{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T12:13:16Z","timestamp":1780315996256,"version":"3.54.1"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2017,10,5]],"date-time":"2017-10-05T00:00:00Z","timestamp":1507161600000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,1,4]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>We present RISE (http:\/\/rise.zhanglab.net), a database of RNA Interactome from Sequencing Experiments. RNA-RNA interactions (RRIs) are essential for RNA regulation and function. RISE provides a comprehensive collection of RRIs that mainly come from recent transcriptome-wide sequencing-based experiments like PARIS, SPLASH, LIGR-seq, and MARIO, as well as targeted studies like RIA-seq, RAP-RNA and CLASH. It also includes interactions aggregated from other primary databases and publications. The RISE database currently contains 328,811 RNA-RNA interactions mainly in human, mouse and yeast. While most existing RNA databases mainly contain interactions of miRNA targeting, notably, more than half of the RRIs in RISE are among mRNA and long non-coding RNAs. We compared different RRI datasets in RISE and found limited overlaps in interactions resolved by different techniques and in different cell lines. It may suggest technology preference and also dynamic natures of RRIs. We also analyzed the basic features of the human and mouse RRI networks and found that they tend to be scale-free, small-world, hierarchical and modular. The analysis may nominate important RNAs or RRIs for further investigation. Finally, RISE provides a Circos plot and several table views for integrative visualization, with extensive molecular and functional annotations to facilitate exploration of biological functions for any RRI of interest.<\/jats:p>","DOI":"10.1093\/nar\/gkx864","type":"journal-article","created":{"date-parts":[[2017,9,29]],"date-time":"2017-09-29T19:10:56Z","timestamp":1506712256000},"page":"D194-D201","source":"Crossref","is-referenced-by-count":107,"title":["RISE: a database of RNA interactome from sequencing experiments"],"prefix":"10.1093","volume":"46","author":[{"given":"Jing","family":"Gong","sequence":"first","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China"},{"name":"Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Di","family":"Shao","sequence":"first","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China"},{"name":"Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kui","family":"Xu","sequence":"first","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China"},{"name":"Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5124-7546","authenticated-orcid":false,"given":"Zhipeng","family":"Lu","sequence":"first","affiliation":[{"name":"Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhi John","family":"Lu","sequence":"first","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yucheng T","family":"Yang","sequence":"first","affiliation":[{"name":"Department of Statistics, University of California Los Angeles, Los Angeles, CA 90095-1554, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4913-0338","authenticated-orcid":false,"given":"Qiangfeng Cliff","family":"Zhang","sequence":"first","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China"},{"name":"Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,10,4]]},"reference":[{"key":"2020041422560251400_B1","doi-asserted-by":"crossref","first-page":"1240","DOI":"10.1126\/science.1252966","article-title":"RNA Function. RNA and dynamic nuclear organization","volume":"345","author":"Rinn","year":"2014","journal-title":"Science"},{"key":"2020041422560251400_B2","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1093\/bib\/bbv031","article-title":"Revealing protein-lncRNA interaction","volume":"17","author":"Ferre","year":"2016","journal-title":"Brief. Bioinform."},{"key":"2020041422560251400_B3","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1016\/j.cell.2011.07.014","article-title":"A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language","volume":"146","author":"Salmena","year":"2011","journal-title":"Cell"},{"key":"2020041422560251400_B4","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1016\/j.tibs.2015.03.001","article-title":"RNA-RNA interactions in gene regulation: the coding and noncoding players","volume":"40","author":"Guil","year":"2015","journal-title":"Trends Biochem. Sci."},{"key":"2020041422560251400_B5","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"Consortium","year":"2012","journal-title":"Nature"},{"key":"2020041422560251400_B6","doi-asserted-by":"crossref","first-page":"1915","DOI":"10.1101\/gad.17446611","article-title":"Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses","volume":"25","author":"Cabili","year":"2011","journal-title":"Genes Dev."