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. 2015 Jul 15;31(14):2400-2.
doi: 10.1093/bioinformatics/btv034. Epub 2015 Jan 22.

Quantitative visualization of alternative exon expression from RNA-seq data

Yarden Katz  1 , Eric T Wang  2 , Jacob Silterra  3 , Schraga Schwartz  3 , Bang Wong  3 , Helga Thorvaldsdóttir  3 , James T Robinson  3 , Jill P Mesirov  3 , Edoardo M Airoldi  4 , Christopher B Burge  5
Affiliations

Quantitative visualization of alternative exon expression from RNA-seq data (V体育安卓版)

VSports - Yarden Katz et al. Bioinformatics. .

"VSports手机版" 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. VSports手机版.

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. V体育安卓版.

Availability and implementation: Software code and documentation freely available here: http://miso. readthedocs. org/en/fastmiso/sashimi. html V体育ios版.

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Figures

Fig. 1.
Fig. 1.
(A) Anatomy of a Sashimi plot. Gene model annotation containing two isoforms differing by inclusion/exclusion of middle exon. Sashimi plot for the two grey exons (blue boxed region) is shown, where genomic reads are converted into read densities (per-base expression on y-axis) and junction reads are plotted as arcs whose width is proportional to the number of reads aligned to the junction spanning the exons connected by arc. Genomic coordinates are shown on x-axis. (B) Inputs required for making a Sashimi plot. Gene model annotations (in GFF format), RNA-Seq read alignments (BAM format) and optionally isoform expression estimates (by MISO) are used to make Sashimi plots. Sashimi plots can be made with a stand-alone program that makes customizable publication quality figures, or dynamically from the IGV browser
Fig. 2.
Fig. 2.
(A) Sashimi plot (stand-alone) for alternatively spliced exon and flanking exons in four samples (colored by experimental condition). Per-base expression is plotted on y-axis of Sashimi plot, genomic coordinates on x-axis, and mRNA isoforms quantified are shown on bottom (exons in black, introns as lines with arrow heads). (B) Optional display of isoform expression information produced by MISO. Posterior distributions over Ψ values are shown as histograms (Ψ values on x-axis, frequency on y-axis). (C) Genomic region of interest in IGV along with two alignment tracks (top). (D) Sashimi plot for region shown in (C). Genomic coordinates are plotted on x-axis and read density (whose value is configurable via IGV) on y-axis
See this image and copyright information in PMC

References

    1. Katz Y., et al. (2010) Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat. Methods , 7, 1009–1015. - PMC - PubMed
    1. Katz Y., et al. (2013) Sashimi plots: quantitative visualization of RNA sequencing read alignments. arXiv, manuscript no. 1306.3466.
    1. Kent J.W., et al. (2002) The human genome browser at UCSC. Genome Res. , 12, 996–1006. - PMC - PubMed
    1. Pan Q., et al. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. , 40, 1413–1415. - PubMed
    1. Stein L. (2010) Generic feature format, Version 3. V体育平台登录 - http://www.sequenceontology.org/gff3.shtml2.

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