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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2018.00433

Classifying included and excluded exons in exon skipping event using histone modifications

 Wei Chen1*, pengmian Feng2,  Hui Ding3 and  Hao Lin3
  • 1North China University of Science and Technology, China
  • 2North China Institute of Science and Technology, China
  • 3University of Electronic Science and Technology of China, China

Alternative splicing (AS) not only ensures the diversity of gene expression products, but also closely correlated with genetic diseases. Therefore, knowledge about regulatory mechanisms of AS will provide useful clues for understanding its biological functions. In the current study, a random forest based method was developed to classify included and excluded exons in exon skipping event. In this method, the samples in the dataset were encoded by using optimal histone modification features which were optimized by using the Maximum Relevance Maximum Distance (MRMD) feature selection technique. The proposed method obtained an accuracy of 72.91% in 10-fold cross validation test and outperformed existing methods. Meanwhile, we also systematically analyzed the distribution of histone modifications between included and excluded exons and discovered their preference in both kinds of exons, which might provide insights into researches on the regulatory mechanisms of alternative splicing.

Keywords: Alternative Splicing, exon skipping, Histone Methylation, histone acetylation, random forest

Received: 30 Jul 2018; Accepted: 12 Sep 2018.

Edited by:

Arun Kumar Sangaiah, VIT University, India

Reviewed by:

Hongbo Liu, University of Pennsylvania, United States
Juexin Wang, University of Missouri, United States  

Copyright: © 2018 Chen, Feng, Ding and Lin. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Wei Chen, North China University of Science and Technology, Tangshan, China, chenweiimu@gmail.com