tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing

Genome Biology
Lorena de la FuenteAna Conesa

Abstract

Recent advances in long-read sequencing solve inaccuracies in alternative transcript identification of full-length transcripts in short-read RNA-Seq data, which encourages the development of methods for isoform-centered functional analysis. Here, we present tappAS, the first framework to enable a comprehensive Functional Iso-Transcriptomics (FIT) analysis, which is effective at revealing the functional impact of context-specific post-transcriptional regulation. tappAS uses isoform-resolved annotation of coding and non-coding functional domains, motifs, and sites, in combination with novel analysis methods to interrogate different aspects of the functional readout of transcript variants and isoform regulation. tappAS software and documentation are available at https://app.tappas.org.

References

May 24, 1991·Science·A LupasJ Stock
Mar 29, 2001·Microscopy Research and Technique·E M KrämerK A Nave
Oct 9, 2001·Human Molecular Genetics·Ami MankodiC A Thornton
Jan 8, 2004·Genome Biology·Anton J EnrightDebora S Marks
Mar 5, 2004·The Journal of Biological Chemistry·Michelle T HarremanAnita H Corbett
Jan 20, 2005·Gene·Stefan StammHermona Soreq
Jun 28, 2005·Nucleic Acids Research·E QuevillonR Lopez
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
May 24, 2006·Human Molecular Genetics·Xiaoyan LinCharles A Thornton
May 24, 2006·Proceedings of the National Academy of Sciences of the United States of America·Pedro R RomeroA Keith Dunker
Aug 29, 2006·Genome Biology·Lauren M McIntyreSergey V Nuzhdin
Dec 5, 2006·Nucleic Acids Research·UniProt Consortium
Sep 25, 2007·Molecular Cell·Jeffrey A PleissChristine Guthrie
Jan 4, 2008·Journal of Molecular Neuroscience : MN·Olaf MaierWia Baron
Feb 5, 2008·Molecular Cell·Irina A VlasovaPaul R Bohjanen
Jul 18, 2008·Human Molecular Genetics·Isabelle GouletJocelyn Côté
Oct 31, 2008·RNA Biology·Irina A Vlasova, Paul R Bohjanen
Nov 4, 2008·Nature·Eric T WangChristopher B Burge
Mar 6, 2009·Cell Adhesion & Migration·Yasushi Shimoda, Kazutada Watanabe
Jun 13, 2009·Proceedings of the National Academy of Sciences of the United States of America·Shunichi KosugiHiroshi Yanagawa
Nov 10, 2009·FEBS Letters·Wia Baron, Dick Hoekstra
Feb 6, 2010·Genome Biology·Matthew D YoungAlicia Oshlack
Mar 4, 2010·Genome Biology·Mark D Robinson, Alicia Oshlack
Apr 9, 2010·International Journal of Biological Sciences·Hitomi YoshidaSatoru Matsuda
May 4, 2010·PloS One·David Montaner, Joaquín Dopazo
Nov 6, 2010·Nucleic Acids Research·Pier L MartelliGraziano Pesole
Nov 9, 2010·Nature Methods·Yarden KatzChristopher B Burge
Dec 25, 2010·Cell Communication and Signaling : CCS·Jonathan D NardozziGino Cingolani
Jan 15, 2011·Trends in Genetics : TIG·Joshua T Witten, Jernej Ule
Feb 4, 2011·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Roeben N MunjiSamuel J Pleasure
Oct 1, 2011·Nature Methods·Thomas Nordahl PetersenHenrik Nielsen
Oct 5, 2011·Proceedings of the National Academy of Sciences of the United States of America·Smaragda LamprianouSheila Harroch
Mar 1, 2012·Methods in Molecular Biology·Sébastien Tempel
Jun 23, 2012·Genome Research·Simon AndersWolfgang Huber
Jul 4, 2012·Molecular Cell·Jonathan D EllisBenjamin J Blencowe
Aug 23, 2012·Gene·Olga KelemenStefan Stamm
Nov 20, 2012·Journal of Neurology·Vincent HuinBernard Sablonnière
Nov 20, 2012·Nucleic Acids Research·Jose Manuel RodriguezMichael Tress
Jan 10, 2013·Nature Communications·Supriya SenNicholas J G Webster
Mar 19, 2013·Cell·Ulrich BraunschweigBenjamin J Blencowe
Mar 23, 2013·International Journal of Molecular Sciences·Yasuko Kitagishi, Satoru Matsuda
Mar 23, 2013·Genome Research·Pedro MiuraEric C Lai
Jun 19, 2013·Nature Reviews. Genetics·Ran ElkonReuven Agami
Nov 28, 2013·Nucleic Acids Research·Ana Kozomara, Sam Griffiths-Jones
Jan 5, 2014·Proceedings of the National Academy of Sciences of the United States of America·Gülsen ÇolakoğluBarbara Ranscht
Mar 29, 2014·BMC Bioinformatics·Fabian AmmanSven Findeiß
Apr 9, 2014·Molecular and Cellular Biology·Huang LiYing Feng
Jun 5, 2014·Bioinformatics·María José NuedaAna Conesa
Sep 27, 2014·Genome Research·Ulrich BraunschweigBenjamin J Blencowe
Dec 7, 2014·Proceedings of the National Academy of Sciences of the United States of America·Shihao ShenYi Xing
Dec 18, 2014·Nucleic Acids Research·Peter V HornbeckElzbieta Skrzypek
Dec 23, 2014·Nature Reviews. Molecular Cell Biology·Peter E Wright, H Jane Dyson
Jan 27, 2015·Bioinformatics·Loredana Le PeraAnna Tramontano
Jan 30, 2015·Wiley Interdisciplinary Reviews. RNA·Benjamin Cieply, Russ P Carstens
Feb 6, 2015·BMC Genomics·Yu-Cheng T YangZhi John Lu
Jul 18, 2015·Nucleic Acids Research·Sonia TarazonaAna Conesa
Aug 1, 2015·Nature Methods·Harsh Dweep, Norbert Gretz
Aug 13, 2015·ELife·Vikram AgarwalDavid P Bartel
Sep 24, 2015·Nature Reviews. Molecular Cell Biology·Søren Lykke-Andersen, Torben Heick Jensen
Nov 25, 2015·Nature Reviews. Genetics·Marina M Scotti, Maurice S Swanson
Feb 7, 2016·The Journal of Biological Chemistry·Alaji Bah, Julie D Forman-Kay
Mar 13, 2016·International Journal of Developmental Neuroscience : the Official Journal of the International Society for Developmental Neuroscience·Sika Zheng
Mar 25, 2016·Molecular Biology of the Cell·Woan-Yuh TarnIng-Ming Chiu
Nov 4, 2016·Nature Reviews. Molecular Cell Biology·Bin Tian, James L Manley
Oct 1, 2016·Cell Death and Differentiation·Maria Paola ParonettoClaudio Sette
Oct 8, 2016·Trends in Biochemical Sciences·Michael TressAlfonso Valencia
Mar 17, 2017·Genome Biology·Robert MiddletonWilliam Ritchie
Apr 20, 2017·Genome Research·Léon-Charles TrancheventDidier Auboeuf
May 10, 2017·Trends in Biochemical Sciences·Michael TressAlfonso Valencia
May 11, 2017·Nature Reviews. Molecular Cell Biology·Francisco E Baralle, Jimena Giudice
Aug 31, 2017·Cell Reports·Héctor Climente-GonzálezEduardo Eyras
Dec 16, 2017·Molecular Systems Biology·Klas HatjeMartin Kollmar
Mar 17, 2018·Nucleic Acids Research·Zhiyi QinYi Xing
Apr 13, 2018·BMC Bioinformatics·Ali OghabianMikko J Frilander
May 18, 2018·Journal of Cell Science·R Eric BlueJimena Giudice
Jun 8, 2018·Nature Communications·Sebastien M Weyn-VanhentenryckChaolin Zhang
Jun 20, 2018·Proceedings of the National Academy of Sciences of the United States of America·Yukio KuriharaMinami Matsui
Jul 20, 2018·G3 : Genes - Genomes - Genetics·Jeremy R B NewmanLauren M McIntyre
Jul 22, 2018·Annual Review of Cell and Developmental Biology·Elisabetta Furlanis, Peter Scheiffele
Nov 6, 2018·Nature Communications·Kristoffer SahlinPaul Medvedev
Nov 10, 2018·Nature Reviews. Neuroscience·Samie R Jaffrey, Miles F Wilkinson
Dec 6, 2018·Frontiers in Molecular Neuroscience·Yi-An ChenJin-Wu Tsai
Jan 31, 2020·Molecular Cell·Thomas Gonatopoulos-PournatzisBenjamin J Blencowe

Related Concepts

Genetic Engineering
Introns
Computer Software
Site
Protein Isoforms
Gene Expression Profiling
Analysis
Post-Transcriptional Regulation
Protein Domain
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