NDLI: Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis

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Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis

Content Provider	ACM Digital Library
Author	Yoon, Byung-Jun Khunlertgit, Navadon
Abstract	Accurate prediction of cancer prognosis based on gene expression data is generally difficult, and identifying robust prognostic markers for cancer remains a challenging problem. Recent studies have shown that modular markers, such as pathway markers and subnetwork markers, can provide better snapshots of the underlying biological mechanisms by incorporating additional biological information, thereby leading to more accurate cancer classification. In this paper, we propose a novel method for simultaneously identifying robust synergistic subnetwork markers that can accurately predict cancer prognosis. The proposed method utilizes an efficient message-passing algorithm called affinity propagation, based on which we identify groups -- or subnetworks -- of discriminative and synergistic genes, whose protein products are closely located in the protein-protein interaction (PPI) network. Unlike other existing subnetwork marker identification methods, our proposed method can simultaneously identify multiple nonoverlapping subnetwork markers that can synergistically predict cancer prognosis. Evaluation results based on multiple breast cancer datasets demonstrate that the proposed message-passing approach can identify robust subnetwork markers in the human PPI network, which have higher discriminative power and better reproducibility compared to those identified by previous methods. The identified subnetwork makers can lead to better cancer classifiers with improved overall performance and consistency across independent cancer datasets.
Starting Page	681
Ending Page	681
Page Count	1
ISBN	9781450328944
DOI	10.1145/2649387.2660826
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2014-09-20
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Protein-protein interaction network Message passing algorithm Subnetwork marker identification Cancer classification
Content Type	Text
Resource Type	Article

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