Using gene pair combinations to improve the accuracy of the PAM classifier

Pankaj Chopra, Jaewoo Kang, Jinseung Lee

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

1 Citation (Scopus)

Abstract

Various classification methods have been used to predict the class of tissue samples based on gene expression data. Prediction Analysis for Microarrays (PAM) is one of the top classifiers that has been extensively used for cancer classification. In this paper a novel method of combining expression data from gene pairs is used to improve the overall accuracy of PAM. Recent studies suggest that deregulation of pathways, rather than individual genes, may be critical in triggering carcinogenesis. The pathway deregulation is often caused by the simultaneous deregulation of more than one genes in the pathway. Robust gene pair combinations may exploit these underlying bio-molecular reactions to provide better biomarkers for cancer, as compared to single genes. In this work, we used gene pair combinations, called doublets, to improve the accuracy of PAM. We validated the proposed approach with nine cancer datasets. The accuracy of PAM, using these doublets, increased consistently across these datasets, in some cases with a significant margin (13%).

Original languageEnglish
Title of host publication2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009
Pages174-177
Number of pages4
DOIs
Publication statusPublished - 2009 Dec 1
Event2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009 - Washington, D.C., United States
Duration: 2009 Nov 12009 Nov 4

Publication series

Name2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009

Other

Other2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009
CountryUnited States
CityWashington, D.C.
Period09/11/109/11/4

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Keywords

  • Cancer classification
  • Doublets
  • Gene pairs
  • Microarray
  • PAM

ASJC Scopus subject areas

  • Artificial Intelligence
  • Software
  • Biomedical Engineering
  • Health Informatics

Cite this

Chopra, P., Kang, J., & Lee, J. (2009). Using gene pair combinations to improve the accuracy of the PAM classifier. In 2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009 (pp. 174-177). [5341823] (2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009). https://doi.org/10.1109/BIBM.2009.47