Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer

Liu, Qi; Chen, Chong; Shen, Enjian; Zhao, Fangqing; Sun, Zhen; Wu, Jinyu

doi:10.1016/j.ygeno.2011.12.003

Cited by 38 publications

(30 citation statements)

References 24 publications

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“…A software SplicingViewer [63] was employed to identify putative AS events in the six different developmental stages of V. dahliae that were examined in this study. This analysis tool enabled detection of potential splicing junctions and identification of seven putative types of AS events, such as skipped exons (SE), mutually exclusive exons (MXE), alternative 5′ splicing sites (A5SS), alternative 3′ splicing sites (A3SS), alternative first exons (AFE), alternative last exons (ALE) and retained intron (RI) [64].…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Deep mRNA sequencing reveals stage-specific transcriptome alterations during microsclerotia development in the smoke tree vascular wilt pathogen, Verticillium dahliae

Xiong

Wang

et al. 2014

BMC Genomics

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BackgroundVerticillium dahliae is a soil-borne fungus that causes vascular wilt diseases in a wide range of plant hosts. V. dahliae produces multicelled, melanized resting bodies, also known as microsclerotia (MS) that can survive for years in the soil. The MS are the primary source of infection of the Verticillium disease cycle. Thus, MS formation marks an important event in the disease cycle of V. dahliae.ResultsIn this study, next generation sequencing technology of RNA-Seq was employed to investigate the global transcriptomic dynamics of MS development to identify differential gene expression at several stages of MS formation in strain XS11 of V. dahliae, isolated from smoke tree. We observed large-scale changes in gene expression during MS formation, such as increased expression of genes involved in protein metabolism and carbohydrate metabolism. Genes involved in glycolytic pathway and melanin biosynthesis were dramatically up-regulated in MS. Cluster analyses revealed increased expression of genes encoding products involved in primary metabolism and stress responses throughout MS development. Differential expression of ubiquitin-dependent protein catabolism and cell death-associated genes during MS development were revealed. Homologs of genes located in the lineage-specific (LS) regions of V. dahliae strain VdLs.17, were either not expressed or showed low expression. Furthermore, alternative splicing (AS) events were analyzed, revealing that over 95.0% AS events involve retention of introns (RI).ConclusionsThese data reveal the dynamics of transcriptional regulation during MS formation and were used to construct a comprehensive high-resolution gene expression map. This map provides a key resource for understanding the biology and molecular basis of MS development of V. dahliae.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-324) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

“…Alternative splicing events were identified by SplicingViewer [63]. First, reads were aligned to the reference genome by Bwa allowing less than two mismatches [77].…”

Section: Methodsmentioning

confidence: 99%

Deep mRNA sequencing reveals stage-specific transcriptome alterations during microsclerotia development in the smoke tree vascular wilt pathogen, Verticillium dahliae

Xiong

Wang

et al. 2014

BMC Genomics

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“…Some tools provide basic analysis-wide summary plots (12,18,33) and/or expression profile plots for individual samples (12,14,34–38), but very few provide methods for directly comparing gene expression profiles between multi-sample experimental groups. Many tools provide little information to the user beyond a text file of raw test statistics (11,13,15–17).…”

Section: Methodsmentioning

confidence: 99%

Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq

2016

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Although RNA-Seq data provide unprecedented isoform-level expression information, detection of alternative isoform regulation (AIR) remains difficult, particularly when working with an incomplete transcript annotation. We introduce JunctionSeq, a new method that builds on the statistical techniques used by the well-established DEXSeq package to detect differential usage of both exonic regions and splice junctions. In particular, JunctionSeq is capable of detecting differential usage of novel splice junctions without the need for an additional isoform assembly step, greatly improving performance when the available transcript annotation is flawed or incomplete. JunctionSeq also provides a powerful and streamlined visualization toolset that allows bioinformaticians to quickly and intuitively interpret their results. We tested our method on publicly available data from several experiments performed on the rat pineal gland and Toxoplasma gondii, successfully detecting known and previously validated AIR genes in 19 out of 19 gene-level hypothesis tests. Due to its ability to query novel splice sites, JunctionSeq is still able to detect these differences even when all alternative isoforms for these genes were not included in the transcript annotation. JunctionSeq thus provides a powerful method for detecting alternative isoform regulation even with low-quality annotations. An implementation of JunctionSeq is available as an R/Bioconductor package.

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“…The Integrative Genomics Viewer that was developed by and is available from the Broad Institute is one of the most widely used tools for visualizing short-read sequence data in the context of rich annotations such as known gene models. Finally, SpliceSeq and SplicingViewer (27) are stand-alone tools that also provide visualization of results besides mapping reads, quantifying events, and differential splicing.…”

Section: Visualizing Alternative Splicingmentioning

confidence: 99%

A survey of computational methods in transcriptome-wide alternative splicing analysis

Wang

Huang³

et al. 2015

Biomolecular Concepts

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Alternative splicing is widely recognized for its roles in regulating genes and creating gene diversity. Consequently the identification and quantification of differentially spliced transcripts is pivotal for transcriptome analysis. Here, we review the currently available computational approaches for the analysis of RNA-sequencing data with a focus on exon-skipping events of alternative splicing and discuss the novelties as well as challenges faced to perform differential splicing analyses. In accordance with operational needs we have classified the software tools, which may be instrumental for a specific analysis based on the experimental objectives and expected outcomes. In addition, we also propose a framework for future directions by pinpointing more extensive experimental validation to assess the accuracy of the software predictions and improvements that would facilitate visualizations, data processing, and downstream analyses along with their associated software implementations.

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Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer

Cited by 38 publications

References 24 publications

Deep mRNA sequencing reveals stage-specific transcriptome alterations during microsclerotia development in the smoke tree vascular wilt pathogen, Verticillium dahliae

Deep mRNA sequencing reveals stage-specific transcriptome alterations during microsclerotia development in the smoke tree vascular wilt pathogen, Verticillium dahliae

Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq

A survey of computational methods in transcriptome-wide alternative splicing analysis

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