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Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis

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submitted on 2024-09-01, 06:37 and posted on 2024-09-01, 06:38 authored by Navadon Khunlertgit, Byung-Jun Yoon

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.

Other Information

Published in: EURASIP Journal on Bioinformatics and Systems Biology
License: http://creativecommons.org/licenses/by/4.0
See article on publisher's website: https://dx.doi.org/10.1186/s13637-014-0019-9

Funding

Royal Thai Government (N/A).

National Science Foundation (CCF-1149544).

History

Language

  • English

Publisher

Springer Nature

Publication Year

  • 2014

License statement

This Item is licensed under the Creative Commons Attribution 4.0 International License.

Institution affiliated with

  • Hamad Bin Khalifa University
  • College of Science and Engineering - HBKU