An optimized cluster validity index for identification of cancer mediating genes

Abstract

One of the major challenges in bioinformatics lies in identification of modified gene expressions of an affected person due to medical ailments. Focused research has been observed till date in such identification, leading to multiple proposals pivoting in clustering of gene expressions. Moreover, while clustering proves to be an effective way to demarcate the affected gene expression vectors, there has been global research on the cluster count that optimizes the gene expression variations among the clusters. This study proposes a new index called mean-max index (MMI) to determine the cluster count which divides the data collection into ideal number of clusters depending on gene expression variations. MMI works on the principle of minimization of the intra cluster variations among the members and maximization of inter cluster variations. In this regard, the study has been conducted on publicly available dataset comprising of gene expressions for three diseases, namely lung disease, leukaemia, and colon cancer. The data count for normal as well as diseased patients lie at 10 and 86 for lung disease patients, 43 and 13 for patients observed with leukaemia, and 18 and 18 for patients with colon cancer respectively. The gene expression vectors for the three diseases comprise of 7129,22283, and 6600 respectively. Three clustering models have been used for this study, namely k-means, partition around medoid, and fuzzy c-means, all using the proposed MMI technique for finalizing the cluster count. The Comparative analysis reflects that the proposed MMI index is able to recognize much more true positives (biologically enriched) cancer mediating genes with respect to other cluster validity indices and it can be considered as superior to other with respect to enhanced accuracy by 85%.