{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T20:01:49Z","timestamp":1772827309370,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2019,5,31]],"date-time":"2019-05-31T00:00:00Z","timestamp":1559260800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"name":"FP7 Marie Curie CIG","award":["631986"],"award-info":[{"award-number":["631986"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Long non-coding RNAs (lncRNAs) can act as molecular sponge or decoys for an RNA-binding protein (RBP) through their RBP-binding sites, thereby modulating the expression of all target genes of the corresponding RBP of interest. Here, we present a web tool named RBPSponge to explore lncRNAs based on their potential to act as a sponge for an RBP of interest. RBPSponge identifies the occurrences of RBP-binding sites and CLIP peaks on lncRNAs, and enables users to run statistical analyses to investigate the regulatory network between lncRNAs, RBPs and targets of RBPs.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The web server is available at https:\/\/www.RBPSponge.com.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz448","type":"journal-article","created":{"date-parts":[[2019,5,28]],"date-time":"2019-05-28T07:18:01Z","timestamp":1559027881000},"page":"4760-4763","source":"Crossref","is-referenced-by-count":16,"title":["RBPSponge: genome-wide identification of lncRNAs that sponge RBPs"],"prefix":"10.1093","volume":"35","author":[{"given":"Saber","family":"HafezQorani","sequence":"first","affiliation":[{"name":"Department of Health Informatics, Graduate School of Informatics, Middle East Technical University , Ankara 06800, Turkey"}]},{"given":"Aissa","family":"Houdjedj","sequence":"additional","affiliation":[{"name":"Graduate School of Electrical and Computer Engineering , Antalya 07190, Turkey"}]},{"given":"Mehmet","family":"Arici","sequence":"additional","affiliation":[{"name":"Department of Computer Engineering, Antalya Bilim University , Antalya 07190, Turkey"}]},{"given":"Abdesselam","family":"Said","sequence":"additional","affiliation":[{"name":"Department of Computer Engineering, Antalya Bilim University , Antalya 07190, Turkey"}]},{"given":"Hilal","family":"Kazan","sequence":"additional","affiliation":[{"name":"Graduate School of Electrical and Computer Engineering , Antalya 07190, Turkey"},{"name":"Department of Computer Engineering, Antalya Bilim University , Antalya 07190, Turkey"}]}],"member":"286","published-online":{"date-parts":[[2019,5,31]]},"reference":[{"key":"2023013108352317000_btz448-B1","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1016\/j.celrep.2018.03.064","article-title":"Pan-cancer analysis of lncRNA regulation supports their targeting of cancer genes in each tumor context","volume":"23","author":"Chiu","year":"2018","journal-title":"Cell Rep"},{"key":"2023013108352317000_btz448-B2","first-page":"854","author":"Dominguez","year":"2017"},{"key":"2023013108352317000_btz448-B3","doi-asserted-by":"crossref","first-page":"W176","DOI":"10.1093\/nar\/gkw443","article-title":"spongeScan: a web for detecting microRNA binding elements in lncRNA sequences","volume":"44","author":"Furio-Tari","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023013108352317000_btz448-B4","doi-asserted-by":"crossref","first-page":"2378","DOI":"10.1093\/nar\/gkw017","article-title":"LncRNA OIP5-AS1\/cyrano sponges RNA-binding protein HuR","volume":"44","author":"Kim","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023013108352317000_btz448-B16","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1016\/j.cell.2018.01.011","article-title":"Functional classification and experimental dissection of long noncoding RNAs","volume":"172","author":"Kopp","year":"2018","journal-title":"Cell"},{"key":"2023013108352317000_btz448-B5","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/j.cell.2015.12.017","article-title":"Noncoding RNA NORAD regulates genomic stability by sequestering PUMILIO proteins","volume":"164","author":"Lee","year":"2016","journal-title":"Cell"},{"key":"2023013108352317000_btz448-B6","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2023013108352317000_btz448-B7","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/nature11928","article-title":"Circular RNAs are a large class of animal RNAs with regulatory potency","volume":"495","author":"Memczak","year":"2013","journal-title":"Nature"},{"key":"2023013108352317000_btz448-B8","first-page":"780","article-title":"Screening and validation of lncRNAs and circRNAs as miRNA sponges","volume":"18","author":"Militello","year":"2017","journal-title":"Brief Bioinform"},{"key":"2023013108352317000_btz448-B9","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1016\/j.molcel.2011.06.007","article-title":"Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability","volume":"43","author":"Mukherjee","year":"2011","journal-title":"Mol. Cell"},{"key":"2023013108352317000_btz448-B10","doi-asserted-by":"crossref","first-page":"W361","DOI":"10.1093\/nar\/gku406","article-title":"RBPmap: a web server for mapping binding sites of RNA-binding proteins","volume":"42","author":"Paz","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023013108352317000_btz448-B11","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":"2023013108352317000_btz448-B12","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms12209","article-title":"A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells","volume":"7","author":"Tichon","year":"2016","journal-title":"Nat. Commun"},{"key":"2023013108352317000_btz448-B13","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1038\/nmeth.3810","article-title":"Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)","volume":"13","author":"van Nostrand","year":"2016","journal-title":"Nat. Methods"},{"key":"2023013108352317000_btz448-B14","first-page":"1","article-title":"circlncRNAnet: an integrated web-based resource for mapping functional networks of long or circular forms of noncoding RNAs","volume":"7","author":"Wu","year":"2018","journal-title":"Gigascience"},{"key":"2023013108352317000_btz448-B15","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1186\/s12864-015-1273-2","article-title":"CLIPdb: a CLIP-seq database for protein-RNA interactions","volume":"16","author":"Yang","year":"2015","journal-title":"BMC Genomics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz448\/28856176\/btz448.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/22\/4760\/48978226\/bioinformatics_35_22_4760.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/22\/4760\/48978226\/bioinformatics_35_22_4760.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T12:46:35Z","timestamp":1675169195000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/22\/4760\/5509522"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,5,31]]},"references-count":16,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2019,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz448","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/566828","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,11,15]]},"published":{"date-parts":[[2019,5,31]]}}}