{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T10:26:07Z","timestamp":1784629567619,"version":"3.55.0"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1136,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Here we introduce catRAPID omics, a server for large-scale calculations of protein\u2013RNA interactions. Our web server allows (i) predictions at proteomic and transcriptomic level; (ii) use of protein and RNA sequences without size restriction; (iii) analysis of nucleic acid binding regions in proteins; and (iv) detection of RNA motifs involved in protein recognition.<\/jats:p>\n               <jats:p>Results: We developed a web server to allow fast calculation of ribonucleoprotein associations in Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae and Xenopus tropicalis (custom libraries can be also generated). The catRAPID omics was benchmarked on the recently published RNA interactomes of Serine\/arginine-rich splicing factor 1 (SRSF1), Histone-lysine N-methyltransferase EZH2 (EZH2), TAR DNA-binding protein 43 (TDP43) and RNA-binding protein FUS (FUS) as well as on the protein interactomes of U1\/U2 small nucleolar RNAs, X inactive specific transcript (Xist) repeat A region (RepA) and Crumbs homolog 3 (CRB3) 3\u2032-untranslated region RNAs. Our predictions are highly significant (P &amp;lt; 0.05) and will help the experimentalist to identify candidates for further validation.<\/jats:p>\n               <jats:p>Availability: \u00a0catRAPID omics can be freely accessed on the Web at http:\/\/s.tartaglialab.com\/catrapid\/omics. Documentation, tutorial and FAQs are available at http:\/\/s.tartaglialab.com\/page\/catrapid_group.<\/jats:p>\n               <jats:p>Contact: \u00a0gian.tartaglia@crg.eu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt495","type":"journal-article","created":{"date-parts":[[2013,8,24]],"date-time":"2013-08-24T04:09:42Z","timestamp":1377317382000},"page":"2928-2930","source":"Crossref","is-referenced-by-count":264,"title":["<i>cat<\/i>RAPID <i>omics<\/i>: a web server for large-scale prediction of protein\u2013RNA interactions"],"prefix":"10.1093","volume":"29","author":[{"given":"Federico","family":"Agostini","sequence":"first","affiliation":[{"name":"1 Gene Function and Evolution, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain"},{"name":"1 Gene Function and Evolution, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Zanzoni","sequence":"additional","affiliation":[{"name":"1 Gene Function and Evolution, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain"},{"name":"1 Gene Function and Evolution, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Petr","family":"Klus","sequence":"additional","affiliation":[{"name":"1 Gene Function and Evolution, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain"},{"name":"1 Gene Function and Evolution, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Domenica","family":"Marchese","sequence":"additional","affiliation":[{"name":"1 Gene Function and Evolution, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain"},{"name":"1 Gene Function and Evolution, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Davide","family":"Cirillo","sequence":"additional","affiliation":[{"name":"1 Gene Function and Evolution, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain"},{"name":"1 Gene Function and Evolution, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gian Gaetano","family":"Tartaglia","sequence":"additional","affiliation":[{"name":"1 Gene Function and Evolution, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain"},{"name":"1 Gene Function and Evolution, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,8,23]]},"reference":[{"key":"2023012810484356800_btt495-B1","doi-asserted-by":"crossref","first-page":"e31","DOI":"10.1093\/nar\/gks968","article-title":"X-inactivation: quantitative predictions of protein interactions in the Xist network","volume":"41","author":"Agostini","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023012810484356800_btt495-B2","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1038\/nmeth.1611","article-title":"Predicting protein associations with long noncoding RNAs","volume":"8","author":"Bellucci","year":"2011","journal-title":"Nat. Methods"},{"key":"2023012810484356800_btt495-B3","doi-asserted-by":"crossref","first-page":"1393","DOI":"10.1016\/j.cell.2012.04.031","article-title":"Insights into RNA biology from an atlas of mammalian mRNA-binding proteins","volume":"149","author":"Castello","year":"2012","journal-title":"Cell"},{"key":"2023012810484356800_btt495-B4","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1261\/rna.034777.112","article-title":"Neurodegenerative diseases: quantitative predictions of protein\u2013RNA interactions","volume":"19","author":"Cirillo","year":"2013","journal-title":"RNA"},{"key":"2023012810484356800_btt495-B5","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1002\/wcms.1119","article-title":"Predictions of protein\u2013RNA interactions","volume":"3","author":"Cirillo","year":"2013","journal-title":"Wiley Interdiscip. Rev. Comput. Mol. Sci."