Systematic evaluation of differential splicing tools for RNA-seq studies

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Fältnamn	Indikatorer	Metadata
000		04268naa a2200457 4500
001		oai:DiVA.org:oru-78549
003		SwePub
008		191213s2020 \| \|\|\|\|\|\|\|\|\|\|\|000 \|\|eng\|
024	7	a https://urn.kb.se/resolve?urn=urn:nbn:se:oru:diva-785492 URI
024	7	a https://doi.org/10.1093/bib/bbz1262 DOI
040		a (SwePub)oru
041		a engb eng
042		9 SwePub
072	7	a ref2 swepub-contenttype
072	7	a art2 swepub-publicationtype
100	1	a Mehmood, Arfau Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; Department of Physiology, University of Turku, Turku, Finland4 aut
245	1 0	a Systematic evaluation of differential splicing tools for RNA-seq studies
264		c 2019-12-05
264	1	b Oxford University Press,c 2020
338		a print2 rdacarrier
500		a 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
520		a 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.
650	7	a TEKNIK OCH TEKNOLOGIERx Industriell bioteknikx Medicinsk bioteknik0 (SwePub)209082 hsv//swe
650	7	a ENGINEERING AND TECHNOLOGYx Industrial Biotechnologyx Medical Biotechnology0 (SwePub)209082 hsv//eng
653		a RNA-seq
653		a differential splicing
653		a event-based methods
653		a exon-based methods
653		a isoform-based methods
653		a splicing events
700	1	a Laiho, Astau Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland4 aut
700	1	a Venäläinen, Mikko S.u Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland4 aut
700	1	a McGlinchey, Aidan J.,d 1984-u Örebro universitet,Institutionen för medicinska vetenskaper,Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland4 aut0 (Swepub:oru)anmy
700	1	a Wang, Ningu Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland4 aut
700	1	a Elo, Laura L.u Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland4 aut
710	2	a Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; Department of Physiology, University of Turku, Turku, Finlandb Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland4 org
773	0	t Briefings in Bioinformaticsd : Oxford University Pressg 21:6, s. 2052-2065q 21:6<2052-2065x 1467-5463x 1477-4054
856	4	u https://doi.org/10.1093/bib/bbz126y Fulltext
856	4	u https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbz126/31221141/bbz126.pdf
856	4 8	u https://urn.kb.se/resolve?urn=urn:nbn:se:oru:diva-78549
856	4 8	u https://doi.org/10.1093/bib/bbz126

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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 ...

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Av lärosätet: Örebro universitet

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