Network propagation in the cytoscape cyberinfrastructure

• Published in: PLoS computational biology Vol. 13; no. 10; p. e1005598
• Main Authors: Carlin, Daniel E, Demchak, Barry, Pratt, Dexter, Sage, Eric, Ideker, Trey
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.10.2017; Public Library of Science (PLoS)
• Subjects: Algorithms; Analysis; Animals; Application programming interface; Bioinformatics; Biology; Biology and Life Sciences; Cancer; Computational biology; Computer and Information Sciences; Drug Resistance, Neoplasm; Genes; Genomes; Genomics; Indoles; Internet; Medicine; Melanoma; Methods; Models, Biological; Mutation; Network analysis; Physical Sciences; Propagation; Protein Interaction Mapping - methods; Proteins; Research and Analysis Methods; Software; Sulfonamides; Systems biology; Systems Biology - methods; California
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1005598

Network propagation is an important and widely used algorithm in systems biology, with applications in protein function prediction, disease gene prioritization, and patient stratification. However, up to this point it has required significant expertise to run. Here we extend the popular network analysis program Cytoscape to perform network propagation as an integrated function. Such integration greatly increases the access to network propagation by putting it in the hands of biologists and linking it to the many other types of network analysis and visualization available through Cytoscape. We demonstrate the power and utility of the algorithm by identifying mutations conferring resistance to Vemurafenib.