• Identification of certain cancer-mediating genes using Gaussian fuzzy cluster validity index

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      https://www.ias.ac.in/article/fulltext/jbsc/040/04/0741-0754

    • Keywords

       

      Biochemical pathways; clustering; fuzzy sets; gene expression; GO-attributes

    • Abstract

       

      In this article, we have used an index, called Gaussian fuzzy index (GFI), recently developed by the authors, based on the notion of fuzzy set theory, for validating the clusters obtained by a clustering algorithm applied on cancer gene expression data. GFI is then used for the identification of genes that have altered quite significantly from normal state to carcinogenic state with respect to their mRNA expression patterns. The effectiveness of the methodology has been demonstrated on three gene expression cancer datasets dealing with human lung, colon and leukemia. The performance of GFI is compared with 19 exiting cluster validity indices. The results are appropriately validated biologically and statistically. In this context, we have used biochemical pathways, 𝑝-value statistics of GO attributes, 𝑡-test and 𝑧-score for the validation of the results. It has been reported that GFI is capable of identifying high-quality enriched clusters of genes, and thereby is able to select more cancer-mediating genes.

    • Author Affiliations

       

      Anupam Ghosh1 Rajat K De2

      1. Department of Computer Science and Engineering, Netaji Subhash Engineering College, Kolkata, India
      2. Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India
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