesha N
authors.initials: AN
authors.lastname: Shajahan-Haq
authors.affiliation: Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University, Washington, DC 20057, USA.
authors.forename: Leena
authors.initials: L
authors.lastname: Hilakivi-Clarke
authors.affiliation: Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University, Washington, DC 20057, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Clarke
authors.affiliation: Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA 22203, USA.
authors.forename: Yue
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA 22203, USA.
authors.forename: Jianhua
authors.initials: J
authors.lastname: Xuan
mesh_terms: D000465:Algorithms; D001943:Breast Neoplasms / Q000235:genetics / Q000378:metabolism; D005260:Female; D015870:Gene Expression; D006801:Humans; D008390:Markov Chains; D025941:Protein Interaction Mapping / Q000379:methods*; D012984:Software