},{"key":"2023012810484356800_btt495-B6","doi-asserted-by":"crossref","first-page":"D301","DOI":"10.1093\/nar\/gkq1069","article-title":"RBPDB: a database of RNA-binding specificities","volume":"39","author":"Cook","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012810484356800_btt495-B7","doi-asserted-by":"crossref","first-page":"D132","DOI":"10.1093\/nar\/gks999","article-title":"Spliceosome database: a tool for tracking components of the spliceosome","volume":"41","author":"Cvitkovic","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023012810484356800_btt495-B8","doi-asserted-by":"crossref","first-page":"D211","DOI":"10.1093\/nar\/gkp985","article-title":"The Pfam protein families database","volume":"38","author":"Finn","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012810484356800_btt495-B9","doi-asserted-by":"crossref","first-page":"W29","DOI":"10.1093\/nar\/gkr367","article-title":"HMMER web server: interactive sequence similarity searching","volume":"39","author":"Finn","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012810484356800_btt495-B10","doi-asserted-by":"crossref","first-page":"D125","DOI":"10.1093\/nar\/gks997","article-title":"SpliceAid-F: a database of human splicing factors and their RNA-binding sites","volume":"41","author":"Giulietti","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023012810484356800_btt495-B11","doi-asserted-by":"crossref","first-page":"768","DOI":"10.1016\/j.cell.2012.04.016","article-title":"Cell-free formation of RNA granules: bound RNAs identify features and components of cellular assemblies","volume":"149","author":"Han","year":"2012","journal-title":"Cell"},{"key":"2023012810484356800_btt495-B12","doi-asserted-by":"crossref","first-page":"e53","DOI":"10.1093\/nar\/gkq1316","article-title":"Efficient detection of RNA-protein interactions using tethered RNAs","volume":"39","author":"Iioka","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012810484356800_btt495-B13","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1016\/j.pneurobio.2012.09.006","article-title":"Neurodegeneration as an RNA disorder","volume":"99","author":"Johnson","year":"2012","journal-title":"Prog. Neurobiol."},{"key":"2023012810484356800_btt495-B14","doi-asserted-by":"crossref","first-page":"e1000832","DOI":"10.1371\/journal.pcbi.1000832","article-title":"RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins","volume":"6","author":"Kazan","year":"2010","journal-title":"PLoS Comput. Biol."},{"key":"2023012810484356800_btt495-B15","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1016\/j.semcdb.2011.02.016","article-title":"RNA-protein interactions in human health and disease","volume":"22","author":"Khalil","year":"2011","journal-title":"Semin. Cell Dev. Biol."},{"key":"2023012810484356800_btt495-B16","doi-asserted-by":"crossref","first-page":"e1000276","DOI":"10.1371\/journal.pbio.1000276","article-title":"2-D structure of the A Region of Xist RNA and its implication for PRC2 association","volume":"8","author":"Maenner","year":"2010","journal-title":"PLoS Biol."},{"key":"2023012810484356800_btt495-B17","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1186\/1471-2105-12-489","article-title":"Predicting RNA-protein interactions using only sequence information","volume":"12","author":"Muppirala","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023012810484356800_btt495-B18","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1038\/nature12311","article-title":"A compendium of RNA-binding motifs for decoding gene regulation","volume":"499","author":"Ray","year":"2013","journal-title":"Nature"},{"key":"2023012810484356800_btt495-B19","doi-asserted-by":"crossref","first-page":"948","DOI":"10.1038\/nsmb.1877","article-title":"The A-repeat links ASF\/SF2-dependent Xist RNA processing with random choice during X inactivation","volume":"17","author":"Royce-Tolland","year":"2010","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2023012810484356800_btt495-B20","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1101\/gr.082503.108","article-title":"Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts","volume":"19","author":"Sanford","year":"2009","journal-title":"Genome Res."},{"key":"2023012810484356800_btt495-B21","doi-asserted-by":"crossref","first-page":"1204","DOI":"10.1074\/jbc.M110.190884","article-title":"Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes","volume":"286","author":"Sephton","year":"2011","journal-title":"J. Biol. Chem."},{"key":"2023012810484356800_btt495-B23","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkt794","article-title":"Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein","author":"Zanzoni","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023012810484356800_btt495-B22","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1016\/j.molcel.2010.12.011","article-title":"Genome-wide identification of polycomb-associated RNAs by RIP-seq","volume":"40","author":"Zhao","year":"2010","journal-title":"Mol. Cell"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/22\/2928\/48894819\/bioinformatics_29_22_2928.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/22\/2928\/48894819\/bioinformatics_29_22_2928.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T12:49:27Z","timestamp":1674910167000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/22\/2928\/314358"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,8,23]]},"references-count":23,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2013,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt495","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,11,15]]},"published":{"date-parts":[[2013,8,23]]}}}