2lpiRNApred: a two-layered integrated algorithm for identifying piRNAs and their functions based on LFE-GM feature selection.

RNA Biology
Yun ZuoXiangrong Liu

Abstract

Piwi-interacting RNAs (piRNAs) are indispensable in the transposon silencing, including in germ cell formation, germline stem cell maintenance, spermatogenesis, and oogenesis. piRNA pathways are amongst the major genome defence mechanisms, which maintain genome integrity. They also have important functions in tumorigenesis, as indicated by aberrantly expressed piRNAs being recently shown to play roles in the process of cancer development. A number of computational methods for this have recently been proposed, but they still have not yielded satisfactory predictive performance. Moreover, only one computational method that identifies whether piRNAs function in inducting target mRNA deadenylation been reported in the literature. In this study, we developed a two-layered integrated classifier algorithm, 2lpiRNApred. It identifies piRNAs in the first layer and determines whether they function in inducting target mRNA deadenylation in the second layer. A new feature selection algorithm, which was based on Luca fuzzy entropy and Gaussian membership function (LFE-GM), was proposed to reduce the dimensionality of the features. Five feature extraction strategies, namely, Kmer, General parallel correlation pseudo-dinucleotide composition,...Continue Reading

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Citations

Apr 23, 2021·Interdisciplinary Sciences, Computational Life Sciences·Yajun LiuXinhong Hei
Aug 28, 2021·International Journal of Molecular Sciences·Muhammad Nabeel AsimSheraz Ahmed
Oct 29, 2021·Biopolymers·Hongliang ZouZhijian Yin

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Methods Mentioned

BETA
feature extraction

Software Mentioned

CarSite
2lpiRNApred
piRNN
Pse
Matlab
NONCODE
WE
in
SVMMRBF3
Piano

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