Computational analysis of muscular dystrophy sub-types using a novel integrative scheme

Chen Wang, Sook Ha, Yue Wang, Jianhua Xuan, Eric Hoffman

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

To construct biologically interpretable features and facilitate Muscular Dystrophy (MD) sub-types classification, we propose a novel integrative scheme utilizing PPI network, functional gene sets information, and mRNA profiling. The workflow of the proposed scheme includes three major steps: First, by combining protein-protein interaction network structure and gene co-expression relationship into new distance metric, we apply affinity propagation clustering to build gene sub-networks. Secondly, we further incorporate functional gene sets knowledge to complement the physical interaction information. Finally, based on constructed subnetwork and gene set features, we apply multi-class support vector machine (MSVM) for MD sub-type classification, and highlight the biomarkers contributing to the sub-type prediction. The experimental results show that our scheme could construct sub-networks that are more relevant to MD than those constructed by conventional approach. Furthermore, our integrative strategy substantially improved the prediction accuracy, especially for those hard-to-classify sub-types.

Original languageEnglish (US)
Title of host publicationProceedings - 9th International Conference on Machine Learning and Applications, ICMLA 2010
Pages287-292
Number of pages6
DOIs
StatePublished - 2010
Event9th International Conference on Machine Learning and Applications, ICMLA 2010 - Washington, DC, United States
Duration: Dec 12 2010Dec 14 2010

Publication series

NameProceedings - 9th International Conference on Machine Learning and Applications, ICMLA 2010

Other

Other9th International Conference on Machine Learning and Applications, ICMLA 2010
CountryUnited States
CityWashington, DC
Period12/12/1012/14/10

Keywords

  • Affinity propagation clustering
  • Biomarker discovery
  • Classification
  • Gene expression
  • Muscular dystrophy

ASJC Scopus subject areas

  • Computer Science Applications
  • Human-Computer Interaction

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  • Cite this

    Wang, C., Ha, S., Wang, Y., Xuan, J., & Hoffman, E. (2010). Computational analysis of muscular dystrophy sub-types using a novel integrative scheme. In Proceedings - 9th International Conference on Machine Learning and Applications, ICMLA 2010 (pp. 287-292). [5708846] (Proceedings - 9th International Conference on Machine Learning and Applications, ICMLA 2010). https://doi.org/10.1109/ICMLA.2010.49