Affiliations: Center for Soft Computing Research, Indian Statistical Institute, 203 B. T. Road, Kolkata- 700108, India. jkp_it08@isical.ac.in; shubhra@isical.ac.in; sankar@isical.ac.in
Note: [] Address for correspondence: Center for Soft Comp. Res., Indian Statistical Institute, 203 B. T. Road, Kolkata- 700108, India
Note: [] Also works: Center for Soft Computing Research, Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India
Note: [] Also works: Center for Soft Computing Research, Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India
Abstract: MicroRNAs (miRNA) are one kind of non-coding RNA which play many important roles in eukaryotic cell. Investigations on miRNAs show that miRNAs are involved in cancer development in animal body. In this article, a threshold based method to check the condition (normal or cancer) of miRNAs of a given sample/patient, using weighted average distance between the normal and cancer miRNA expressions, is proposed. For each miRNA, the city block distance between two representatives, corresponding to scaled normal and cancer expressions, is obtained. The average of all such distances for different miRNAs is weighted by a factor, to generate the threshold. The weight factor, which is cancer dependent, is determined through an exhaustive search by maximizing the F score during training. In a part of the investigation, a ranking algorithm for cancer specific miRNAs is also discussed. The performance of the proposed method is evaluated in terms of Matthews Correlation Coefficient (MCC) and by plotting points (1 – Specificity vs: Sensitivity) in Receiver Operating Characteristic (ROC) space, besides the F score. Its efficiency is demonstrated on breast, colorectal, melanoma lung, prostate and renal cancer data sets and it is observed to be superior to some of the existing classifiers in terms of the said indices.
Keywords: miRNA expression analysis, cancer detection, pattern recognition, bioinformatics
