title: Computational Analysis of Muscular Dystrophy Sub-types Using A Novel Integrative Scheme.
abstract: To construct biologically interpretable gene sets for muscular dystrophy (MD) sub-type classification, we propose a novel computational scheme to integrate protein-protein interaction (PPI) network, functional gene set information, and mRNA profiling data. The workflow of the proposed scheme includes the following three major steps: firstly, we apply an affinity propagation clustering (APC) approach to identify gene sub-networks associated with each MD sub-type, in which a new distance metric is proposed for APC to combine PPI network information and gene-gene co-expression relationship; secondly, we further incorporate functional gene set knowledge, which complements the physical PPI information, into our scheme for biomarker identification; finally, based on the constructed sub-networks and gene set features, we apply multi-class support vector machines (MSVMs) for MD sub-type classification, with which to highlight the biomarkers contributing to sub-type prediction. The experimental results show that our scheme can help identify sub-networks and gene sets that are more relevant to MD than those constructed by other conventional approaches. Moreover, our integrative strategy improves the prediction accuracy substantially, especially for those 'hard-to-classify' sub-types.
authors: Department of Electrical and Computer Engineering Virginia Polytechnic Institute and State University Arlington, Virginia, U.S.A.
authors: Chen
authors: C
authors: Wang
authors: Sook
authors: S
authors: Ha
authors: Jianhua
authors: J
authors: Xuan
authors: Yue
authors: Y
authors: Wang
authors: Eric
authors: E
authors: Hoffman