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Network propagation in the cytoscape cyberinfrastructure

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  • Daniel E Carlin
  • Barry Demchak
  • Dexter Pratt
  • Eric Sage
  • Trey Ideker

Abstract

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.

Suggested Citation

  • Daniel E Carlin & Barry Demchak & Dexter Pratt & Eric Sage & Trey Ideker, 2017. "Network propagation in the cytoscape cyberinfrastructure," PLOS Computational Biology, Public Library of Science, vol. 13(10), pages 1-9, October.
    • Handle: RePEc:plo:pcbi00:1005598
    DOI: 10.1371/journal.pcbi.1005598
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    1. Ravid Straussman & Teppei Morikawa & Kevin Shee & Michal Barzily-Rokni & Zhi Rong Qian & Jinyan Du & Ashli Davis & Margaret M. Mongare & Joshua Gould & Dennie T. Frederick & Zachary A. Cooper & Paul B, 2012. "Tumour micro-environment elicits innate resistance to RAF inhibitors through HGF secretion," Nature, Nature, vol. 487(7408), pages 500-504, July.
    2. Timothy R. Wilson & Jane Fridlyand & Yibing Yan & Elicia Penuel & Luciana Burton & Emily Chan & Jing Peng & Eva Lin & Yulei Wang & Jeff Sosman & Antoni Ribas & Jiang Li & John Moffat & Daniel P. Suthe, 2012. "Widespread potential for growth-factor-driven resistance to anticancer kinase inhibitors," Nature, Nature, vol. 487(7408), pages 505-509, July.
    3. Oron Vanunu & Oded Magger & Eytan Ruppin & Tomer Shlomi & Roded Sharan, 2010. "Associating Genes and Protein Complexes with Disease via Network Propagation," PLOS Computational Biology, Public Library of Science, vol. 6(1), pages 1-9, January.
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    1. Konstantina Charmpi & Manopriya Chokkalingam & Ronja Johnen & Andreas Beyer, 2021. "Optimizing network propagation for multi-omics data integration," PLOS Computational Biology, Public Library of Science, vol. 17(11), pages 1-26, November.

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