Systematic evaluation of differential splicing tools for RNA-seq studies

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Mehmood, ArfaTurku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; Department of Physiology, University of Turku, Turku, Finland (författare)

Systematic evaluation of differential splicing tools for RNA-seq studies

Artikel/kapitelEngelska2020

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2019-12-05
Oxford University Press,2020
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LIBRIS-ID:oai:DiVA.org:oru-78549
https://urn.kb.se/resolve?urn=urn:nbn:se:oru:diva-78549URI
https://doi.org/10.1093/bib/bbz126DOI

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Språk:engelska
Sammanfattning på:engelska

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Ämneskategori:ref swepub-contenttype
Ämneskategori:art swepub-publicationtype

Anmärkningar

Funding Agencies:European Research Council (ERC)677943Academy of Finland 296801 304995 314443 310561Juvenile Diabetes Research Foundation 2-2013-32Finnish Funding Agency for Technology & Innovation (TEKES) 1877/31/2016Sigrid Juselius FoundationTurku Graduate School University of Turku Åbo Akademi University Biocenter Finland ELIXIR Finland
Differential splicing (DS) is a post-transcriptional biological process with critical, wide-ranging effects on a plethora of cellular activities and disease processes. To date, a number of computational approaches have been developed to identify and quantify differentially spliced genes from RNA-seq data, but a comprehensive intercomparison and appraisal of these approaches is currently lacking. In this study, we systematically evaluated 10 DS analysis tools for consistency and reproducibility, precision, recall and false discovery rate, agreement upon reported differentially spliced genes and functional enrichment. The tools were selected to represent the three different methodological categories: exon-based (DEXSeq, edgeR, JunctionSeq, limma), isoform-based (cuffdiff2, DiffSplice) and event-based methods (dSpliceType, MAJIQ, rMATS, SUPPA). Overall, all the exon-based methods and two event-based methods (MAJIQ and rMATS) scored well on the selected measures. Of the 10 tools tested, the exon-based methods performed generally better than the isoform-based and event-based methods. However, overall, the different data analysis tools performed strikingly differently across different data sets or numbers of samples.

Ämnesord och genrebeteckningar

TEKNIK OCH TEKNOLOGIER Industriell bioteknik Medicinsk bioteknik hsv//swe
ENGINEERING AND TECHNOLOGY Industrial Biotechnology Medical Biotechnology hsv//eng
RNA-seq
differential splicing
event-based methods
exon-based methods
isoform-based methods
splicing events

Biuppslag (personer, institutioner, konferenser, titlar ...)

Laiho, AstaTurku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland (författare)
Venäläinen, Mikko S.Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland (författare)
McGlinchey, Aidan J.,1984-Örebro universitet,Institutionen för medicinska vetenskaper,Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland(Swepub:oru)anmy (författare)
Wang, NingTurku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland (författare)
Elo, Laura L.Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland (författare)
Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; Department of Physiology, University of Turku, Turku, FinlandTurku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland (creator_code:org_t)

Sammanhörande titlar

Ingår i:Briefings in Bioinformatics: Oxford University Press21:6, s. 2052-20651467-54631477-4054

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Av författaren/redakt...: Mehmood, Arfa; Laiho, Asta; Venäläinen, Mikk ...; McGlinchey, Aida ...; Wang, Ning; Elo, Laura L.

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TEKNIK OCH TEKNOLOGIER: TEKNIK OCH TEKNO ...; och Industriell biot ...; och Medicinsk biotek ...

Artiklar i publikationen: Briefings in Bio ...

Av lärosätet: Örebro universitet

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