},{"key":"2020041422560251400_B7","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1038\/nature07672","article-title":"Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals","volume":"458","author":"Guttman","year":"2009","journal-title":"Nature"},{"key":"2020041422560251400_B8","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1534\/genetics.112.146704","article-title":"Long noncoding RNAs: past, present, and future","volume":"193","author":"Kung","year":"2013","journal-title":"Genetics"},{"key":"2020041422560251400_B9","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1038\/nature10887","article-title":"Modular regulatory principles of large non-coding RNAs","volume":"482","author":"Guttman","year":"2012","journal-title":"Nature"},{"key":"2020041422560251400_B10","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/nrg2521","article-title":"Long non-coding RNAs: insights into functions","volume":"10","author":"Mercer","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"2020041422560251400_B11","doi-asserted-by":"crossref","first-page":"7112","DOI":"10.1073\/pnas.1305322110","article-title":"Deciphering the rules of ceRNA networks","volume":"110","author":"Cesana","year":"2013","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2020041422560251400_B12","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1016\/j.cell.2013.03.043","article-title":"Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding","volume":"153","author":"Helwak","year":"2013","journal-title":"Cell"},{"key":"2020041422560251400_B13","doi-asserted-by":"crossref","first-page":"10010","DOI":"10.1073\/pnas.1017386108","article-title":"Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast","volume":"108","author":"Kudla","year":"2011","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2020041422560251400_B14","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/nature14280","article-title":"hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1","volume":"519","author":"Sugimoto","year":"2015","journal-title":"Nature"},{"key":"2020041422560251400_B15","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1038\/nature11661","article-title":"Control of somatic tissue differentiation by the long non-coding RNA TINCR","volume":"493","author":"Kretz","year":"2013","journal-title":"Nature"},{"key":"2020041422560251400_B16","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1016\/j.cell.2014.08.018","article-title":"RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent Pre-mRNAs and chromatin sites","volume":"159","author":"Engreitz","year":"2014","journal-title":"Cell"},{"key":"2020041422560251400_B17","doi-asserted-by":"crossref","first-page":"1267","DOI":"10.1016\/j.cell.2016.04.028","article-title":"RNA duplex map in living cells reveals higher-order transcriptome structure","volume":"165","author":"Lu","year":"2016","journal-title":"Cell"},{"key":"2020041422560251400_B18","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1016\/j.molcel.2016.04.028","article-title":"In vivo mapping of eukaryotic RNA interactomes reveals principles of higher-order organization and regulation","volume":"62","author":"Aw","year":"2016","journal-title":"Mol. Cell"},{"key":"2020041422560251400_B19","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1016\/j.molcel.2016.04.030","article-title":"Global mapping of human RNA-RNA interactions","volume":"62","author":"Sharma","year":"2016","journal-title":"Mol. Cell"},{"key":"2020041422560251400_B20","doi-asserted-by":"crossref","first-page":"12023","DOI":"10.1038\/ncomms12023","article-title":"Mapping RNA-RNA interactome and RNA structure in vivo by MARIO","volume":"7","author":"Nguyen","year":"2016","journal-title":"Nat. Commun."},{"key":"2020041422560251400_B21","doi-asserted-by":"crossref","first-page":"baw057","DOI":"10.1093\/database\/baw057","article-title":"NPInter v3.0: an upgraded database of noncoding RNA-associated interactions","volume":"2016","author":"Hao","year":"2016","journal-title":"Database (Oxford)"},{"key":"2020041422560251400_B22","doi-asserted-by":"crossref","first-page":"D115","DOI":"10.1093\/nar\/gkw1052","article-title":"RAID v2.0: an updated resource of RNA-associated interactions across organisms","volume":"45","author":"Yi","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2020041422560251400_B23","doi-asserted-by":"crossref","first-page":"baw167","DOI":"10.1093\/database\/baw167","article-title":"RAIN: RNA-protein association and interaction networks","volume":"2017","author":"Junge","year":"2017","journal-title":"Database (Oxford)"},{"key":"2020041422560251400_B24","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2020041422560251400_B25","doi-asserted-by":"crossref","first-page":"e61","DOI":"10.1093\/nar\/gkv1477","article-title":"A comprehensive comparison of general RNA-RNA interaction prediction methods","volume":"44","author":"Lai","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2020041422560251400_B26","doi-asserted-by":"crossref","first-page":"1006","DOI":"10.1093\/bioinformatics\/btt730","article-title":"CrossMap: a versatile tool for coordinate conversion between genome