Identifying Drug Resistant miRNAs Using Entropy Based Ranking

• Published in: IEEE/ACM transactions on computational biology and bioinformatics 2021-05, Vol.18 (3), p.973-984
• Main Authors: Pal, Jayanta Kumar, Ray, Shubhra Sankar, Pal, Sankar K.
• Format: Article
• Language: English
• Subjects: <inline-formula xmlns:ali="http://www.niso.org/schemas/ali/1.0/" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> <tex-math notation="LaTeX"> mathbf {Z^+}</tex-math> <mml:math> <mml:msup> <mml:mi mathvariant="bold">Z</mml:mi> <mml:mo>+</mml:mo> </mml:msup> </mml:math> <inline-graphic xlink:href="pal-ieq3-2933205.gif" xlink:type="simple"/> </inline-formula> number; Algorithms; bioinformatics; Cancer; Computational Biology - methods; Confidence intervals; Databases, Genetic; DNA; Drug resistance; Drug Resistance, Neoplasm - genetics; Drugs; Entropy; Fuzzy Logic; fuzzy set; Fuzzy sets; Granular materials; granular probability; histogram; Histograms; Humans; Immune system; MicroRNAs - genetics; miRNA; Neoplasms - genetics; Source code; Statistical analysis; Support vector machines
• ISSN: 1545-5963; 1557-9964
• DOI: 10.1109/TCBB.2019.2933205

MicroRNAs play an important role in controlling drug sensitivity and resistance in cancer. Identification of responsible miRNAs for drug resistance can enhance the effectiveness of treatment. A new set theoretic entropy measure (SPEM) is defined to determine the relevance and level of confidence of miRNAs in deciding their drug resistant nature. Here, a pattern is represented by a pair of values. One of them implies the degree of its belongingness (fuzzy membership) to a class and the other represents the actual class of origin (crisp membership). A measure, called granular probability, is defined that determines the confidence level of having a particular pair of membership values. The granules used to compute the said probability are formed by a histogram based method where each bin of a histogram is considered as one granule. The width and number of the bins are automatically determined by the algorithm. The set thus defined, comprising a pair of membership values and the confidence level for having them, is used for the computation of SPEM and thereby identifying the drug resistant miRNAs. The efficiency of SPEM is demonstrated extensively on six data sets. While the achieved F F -score in classifying sensitive and resistant samples ranges between 0.31 & 0.50 using all the miRNAs by SVM classifier, the same score varies from 0.67 to 0.94 using only the top 1 percent drug resistant miRNAs. Superiority of the proposed method as compared to some existing ones is established in terms of F F -score. The significance of the top 1 percent miRNAs in corresponding cancer is also verified by the different articles based on biological investigations. Source code of SPEM is available at http://www.jayanta.droppages.com/SPEM.html .