The Usage of Exon-Exon Splice Junctions for the Detection of Alternative Splicing using the REIDS model

Scientific Reports
Marijke Van MoerbekeZiv Shkedy

Abstract

Alternative gene splicing is a common phenomenon in which a single gene gives rise to multiple transcript isoforms. The process is strictly guided and involves a multitude of proteins and regulatory complexes. Unfortunately, aberrant splicing events have been linked to genetic disorders. Therefore, understanding mechanisms of alternative splicing regulation and differences in splicing events between diseased and healthy tissues is crucial in advancing personalized medicine and drug developments. We propose a linear mixed model, Random Effects for the Identification of Differential Splicing (REIDS), for the identification of alternative splicing events using Human Transcriptome Arrays (HTA). For each exon, a splicing score is calculated based on two scores, an exon score and an array score. The junction information is used to rank the identified exons from strongly confident to less confident candidates for alternative splicing. The design of junctions was also discussed to highlight the complexity of exon-exon and exon-junction interactions. Based on a list of Rt-PCR validated probe sets, REIDS outperforms AltAnalyze and iGems in the % recall rate.

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Citations

Aug 11, 2021·Molecular Reproduction and Development·David Cornet-BartoloméRita Vassena

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Datasets Mentioned

BETA
JUC0100236573
PSR010025632
JUC0100236756
PSR010025634
PSR010025633
PSR080007308

Methods Mentioned

BETA
RNASeq

Software Mentioned

R
mathrm
Ensembl
REIDScon
REIDS
R package aroma
RASA
affymetrix
iGEMS
DEXSeq

Related Concepts

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Alternative splicing

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