Minimizing Redundancy Among Genes Selected Based on the Overlapping Analysis

  • Osama MahmoudEmail author
  • Andrew Harrison
  • Asma Gul
  • Zardad Khan
  • Metodi V. Metodiev
  • Berthold Lausen
Conference paper
Part of the Studies in Classification, Data Analysis, and Knowledge Organization book series (STUDIES CLASS)


For many functional genomic experiments, identifying the most characterizing genes is a main challenge. Both the prediction accuracy and interpretability of a classifier could be enhanced by performing the classification based only on a set of discriminative genes. Analyzing overlapping between gene expression of different classes is an effective criterion for identifying relevant genes. However, genes selected according to maximizing a relevance score could have rich redundancy. We propose a scheme for minimizing selection redundancy, in which the Proportional Overlapping Score (POS) technique is extended by using a recursive approach to assign a set of complementary discriminative genes. The proposed scheme exploits the gene masks defined by POS to identify more integrated genes in terms of their classification patterns. The approach is validated by comparing its classification performance with other feature selection methods, Wilcoxon Rank Sum, mRMR, MaskedPainter and POS, for several benchmark gene expression datasets using three different classifiers: Random Forest; k Nearest Neighbour; Support Vector Machine. The experimental results of classification error rates show that our proposal achieves a better performance.


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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Osama Mahmoud
    • 1
    • 2
    Email author
  • Andrew Harrison
    • 1
  • Asma Gul
    • 1
    • 3
  • Zardad Khan
    • 1
  • Metodi V. Metodiev
    • 4
  • Berthold Lausen
    • 1
  1. 1.Department of Mathematical SciencesUniversity of EssexColchesterUK
  2. 2.Department of Applied StatisticsHelwan UniversityCairoEgypt
  3. 3.Department of StatisticsShaheed Benazir Bhutto Women University PeshawarKhyber PukhtoonkhwaPakistan
  4. 4.School of Biological Sciences/Proteomics UnitUniversity of EssexColchesterUK

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