title: Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Electrical and Computer Engineering, Texas A&M University, College Station, 77843-3128 TX USA.
authors.forename: Navadon
authors.initials: N
authors.lastname: Khunlertgit
authors.affiliation: Department of Electrical and Computer Engineering, Texas A&M University, College Station, 77843-3128 TX USA.|College of Science, Engineering, and Technology, Hamad Bin Khalifa University (HBKU), Doha, P.O. Box 5825 Qatar.
authors.forename: Byung-Jun
authors.initials: BJ
authors.lastname: Yoon
keywords: Cancer classification; Message-passing algorithm; Protein-protein interaction network; Subnetwork marker identification