Neighborhood rough set reduction-based gene selection and prioritization for gene expression profile analysis and molecular cancer classification.

Journal of Biomedicine & Biotechnology
Mei-Ling HouYing-Ke Lei

Abstract

Selection of reliable cancer biomarkers is crucial for gene expression profile-based precise diagnosis of cancer type and successful treatment. However, current studies are confronted with overfitting and dimensionality curse in tumor classification and false positives in the identification of cancer biomarkers. Here, we developed a novel gene-ranking method based on neighborhood rough set reduction for molecular cancer classification based on gene expression profile. Comparison with other methods such as PAM, ClaNC, Kruskal-Wallis rank sum test, and Relief-F, our method shows that only few top-ranked genes could achieve higher tumor classification accuracy. Moreover, although the selected genes are not typical of known oncogenes, they are found to play a crucial role in the occurrence of tumor through searching the scientific literature and analyzing protein interaction partners, which may be used as candidate cancer biomarkers.

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Citations

Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Jun MengYushi Luan

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Methods Mentioned

BETA
GTPases

Software Mentioned

ClaNC
KWRST
FARNeM
PAM
Relief
HBFSNRS
GA

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