Classifying tumors by supervised network propagation.
Ontology highlight
ABSTRACT: Motivation
Network propagation has been widely used to aggregate and amplify the effects of tumor mutations using knowledge of molecular interaction networks. However, propagating mutations through interactions irrelevant to cancer leads to erosion of pathway signals and complicates the identification of cancer subtypes.Results
To address this problem we introduce a propagation algorithm, Network-Based Supervised Stratification (NBS2), which learns the mutated subnetworks underlying tumor subtypes using a supervised approach. Given an annotated molecular network and reference tumor mutation profiles for which subtypes have been predefined, NBS2 is trained by adjusting the weights on interaction features such that network propagation best recovers the provided subtypes. After training, weights are fixed such that mutation profiles of new tumors can be accurately classified. We evaluate NBS2 on breast and glioblastoma tumors, demonstrating that it outperforms the best network-based approaches in classifying tumors to known subtypes for these diseases. By interpreting the interaction weights, we highlight characteristic molecular pathways driving selected subtypes.Availability and implementation
The NBS2 package is freely available at: https://github.com/wzhang1984/NBSS.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Zhang W
PROVIDER: S-EPMC6022559 | biostudies-literature | 2018 Jul
REPOSITORIES: biostudies-literature
Publications
Classifying tumors by supervised network propagation.
Zhang Wei W Ma Jianzhu J Ideker Trey T
Bioinformatics (Oxford, England) 20180701 13
<h4>Motivation</h4>Network propagation has been widely used to aggregate and amplify the effects of tumor mutations using knowledge of molecular interaction networks. However, propagating mutations through interactions irrelevant to cancer leads to erosion of pathway signals and complicates the identification of cancer subtypes.<h4>Results</h4>To address this problem we introduce a propagation algorithm, Network-Based Supervised Stratification (NBS2), which learns the mutated subnetworks underly ...[more]
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