assemblies","volume":"30","author":"Zhao","year":"2014","journal-title":"Bioinformatics"},{"key":"2020041422560251400_B27","doi-asserted-by":"crossref","first-page":"bar049","DOI":"10.1093\/database\/bar049","article-title":"BioMart: driving a paradigm change in biological data management","volume":"2011","author":"Kasprzyk","year":"2011","journal-title":"Database (Oxford)"},{"key":"2020041422560251400_B28","doi-asserted-by":"crossref","first-page":"D68","DOI":"10.1093\/nar\/gkt1181","article-title":"miRBase: annotating high confidence microRNAs using deep sequencing data","volume":"42","author":"Kozomara","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2020041422560251400_B29","doi-asserted-by":"crossref","first-page":"11","DOI":"10.25080\/TCWV9851","article-title":"Exploring network structure, dynamics, and function using NetworkX","author":"Hagberg","year":"2008","journal-title":"In Proceedings of the 7th Python in Science Conference (SciPy)"},{"key":"2020041422560251400_B30","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"},{"key":"2020041422560251400_B31","doi-asserted-by":"crossref","first-page":"D109","DOI":"10.1093\/nar\/gkt996","article-title":"RADAR: a rigorously annotated database of A-to-I RNA editing","volume":"42","author":"Ramaswami","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2020041422560251400_B32","doi-asserted-by":"crossref","first-page":"1772","DOI":"10.1093\/bioinformatics\/btq285","article-title":"DARNED: a DAtabase of RNa EDiting in humans","volume":"26","author":"Kiran","year":"2010","journal-title":"Bioinformatics"},{"key":"2020041422560251400_B33","doi-asserted-by":"crossref","first-page":"D259","DOI":"10.1093\/nar\/gkv1036","article-title":"RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data","volume":"44","author":"Sun","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2020041422560251400_B34","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1093\/nar\/29.1.308","article-title":"dbSNP: the NCBI database of genetic variation","volume":"29","author":"Sherry","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2020041422560251400_B35","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/nbt.3391","article-title":"Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity","volume":"34","author":"Chang","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"2020041422560251400_B36","first-page":"1657","article-title":"Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell states","volume":"45","author":"Yang","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2020041422560251400_B37","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information aesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Genome Res."},{"key":"2020041422560251400_B38","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1016\/j.cell.2005.08.029","article-title":"A human protein-protein interaction network: a resource for annotating the proteome","volume":"122","author":"Stelzl","year":"2005","journal-title":"Cell"},{"key":"2020041422560251400_B39","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/nrg1272","article-title":"Network biology: understanding the cell's functional organization","volume":"5","author":"Barabasi","year":"2004","journal-title":"Nat. Rev. Genet."},{"key":"2020041422560251400_B40","doi-asserted-by":"crossref","first-page":"1479","DOI":"10.1261\/rna.060996.117","article-title":"Yeast non-coding RNA interaction network","volume":"23","author":"Panni","year":"2017","journal-title":"RNA"},{"key":"2020041422560251400_B41","doi-asserted-by":"crossref","first-page":"1112","DOI":"10.1101\/gr.219741.116","article-title":"Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers","volume":"27","author":"Wang","year":"2017","journal-title":"Genome Res."},{"key":"2020041422560251400_B42","doi-asserted-by":"crossref","first-page":"3418","DOI":"10.1093\/hmg\/ddv090","article-title":"A 3\u2032-UTR mutation creates a microRNA target site in the GFPT1 gene of patients with congenital myasthenic syndrome","volume":"24","author":"Dusl","year":"2015","journal-title":"Hum. Mol. Genet."},{"key":"2020041422560251400_B43","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1038\/nrd.2016.117","article-title":"Non-coding RNAs as drug targets","volume":"16","author":"Matsui","year":"2017","journal-title":"Nat. Rev. Drug Discov."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/46\/D1\/D194\/33043705\/gkx864.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/46\/D1\/D194\/33043705\/gkx864.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,25]],"date-time":"2025-06-25T23:20:57Z","timestamp":1750893657000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/46\/D1\/D194\/4344571"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,10,4]]},"references-count":43,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2017,10,4]]},"published-print":{"date-parts":[[2018,1,4]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkx864","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,1,4]]},"published":{"date-parts":[[2017,10,4]]}}}