RNAInter in 2020: RNA interactome repository with increased coverage and annotation
Abstract Research on RNA-associated interactions has exploded in recent years, and increasing numbers of studies are not limited to RNA–RNA and RNA–protein interactions but also include RNA–DNA/compound interactions. To facilitate the development of the interactome and promote understanding of the b...
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| Veröffentlicht in: | Nucleic acids research 2020-01, Vol.48 (D1), p.D189-D197 |
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| container_title | Nucleic acids research |
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| creator | Lin, Yunqing Liu, Tianyuan Cui, Tianyu Wang, Zhao Zhang, Yuncong Tan, Puwen Huang, Yan Yu, Jia Wang, Dong |
| description | Abstract
Research on RNA-associated interactions has exploded in recent years, and increasing numbers of studies are not limited to RNA–RNA and RNA–protein interactions but also include RNA–DNA/compound interactions. To facilitate the development of the interactome and promote understanding of the biological functions and molecular mechanisms of RNA, we updated RAID v2.0 to RNAInter (RNA Interactome Database), a repository for RNA-associated interactions that is freely accessible at http://www.rna-society.org/rnainter/ or http://www.rna-society.org/raid/. Compared to RAID v2.0, new features in RNAInter include (i) 8-fold more interaction data and 94 additional species; (ii) more definite annotations organized, including RNA editing/localization/modification/structure and homology interaction; (iii) advanced functions including fuzzy/batch search, interaction network and RNA dynamic expression and (iv) four embedded RNA interactome tools: RIscoper, IntaRNA, PRIdictor and DeepBind. Consequently, RNAInter contains >41 million RNA-associated interaction entries, involving more than 450 thousand unique molecules, including RNA, protein, DNA and compound. Overall, RNAInter provides a comprehensive RNA interactome resource for researchers and paves the way to investigate the regulatory landscape of cellular RNAs. |
| doi_str_mv | 10.1093/nar/gkz804 |
| format | Article |
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Research on RNA-associated interactions has exploded in recent years, and increasing numbers of studies are not limited to RNA–RNA and RNA–protein interactions but also include RNA–DNA/compound interactions. To facilitate the development of the interactome and promote understanding of the biological functions and molecular mechanisms of RNA, we updated RAID v2.0 to RNAInter (RNA Interactome Database), a repository for RNA-associated interactions that is freely accessible at http://www.rna-society.org/rnainter/ or http://www.rna-society.org/raid/. Compared to RAID v2.0, new features in RNAInter include (i) 8-fold more interaction data and 94 additional species; (ii) more definite annotations organized, including RNA editing/localization/modification/structure and homology interaction; (iii) advanced functions including fuzzy/batch search, interaction network and RNA dynamic expression and (iv) four embedded RNA interactome tools: RIscoper, IntaRNA, PRIdictor and DeepBind. Consequently, RNAInter contains >41 million RNA-associated interaction entries, involving more than 450 thousand unique molecules, including RNA, protein, DNA and compound. Overall, RNAInter provides a comprehensive RNA interactome resource for researchers and paves the way to investigate the regulatory landscape of cellular RNAs.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkz804</identifier><identifier>PMID: 31906603</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Animals ; Database Issue ; Databases, Nucleic Acid ; DNA - metabolism ; Humans ; Mice ; Molecular Sequence Annotation ; RNA - chemistry ; RNA - metabolism ; RNA-Binding Proteins - metabolism ; Software ; Spermatogenesis - genetics</subject><ispartof>Nucleic acids research, 2020-01, Vol.48 (D1), p.D189-D197</ispartof><rights>The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. 2019</rights><rights>The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c408t-79d680bd890e1c84ec8831bdd6a555d81059a5d5f0f99ef90a9dd17b9f299ef93</citedby><cites>FETCH-LOGICAL-c408t-79d680bd890e1c84ec8831bdd6a555d81059a5d5f0f99ef90a9dd17b9f299ef93</cites><orcidid>0000-0001-7949-5285</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943043/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943043/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,1604,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31906603$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lin, Yunqing</creatorcontrib><creatorcontrib>Liu, Tianyuan</creatorcontrib><creatorcontrib>Cui, Tianyu</creatorcontrib><creatorcontrib>Wang, Zhao</creatorcontrib><creatorcontrib>Zhang, Yuncong</creatorcontrib><creatorcontrib>Tan, Puwen</creatorcontrib><creatorcontrib>Huang, Yan</creatorcontrib><creatorcontrib>Yu, Jia</creatorcontrib><creatorcontrib>Wang, Dong</creatorcontrib><title>RNAInter in 2020: RNA interactome repository with increased coverage and annotation</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract
