Quantitative visualization of alternative exon expression from RNA-seq data

Yarden Katz; Eric T. Wang; Jacob Silterra; Schraga Schwartz; Bang Wong; Helga Thorvaldsdottir; James T. Robinson; Jill P. Mesirov; Edoardo M. Airoldi; Christopher B. Burge

doi:10.1093/bioinformatics/btv034

Quantitative visualization of alternative exon expression from RNA-seq data

Yarden Katz, Eric T. Wang, Jacob Silterra, Schraga Schwartz, Bang Wong, Helga Thorvaldsdottir, James T. Robinson, Jill P. Mesirov, Edoardo M. Airoldi, Christopher B. Burge

Department of Molecular Genetics

Weizmann Institute of Science

Research output: Contribution to journal › Article › peer-review

Abstract

Motivation: Analysis of RNA sequencing (RNA-Seq) data revealed that the vast majority of human genes express multiple mRNA isoforms, produced by alternative pre-mRNA splicing and other mechanisms, and that most alternative isoforms vary in expression between human tissues. As RNA-Seq datasets grow in size, it remains challenging to visualize isoform expression across multiple samples. Results: To help address this problem, we present Sashimi plots, a quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions. Sashimi plots can be made using the Broad Integrated Genome Viewer or with a stand-alone command line program.

Original language	English
Pages (from-to)	2400-2402
Number of pages	3
Journal	Bioinformatics
Volume	31
Issue number	14
DOIs	https://doi.org/10.1093/bioinformatics/btv034
State	Published - 15 Jul 2015

All Science Journal Classification (ASJC) codes

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btv034

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title = "Quantitative visualization of alternative exon expression from RNA-seq data",

abstract = "Motivation: Analysis of RNA sequencing (RNA-Seq) data revealed that the vast majority of human genes express multiple mRNA isoforms, produced by alternative pre-mRNA splicing and other mechanisms, and that most alternative isoforms vary in expression between human tissues. As RNA-Seq datasets grow in size, it remains challenging to visualize isoform expression across multiple samples. Results: To help address this problem, we present Sashimi plots, a quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions. Sashimi plots can be made using the Broad Integrated Genome Viewer or with a stand-alone command line program.",

author = "Yarden Katz and Wang, {Eric T.} and Jacob Silterra and Schraga Schwartz and Bang Wong and Helga Thorvaldsdottir and Robinson, {James T.} and Mesirov, {Jill P.} and Airoldi, {Edoardo M.} and Burge, {Christopher B.}",

year = "2015",

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doi = "10.1093/bioinformatics/btv034",

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T1 - Quantitative visualization of alternative exon expression from RNA-seq data

AU - Katz, Yarden

AU - Wang, Eric T.

AU - Silterra, Jacob

AU - Schwartz, Schraga

AU - Wong, Bang

AU - Thorvaldsdottir, Helga

AU - Robinson, James T.

AU - Mesirov, Jill P.

AU - Airoldi, Edoardo M.

AU - Burge, Christopher B.

PY - 2015/7/15

Y1 - 2015/7/15

N2 - Motivation: Analysis of RNA sequencing (RNA-Seq) data revealed that the vast majority of human genes express multiple mRNA isoforms, produced by alternative pre-mRNA splicing and other mechanisms, and that most alternative isoforms vary in expression between human tissues. As RNA-Seq datasets grow in size, it remains challenging to visualize isoform expression across multiple samples. Results: To help address this problem, we present Sashimi plots, a quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions. Sashimi plots can be made using the Broad Integrated Genome Viewer or with a stand-alone command line program.

AB - Motivation: Analysis of RNA sequencing (RNA-Seq) data revealed that the vast majority of human genes express multiple mRNA isoforms, produced by alternative pre-mRNA splicing and other mechanisms, and that most alternative isoforms vary in expression between human tissues. As RNA-Seq datasets grow in size, it remains challenging to visualize isoform expression across multiple samples. Results: To help address this problem, we present Sashimi plots, a quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions. Sashimi plots can be made using the Broad Integrated Genome Viewer or with a stand-alone command line program.

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U2 - 10.1093/bioinformatics/btv034

DO - 10.1093/bioinformatics/btv034

M3 - مقالة

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VL - 31

SP - 2400

EP - 2402

JO - Bioinformatics

JF - Bioinformatics

IS - 14

ER -

Quantitative visualization of alternative exon expression from RNA-seq data

Abstract

All Science Journal Classification (ASJC) codes

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