A novel gene selection method for gene expression data for the task of cancer type classification

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Abstract

Cancer is a poligenetic disease with each cancer type having a different mutation profile. Genomic data can be utilized to detect these profiles and to diagnose and differentiate cancer types. Variant calling provide mutation information. Gene expression data reveal the altered cell behaviour. The combination of the mutation and expression information can lead to accurate discrimination of different cancer types. In this study, we utilized and transferred the information of existing mutations for a novel gene selection method for gene expression data. We tested the proposed method in order to diagnose and differentiate cancer types. It is a disease specific method as both the mutations and expressions are filtered according to the selected cancer types. Our experiment results show that the proposed gene selection method leads to similar or improved performance metrics compared to classical feature selection methods and curated gene sets.

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Özcan Şimşek, N. Ö., Özgür, A., & Gürgen, F. (2021). A novel gene selection method for gene expression data for the task of cancer type classification. Biology Direct, 16(1). https://doi.org/10.1186/s13062-020-00290-3

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