Genetic variants or mutations that otherwise would not pass a test for statistical significance, due to low power of association with the disease phenotype, can be prioritized due to their close association with each other in molecular networks. Of the many applications of network propagation in systems biology, one of the most critical has been disease gene prioritization in genome-wide association studies. In computational biology, the most common meaning for the nodes is genes, and the edges usually represent various types of functional relationships between genes, for instance protein binding interaction, transcriptional regulation or signaling by phosphorylation. More abstractly, network propagation supplies a robust estimate of network closeness, which can be used for many different applications. By examining the final distribution of values, we can, for instance, find a subnetwork where the nodes are closely related by the network to the original query. The query nodes are given some initial value, then a smoothing process is applied to the initial values on those query nodes, passing some of the value to neighboring nodes. Most commonly, the basic network propagation process starts with some query nodes, and a network. Network propagation has become a critical analysis technique in computational systems biology. “This is a PLOS Computational Biology Software paper.” The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: The authors have declared that no competing interests exist. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: All relevant data are within the paper and its Supporting Information files.įunding: This work was supported by: Department of Defense Big Mechanism (W911-NF-14-1-0397), National Cancer Institute (U24 CA-184427F), National Institute of General Medical Sciences (P41 GM103504). Received: DecemAccepted: Published: October 12, 2017Ĭopyright: © 2017 Carlin et al. PLoS Comput Biol 13(10):Įditor: Xianghong Jasmine Zhou, University of Southern California, UNITED STATES Citation: Carlin DE, Demchak B, Pratt D, Sage E, Ideker T (2017) Network propagation in the cytoscape cyberinfrastructure.
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