Research on RNA-associated interactions has exploded in recent years, and increasing numbers of studies are not limited to RNA–RNA and RNA–protein interactions but also include RNA–DNA/compound interactions. To facilitate the development of the interactome and promote understanding of the biological functions and molecular mechanisms of RNA, we updated RAID v2.0 to RNAInter (RNA Interactome Database), a repository for RNA-associated interactions that is freely accessible at http://www.rna-society.org/rnainter/ or http://www.rna-society.org/raid/. Compared to RAID v2.0, new features in RNAInter include (i) 8-fold more interaction data and 94 additional species; (ii) more definite annotations organized, including RNA editing/localization/modification/structure and homology interaction; (iii) advanced functions including fuzzy/batch search, interaction network and RNA dynamic expression and (iv) four embedded RNA interactome tools: RIscoper, IntaRNA, PRIdictor and DeepBind. Consequently, RNAInter contains >41 million RNA-associated interaction entries, involving more than 450 thousand unique molecules, including RNA, protein, DNA and compound. Overall, RNAInter provides a comprehensive RNA interactome resource for researchers and paves the way to investigate the regulatory landscape of cellular RNAs.</description><subject>Animals</subject><subject>Database Issue</subject><subject>Databases, Nucleic Acid</subject><subject>DNA - metabolism</subject><subject>Humans</subject><subject>Mice</subject><subject>Molecular Sequence Annotation</subject><subject>RNA - chemistry</subject><subject>RNA - metabolism</subject><subject>RNA-Binding Proteins - metabolism</subject><subject>Software</subject><subject>Spermatogenesis - genetics</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kU1LxDAQhoMo7vpx8QdIL4IIdSdN2k08CIv4BaLgxzmkSbpWd5M1SRX99UarohcPwzAzD-8M8yK0hWEfAycjK_1o-vjGgC6hISZVkVNeFctoCATKHANlA7QWwgMAprikq2hAMIeqAjJEN9eXk3Mbjc9amxVQwEGWOqlILamim5vMm4ULbXT-NXtp432aKW9kMDpT7jlRU5NJq1NYF2Vsnd1AK42cBbP5ldfR3cnx7dFZfnF1en40ucgVBRbzMdcVg1ozDgYrRo1ijOBa60qWZakZhpLLUpcNNJybhoPkWuNxzZvisybr6LDXXXT13GhlbPRyJha-nUv_Kpxsxd-Jbe_F1D2LilMClCSB3S8B7546E6KYt0GZ2Uxa47ogCkJokcjxOKF7Paq8C8Gb5mcNBvHhgkguiN6FBG__PuwH_X57AnZ6wHWL_4TeAQxQkWM</recordid><startdate>20200108</startdate><enddate>20200108</enddate><creator>Lin, Yunqing</creator><creator>Liu, Tianyuan</creator><creator>Cui, Tianyu</creator><creator>Wang, Zhao</creator><creator>Zhang, Yuncong</creator><creator>Tan, Puwen</creator><creator>Huang, Yan</creator><creator>Yu, Jia</creator><creator>Wang, Dong</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0001-7949-5285</orcidid></search><sort><creationdate>20200108</creationdate><title>RNAInter in 2020: RNA interactome repository with increased coverage and annotation</title><author>Lin, Yunqing ; Liu, Tianyuan ; Cui, Tianyu ; Wang, Zhao ; Zhang, Yuncong ; Tan, Puwen ; Huang, Yan ; Yu, Jia ; Wang, Dong</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c408t-79d680bd890e1c84ec8831bdd6a555d81059a5d5f0f99ef90a9dd17b9f299ef93</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Animals</topic><topic>Database Issue</topic><topic>Databases, Nucleic Acid</topic><topic>DNA - metabolism</topic><topic>Humans</topic><topic>Mice</topic><topic>Molecular Sequence Annotation</topic><topic>RNA - chemistry</topic><topic>RNA - metabolism</topic><topic>RNA-Binding Proteins - metabolism</topic><topic>Software</topic><topic>Spermatogenesis - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lin, Yunqing</creatorcontrib><creatorcontrib>Liu, Tianyuan</creatorcontrib><creatorcontrib>Cui, Tianyu</creatorcontrib><creatorcontrib>Wang, Zhao</creatorcontrib><creatorcontrib>Zhang, Yuncong</creatorcontrib><creatorcontrib>Tan, Puwen</creatorcontrib><creatorcontrib>Huang, Yan</creatorcontrib><creatorcontrib>Yu, Jia</creatorcontrib><creatorcontrib>Wang, Dong</creatorcontrib><collection>Access via Oxford University Press (Open Access Collection)</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lin, Yunqing</au><au>Liu, Tianyuan</au><au>Cui, Tianyu</au><au>Wang, Zhao</au><au>Zhang, Yuncong</au><au>Tan, Puwen</au><au>Huang, Yan</au><au>Yu, Jia</au><au>Wang, Dong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>RNAInter in 2020: RNA interactome repository with increased coverage and annotation</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2020-01-08</date><risdate>2020</risdate><volume>48</volume><issue>D1</issue><spage>D189</spage><epage>D197</epage><pages>D189-D197</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>Abstract
Research on RNA-associated interactions has exploded in recent years, and increasing numbers of studies are not limited to RNA–RNA and RNA–protein interactions but also include RNA–DNA/compound interactions. To facilitate the development of the interactome and promote understanding of the biological functions and molecular mechanisms of RNA, we updated RAID v2.0 to RNAInter (RNA Interactome Database), a repository for RNA-associated interactions that is freely accessible at http://www.rna-society.org/rnainter/ or http://www.rna-society.org/raid/. Compared to RAID v2.0, new features in RNAInter include (i) 8-fold more interaction data and 94 additional species; (ii) more definite annotations organized, including RNA editing/localization/modification/structure and homology interaction; (iii) advanced functions including fuzzy/batch search, interaction network and RNA dynamic expression and (iv) four embedded RNA interactome tools: RIscoper, IntaRNA, PRIdictor and DeepBind. Consequently, RNAInter contains >41 million RNA-associated interaction entries, involving more than 450 thousand unique molecules, including RNA, protein, DNA and compound. Overall, RNAInter provides a comprehensive RNA interactome resource for researchers and paves the way to investigate the regulatory landscape of cellular RNAs.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>31906603</pmid><doi>10.1093/nar/gkz804</doi><orcidid>https://orcid.org/0000-0001-7949-5285</orcidid><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Access via Oxford University Press (Open Access Collection); PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Animals Database Issue Databases, Nucleic Acid DNA - metabolism Humans Mice Molecular Sequence Annotation RNA - chemistry RNA - metabolism RNA-Binding Proteins - metabolism Software Spermatogenesis - genetics |
| title | RNAInter in 2020: RNA interactome repository with increased coverage and annotation |
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