title: CyNetSVM: A Cytoscape App for Cancer Biomarker Identification Using Network Constrained Support Vector Machines.
abstract: One of the important tasks in cancer research is to identify biomarkers and build classification models for clinical outcome prediction. In this paper, we develop a CyNetSVM software package, implemented in Java and integrated with Cytoscape as an app, to identify network biomarkers using network-constrained support vector machines (NetSVM). The Cytoscape app of NetSVM is specifically designed to improve the usability of NetSVM with the following enhancements: (1) user-friendly graphical user interface (GUI), (2) computationally efficient core program and (3) convenient network visualization capability. The CyNetSVM app has been used to analyze breast cancer data to identify network genes associated with breast cancer recurrence. The biological function of these network genes is enriched in signaling pathways associated with breast cancer progression, showing the effectiveness of CyNetSVM for cancer biomarker identification. The CyNetSVM package is available at Cytoscape App Store and http://sourceforge.net/projects/netsvmjava; a sample data set is also provided at sourceforge.net.
authors.affiliation: Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, Virginia, United States of America.
authors.forename: Xu
authors.initials: X
authors.lastname: Shi
authors.affiliation: Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, Virginia, United States of America.
authors.forename: Sharmi
authors.initials: S
authors.lastname: Banerjee
authors.affiliation: Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America.
authors.forename: Li
authors.initials: L
authors.lastname: Chen
authors.affiliation: Departments of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States of America.
authors.forename: Leena
authors.initials: L
authors.lastname: Hilakivi-Clarke
authors.affiliation: Departments of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States of America.
authors.forename: Robert
authors.initials: R
authors.lastname: Clarke
authors.affiliation: Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, Virginia, United States of America.
authors.forename: Jianhua
authors.identifier: http://orcid.org/0000-0001-7256-1374
authors.initials: J
authors.lastname: Xuan
mesh_terms: D000465:Algorithms; D014408:Biomarkers, Tumor; D053263:Gene Regulatory Networks; D006801:Humans; D009369:Neoplasms / Q000175:diagnosis* / Q000235:genetics; D012984:Software; D060388:Support Vector Machine
chemical_list: D014408:Biomarkers, Tumor