LncRBase V.2: an updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients
The recent discovery of long non-coding RNA as a regulatory molecule in the cellular system has altered the concept of the functional aptitude of the genome. Since our publication of the first version of LncRBase in 2014, there has been an enormous increase in the number of annotated lncRNAs of mult...
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| Veröffentlicht in: | RNA biology 2021-08, Vol.18 (8), p.1136-1151 |
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| creator | Das, Troyee Deb, Aritra Parida, Sibun Mondal, Sudip Khatua, Sunirmal Ghosh, Zhumur |
| description | The recent discovery of long non-coding RNA as a regulatory molecule in the cellular system has altered the concept of the functional aptitude of the genome. Since our publication of the first version of LncRBase in 2014, there has been an enormous increase in the number of annotated lncRNAs of multiple species other than Human and Mouse. LncRBase V.2 hosts information of 549,648 lncRNAs corresponding to six additional species besides Human and Mouse, viz. Rat, Fruitfly, Zebrafish, Chicken, Cow and C.elegans. It provides additional distinct features such as (i) Transcription Factor Binding Site (TFBS) in the lncRNA promoter region, (ii) sub-cellular localization pattern of lncRNAs (iii) lnc-pri-miRNAs (iv) Possible small open reading frames (sORFs) within lncRNA. (v) Manually curated information of interacting target molecules and disease association of lncRNA genes (vi) Distribution of lncRNAs across multiple tissues of all species. Moreover, we have hosted ClinicLSNP within LncRBase V.2. ClinicLSNP has a comprehensive catalogue of lncRNA variants present within breast, ovarian, and cervical cancer inferred from 561 RNA-Seq data corresponding to these cancers. Further, we have checked whether these lncRNA variants overlap with (i)Repeat elements,(ii)CGI, (iii)TFBS within lncRNA loci (iv)SNP localization in trait-associated Linkage Disequilibrium(LD) region, (v)predicted the potentially pathogenic variants and (vi)effect of SNP on lncRNA secondary structure. Overall, LncRBaseV.2 is a user-friendly database to survey, search and retrieve information about multi-species lncRNAs. Further, ClinicLSNP will serve as a useful resource for cancer specific lncRNA variants and their related information. The database is freely accessible and available at
http://dibresources.jcbose.ac.in/zhumur/lncrbase2/
. |
| doi_str_mv | 10.1080/15476286.2020.1833529 |
| format | Article |
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http://dibresources.jcbose.ac.in/zhumur/lncrbase2/
.</description><identifier>ISSN: 1547-6286</identifier><identifier>EISSN: 1555-8584</identifier><identifier>DOI: 10.1080/15476286.2020.1833529</identifier><identifier>PMID: 33112702</identifier><language>eng</language><publisher>PHILADELPHIA: Taylor & Francis</publisher><subject>Animals ; Biochemistry & Molecular Biology ; Breast Neoplasms - genetics ; Breast Neoplasms - metabolism ; Breast Neoplasms - pathology ; Caenorhabditis elegans - genetics ; Caenorhabditis elegans - metabolism ; Cattle ; Chickens - genetics ; Chickens - metabolism ; clinicLSNP ; Databases, Nucleic Acid ; Drosophila melanogaster - genetics ; Drosophila melanogaster - metabolism ; Female ; female cancer ; Genome ; Humans ; Life Sciences & Biomedicine ; lncrbase ; lncRNA variant ; Long non-coding RNA ; Male ; Mice ; MicroRNAs - classification ; MicroRNAs - genetics ; MicroRNAs - metabolism ; Molecular Sequence Annotation ; Ovarian Neoplasms - genetics ; Ovarian Neoplasms - metabolism ; Ovarian Neoplasms - pathology ; Polymorphism, Single Nucleotide ; Rats ; Research Paper ; RNA, Long Noncoding - classification ; RNA, Long Noncoding - genetics ; RNA, Long Noncoding - metabolism ; RNA, Small Interfering - classification ; RNA, Small Interfering - genetics ; RNA, Small Interfering - metabolism ; Science & Technology ; sORFs ; Species Specificity ; sub-cellular localization ; Uterine Cervical Neoplasms - genetics ; Uterine Cervical Neoplasms - metabolism ; Uterine Cervical Neoplasms - pathology ; Zebrafish - genetics ; Zebrafish - metabolism</subject><ispartof>RNA biology, 2021-08, Vol.18 (8), p.1136-1151</ispartof><rights>2020 Informa UK Limited, trading as Taylor & Francis Group 2020</rights><rights>2020 Informa UK Limited, trading as Taylor & Francis Group 2020 Informa UK Limited, trading as Taylor & Francis Group</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>true</woscitedreferencessubscribed><woscitedreferencescount>13</woscitedreferencescount><woscitedreferencesoriginalsourcerecordid>wos000584683100001</woscitedreferencesoriginalsourcerecordid><citedby>FETCH-LOGICAL-c468t-25b67ad6cbd217025869ef3ad8deaeac2bc3f8bcd31de7026fdf1fbb9eb9116a3</citedby><cites>FETCH-LOGICAL-c468t-25b67ad6cbd217025869ef3ad8deaeac2bc3f8bcd31de7026fdf1fbb9eb9116a3</cites><orcidid>0000-0002-0624-9718</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/PMC8244770/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8244770/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,315,729,782,786,887,27931,27932,39265,53798,53800</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33112702$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Das, Troyee</creatorcontrib><creatorcontrib>Deb, Aritra</creatorcontrib><creatorcontrib>Parida, Sibun</creatorcontrib><creatorcontrib>Mondal, Sudip</creatorcontrib><creatorcontrib>Khatua, Sunirmal</creatorcontrib><creatorcontrib>Ghosh, Zhumur</creatorcontrib><title>LncRBase V.2: an updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients</title><title>RNA biology</title><addtitle>RNA BIOL</addtitle><addtitle>RNA Biol</addtitle><description>The recent discovery of long non-coding RNA as a regulatory molecule in the cellular system has altered the concept of the functional aptitude of the genome. Since our publication of the first version of LncRBase in 2014, there has been an enormous increase in the number of annotated lncRNAs of multiple species other than Human and Mouse. LncRBase V.2 hosts information of 549,648 lncRNAs corresponding to six additional species besides Human and Mouse, viz. Rat, Fruitfly, Zebrafish, Chicken, Cow and C.elegans. It provides additional distinct features such as (i) Transcription Factor Binding Site (TFBS) in the lncRNA promoter region, (ii) sub-cellular localization pattern of lncRNAs (iii) lnc-pri-miRNAs (iv) Possible small open reading frames (sORFs) within lncRNA. (v) Manually curated information of interacting target molecules and disease association of lncRNA genes (vi) Distribution of lncRNAs across multiple tissues of all species. Moreover, we have hosted ClinicLSNP within LncRBase V.2. ClinicLSNP has a comprehensive catalogue of lncRNA variants present within breast, ovarian, and cervical cancer inferred from 561 RNA-Seq data corresponding to these cancers. Further, we have checked whether these lncRNA variants overlap with (i)Repeat elements,(ii)CGI, (iii)TFBS within lncRNA loci (iv)SNP localization in trait-associated Linkage Disequilibrium(LD) region, (v)predicted the potentially pathogenic variants and (vi)effect of SNP on lncRNA secondary structure. Overall, LncRBaseV.2 is a user-friendly database to survey, search and retrieve information about multi-species lncRNAs. