{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T07:08:01Z","timestamp":1773644881709,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1008287","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,10,15]],"date-time":"2020-10-15T00:00:00Z","timestamp":1602720000000}}],"reference-count":48,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2020,10,5]],"date-time":"2020-10-05T00:00:00Z","timestamp":1601856000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","award":["2 U41 HG007234"],"award-info":[{"award-number":["2 U41 HG007234"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1008287","type":"journal-article","created":{"date-parts":[[2020,10,5]],"date-time":"2020-10-05T17:59:53Z","timestamp":1601920793000},"page":"e1008287","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":77,"title":["An analysis of tissue-specific alternative splicing at the protein level"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9948-5073","authenticated-orcid":true,"given":"Jose Manuel","family":"Rodriguez","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7688-6045","authenticated-orcid":true,"given":"Fernando","family":"Pozo","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2887-815X","authenticated-orcid":true,"given":"Tomas","family":"di Domenico","sequence":"additional","affiliation":[]},{"given":"Jesus","family":"Vazquez","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9046-6370","authenticated-orcid":true,"given":"Michael L.","family":"Tress","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2020,10,5]]},"reference":[{"key":"pcbi.1008287.ref001","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1038\/nature07509","article-title":"Alternative isoform regulation in human tissue transcriptomes","volume":"456","author":"E Wang","year":"2008","journal-title":"Nature"},{"key":"pcbi.1008287.ref002","doi-asserted-by":"crossref","first-page":"1593","DOI":"10.1126\/science.1228186","article-title":"Evolutionary dynamics of gene and isoform regulation in Mammalian tissues","volume":"338","author":"J Merkin","year":"2012","journal-title":"Science"},{"key":"pcbi.1008287.ref003","doi-asserted-by":"crossref","first-page":"D766","DOI":"10.1093\/nar\/gky955","article-title":"GENCODE reference annotation for the human and mouse genomes","volume":"47","author":"A Frankish","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008287.ref004","first-page":"10940","article-title":"Revealing missing human protein isoforms based on ab initio prediction","volume":"5","author":"Z Hu","year":"2015","journal-title":"RNA-seq and proteomics. Sci Rep"},{"key":"pcbi.1008287.ref005","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1186\/s13059-018-1590-2","article-title":"CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise","volume":"19","author":"M Pertea","year":"2018","journal-title":"Genome Biol"},{"key":"pcbi.1008287.ref006","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1016\/j.cell.2016.01.029","article-title":"Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing","volume":"164","author":"X Yang","year":"2016","journal-title":"Cell"},{"key":"pcbi.1008287.ref007","doi-asserted-by":"crossref","first-page":"R70","DOI":"10.1186\/gb-2013-14-7-r70","article-title":"Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene","volume":"14","author":"M Gonz\u00e0lez-Porta","year":"2013","journal-title":"Genome Biol"},{"key":"pcbi.1008287.ref008","doi-asserted-by":"crossref","first-page":"15377","DOI":"10.1073\/pnas.1307202110","article-title":"Drift and conservation of differential exon usage across tissues in primate species","volume":"110","author":"A Reyes","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1008287.ref009","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1016\/j.molcel.2012.05.039","article-title":"Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks","volume":"46","author":"M Buljan","year":"2012","journal-title":"Mol Cell"},{"key":"pcbi.1008287.ref010","doi-asserted-by":"crossref","first-page":"e1005717","DOI":"10.1371\/journal.pcbi.1005717","article-title":"Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing.","volume":"13","author":"MA Ghadie","year":"2017","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1008287.ref011","doi-asserted-by":"crossref","first-page":"660","DOI":"10.1126\/science.aaa0355","article-title":"Human genomics. The human transcriptome across tissues and individuals","volume":"348","author":"M Mel\u00e9","year":"2015","journal-title":"Science"},{"key":"pcbi.1008287.ref012","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1093\/nar\/gkx1165","article-title":"Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues","volume":"46","author":"A Reyes","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008287.ref013","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.gene.2012.07.083","article-title":"Function of alternative splicing","volume":"514","author":"O Kelemen","year":"2013","journal-title":"Gene"},{"key":"pcbi.1008287.ref014","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1186\/s12864-018-5013-2","article-title":"Systematic evaluation of isoform function in literature reports of alternative splicing","volume":"19","author":"SA Bhuiyan","year":"2018","journal-title":"BMC Genomics"},{"key":"pcbi.1008287.ref015","doi-asserted-by":"crossref","first-page":"1880","DOI":"10.1021\/pr501286b","article-title":"Most highly expressed protein-coding genes have a single dominant isoform","volume":"14","author":"I Ezkurdia","year":"2015","journal-title":"J Proteome Res"},{"key":"pcbi.1008287.ref016","doi-asserted-by":"crossref","first-page":"2265","DOI":"10.1093\/molbev\/mss100","article-title":"Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function","volume":"29","author":"I Ezkurdia","year":"2012","journal-title":"Mol Biol Evol"},{"key":"pcbi.1008287.ref017","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1038\/nsmb.3317","article-title":"The ribosome-engaged landscape of alternative splicing","volume":"23","author":"RJ Weatheritt","year":"2016","journal-title":"Nat Struct Mol Biol"},{"key":"pcbi.1008287.ref018","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1186\/s13059-018-1451-z","article-title":"Post-translational buffering leads to convergent protein expression levels between primates","volume":"19","author":"SH Wang","year":"2018","journal-title":"Genome Biol"},{"key":"pcbi.1008287.ref019","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1016\/j.tibs.2016.09.005","article-title":"The ribosome as a platform for mRNA and nascent polypeptide quality control","volume":"42","author":"T Inada","year":"2017","journal-title":"Trends Biochem Sci."},{"key":"pcbi.1008287.ref020","doi-asserted-by":"crossref","first-page":"D213","DOI":"10.1093\/nar\/gkx997","article-title":"Rodriguez-Rivas J, Di Domenico T, V\u00e1zquez J, Valencia A, Tress ML. APPRIS 2017: principal isoforms for multiple gene sets","volume":"46","author":"JM Rodriguez","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008287.ref021","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1038\/nature13302","article-title":"A draft map of the human proteome","volume":"509","author":"MS Kim","year":"2014","journal-title":"Nature"},{"key":"pcbi.1008287.ref022","doi-asserted-by":"crossref","first-page":"11778","DOI":"10.1038\/ncomms11778","article-title":"Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow","volume":"7","author":"JC Wright","year":"2016","journal-title":"Nat Commun"},{"key":"pcbi.1008287.ref023","doi-asserted-by":"crossref","first-page":"e1004325","DOI":"10.1371\/journal.pcbi.1004325","article-title":"Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level.","volume":"11","author":"F Abascal","year":"2015","journal-title":"PLoS Comput Biol."},{"key":"pcbi.1008287.ref024","doi-asserted-by":"crossref","first-page":"3751","DOI":"10.1016\/j.celrep.2019.11.026","article-title":"Splice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome","volume":"29","author":"E Lau","year":"2019","journal-title":"Cell Rep"},{"key":"pcbi.1008287.ref025","doi-asserted-by":"crossref","first-page":"e1001229","DOI":"10.1371\/journal.pbio.1001229","article-title":"Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution","volume":"10","author":"RK Bradley","year":"2012","journal-title":"PLoS Biol"},{"key":"pcbi.1008287.ref026","doi-asserted-by":"crossref","first-page":"2661","DOI":"10.1093\/hmg\/10.23.2661","article-title":"Origin of alternative splicing by tandem exon duplication","volume":"10","author":"FA Kondrashov","year":"2001","journal-title":"Hum Mol Genet"},{"key":"pcbi.1008287.ref027","doi-asserted-by":"crossref","first-page":"8390","DOI":"10.1073\/pnas.0507916103","article-title":"Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms","volume":"103","author":"PR Romero","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1008287.ref028","doi-asserted-by":"crossref","first-page":"5866","DOI":"10.1093\/hmg\/ddu309","article-title":"Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes","volume":"23","author":"I Ezkurdia","year":"2014","journal-title":"Hum Mol Genet"},{"key":"pcbi.1008287.ref029","doi-asserted-by":"crossref","first-page":"7070","DOI":"10.1093\/nar\/gky587","article-title":"Loose ends: almost one in five human genes still have unresolved coding status","volume":"46","author":"F Abascal","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008287.ref030","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1038\/msb.2011.81","article-title":"Deep proteome and transcriptome mapping of a human cancer cell line","volume":"7","author":"N Nagaraj","year":"2011","journal-title":"Mol Syst Biol"},{"key":"pcbi.1008287.ref031","doi-asserted-by":"crossref","first-page":"1260419","DOI":"10.1126\/science.1260419","article-title":"Tissue-based map of the human proteome","volume":"347","author":"M Uhl\u00e9n","year":"2015","journal-title":"Science"},{"key":"pcbi.1008287.ref032","doi-asserted-by":"crossref","first-page":"884","DOI":"10.1016\/j.molcel.2012.05.037","article-title":"Tissue-specific alternative splicing remodels protein-protein interaction