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Genes (Basel). 2019 Aug 1;10(8). pii: E587. doi: 10.3390/genes10080587.

Deep Splicing Code: Classifying Alternative Splicing Events Using Deep Learning.

Author information

1
Department of Electronics and Information Engineering, Chonbuk National University, Jeonju 54896, Korea.
2
Department of Electronics and Information Engineering, Chonbuk National University, Jeonju 54896, Korea. hilaltayara@jbnu.ac.kr.
3
Department of Electronics and Information Engineering, Chonbuk National University, Jeonju 54896, Korea. kitchong@jbnu.ac.kr.
4
Advanced Electronics and Information Research Center, Chonbuk National University, Jeonju 54896, Korea. kitchong@jbnu.ac.kr.

Abstract

Alternative splicing (AS) is the process of combining different parts of the pre-mRNA to produce diverse transcripts and eventually different protein products from a single gene. In computational biology field, researchers try to understand AS behavior and regulation using computational models known as "Splicing Codes". The final goal of these algorithms is to make an in-silico prediction of AS outcome from genomic sequence. Here, we develop a deep learning approach, called Deep Splicing Code (DSC), for categorizing the well-studied classes of AS namely alternatively skipped exons, alternative 5'ss, alternative 3'ss, and constitutively spliced exons based only on the sequence of the exon junctions. The proposed approach significantly improves the prediction and the obtained results reveal that constitutive exons have distinguishable local characteristics from alternatively spliced exons. Using the motif visualization technique, we show that the trained models learned to search for competitive alternative splice sites as well as motifs of important splicing factors with high precision. Thus, the proposed approach greatly expands the opportunities to improve alternative splicing modeling. In addition, a web-server for AS events prediction has been developed based on the proposed method and made available at https://home.jbnu.ac.kr/NSCL/dsc.htm.

KEYWORDS:

alternative splicing; computational biology; deep learning; splicing code; splicing predictor

PMID:
31374967
DOI:
10.3390/genes10080587
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