PennDiff: detecting differential alternative splicing and transcription by RNA sequencing

Bioinformatics
Yu HuMingyao Li

Abstract

Alternative splicing and alternative transcription are a major mechanism for generating transcriptome diversity. Differential alternative splicing and transcription (DAST), which describe different usage of transcript isoforms across different conditions, can complement differential expression in characterizing gene regulation. However, the analysis of DAST is challenging because only a small fraction of RNA-seq reads is informative for isoforms. Several methods have been developed to detect exon-based and gene-based DAST, but they suffer from power loss for genes with many isoforms. We present PennDiff, a novel statistical method that makes use of information on gene structures and pre-estimated isoform relative abundances, to detect DAST from RNA-seq data. PennDiff has several advantages. First, grouping exons avoids multiple testing for 'exons' originated from the same isoform(s). Second, it utilizes all available reads in exon-inclusion level estimation, which is different from methods that only use junction reads. Third, collapsing isoforms sharing the same alternative exons reduces the impact of isoform expression estimation uncertainty. PennDiff is able to detect DAST at both exon and gene levels, thus offering more flex...Continue Reading

References

May 31, 2008·Biometrics·Peter X-K SongYing Yuan
Feb 27, 2009·Bioinformatics·Hui Jiang, Wing Hung Wong
Mar 18, 2009·Bioinformatics·Cole TrapnellSteven L Salzberg
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
Nov 9, 2010·Nature Methods·Yarden KatzChristopher B Burge
Apr 26, 2011·Trends in Cell Biology·Joonhee HanXiang-Dong Fu
Sep 11, 2012·Nucleic Acids Research·Thasso GriebelMichael Sammeth
Mar 2, 2013·Bioinformatics·Moritz AschoffRainer König
Mar 19, 2014·Human Molecular Genetics·Mingyao LiDwight Stambolian
Aug 21, 2014·Nature Communications·Jean MonlongRoderic Guigó
Sep 10, 2014·Nature Biotechnology·Anton Kratz, Piero Carninci
Dec 7, 2014·Proceedings of the National Academy of Sciences of the United States of America·Shihao ShenYi Xing

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Citations

Mar 7, 2019·Frontiers in Cardiovascular Medicine·Adam W TurnerClint L Miller
Dec 6, 2019·Briefings in Bioinformatics·Arfa MehmoodLaura L Elo
Jun 19, 2021·Genome Biology·Yu HuKai Wang
Sep 29, 2021·Nucleic Acids Research·Madalee G WulfIvan R Corrêa

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