networks","volume":"46","author":"JD Ellis","year":"2012","journal-title":"Mol Cell"},{"key":"pcbi.1008287.ref033","doi-asserted-by":"crossref","first-page":"20333","DOI":"10.1073\/pnas.0809045105","article-title":"A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart","volume":"105","author":"A Kalsotra","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1008287.ref034","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/nrn.2016.27","article-title":"The neurogenetics of alternative splicing","volume":"17","author":"CK Vuong","year":"2016","journal-title":"Nat Rev Neurosci"},{"key":"pcbi.1008287.ref035","doi-asserted-by":"crossref","first-page":"715","DOI":"10.1038\/nrg3052","article-title":"Functional consequences of developmentally regulated alternative splicing","volume":"12","author":"A Kalsotra","year":"2011","journal-title":"Nat Rev Genet"},{"key":"pcbi.1008287.ref036","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1007\/s12265-013-9482-z","article-title":"The alternative heart: impact of alternative splicing in heart disease","volume":"6","author":"E Lara-Pezzi","year":"2013","journal-title":"J Cardiovasc Transl Res"},{"key":"pcbi.1008287.ref037","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1016\/j.neuron.2018.01.020","article-title":"Rbfox Splicing Factors Promote Neuronal Maturation and Axon Initial Segment Assembly","volume":"97","author":"M Jacko","year":"2018","journal-title":"Neuron"},{"key":"pcbi.1008287.ref038","doi-asserted-by":"crossref","first-page":"3869","DOI":"10.1091\/mbc.E16-04-0237","article-title":"Conover,G.M. Nebulette is a powerful cytolinker organizing desmin and actin in mouse hearts","volume":"27","author":"DA Hernandez","year":"2016","journal-title":"Mol Biol Cell"},{"key":"pcbi.1008287.ref039","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1523\/JNEUROSCI.0334-19.2019","article-title":"The Nebulin Family LIM and SH3 Proteins Regulate Postsynaptic Development and Function","volume":"40","author":"KR Myers","year":"2020","journal-title":"J Neurosci"},{"key":"pcbi.1008287.ref040","doi-asserted-by":"crossref","first-page":"D1100","DOI":"10.1093\/nar\/gkw936","article-title":"The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition","volume":"45","author":"EW Deutsch","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008287.ref041","doi-asserted-by":"crossref","first-page":"176","DOI":"10.4172\/jpb.1000404","article-title":"DecoyPyrat: Fast Non-redundant Hybrid Decoy Sequence Generation for Large Scale Proteomics.","volume":"9","author":"JC Wright","year":"2016","journal-title":"J Proteomics Bioinform"},{"key":"pcbi.1008287.ref042","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1002\/pmic.201200439","article-title":"Hoopmann, MR. Comet: an open-source MS\/MS sequence database search tool","volume":"13","author":"JK Eng","year":"2013","journal-title":"Proteomics"},{"key":"pcbi.1008287.ref043","doi-asserted-by":"crossref","first-page":"1719","DOI":"10.1007\/s13361-016-1460-7","article-title":"Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0","volume":"27","author":"M The","year":"2016","journal-title":"J Am Soc Mass Spectrom"},{"key":"pcbi.1008287.ref044","doi-asserted-by":"crossref","first-page":"3938","DOI":"10.1093\/bioinformatics\/btv488","article-title":"Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data","volume":"31","author":"KE Hayer","year":"2015","journal-title":"Bioinformatics"},{"key":"pcbi.1008287.ref045","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"A Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"pcbi.1008287.ref046","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"SF Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"pcbi.1008287.ref047","doi-asserted-by":"crossref","first-page":"W329","DOI":"10.1093\/nar\/gky384","article-title":"IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding","volume":"46","author":"B M\u00e9sz\u00e1ros","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008287.ref048","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1186\/1471-2105-8-426","article-title":"DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis","volume":"8","author":"BT Sherman","year":"2007","journal-title":"BMC Bioinformatics"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1008287","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,10,15]],"date-time":"2020-10-15T00:00:00Z","timestamp":1602720000000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1008287","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,9]],"date-time":"2023-10-09T02:18:55Z","timestamp":1696817935000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1008287"}},"subtitle":[],"editor":[{"given":"Christine A.","family":"Orengo","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,10,5]]},"references-count":48,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2020,10,5]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1008287","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1008287","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,10,5]]}}}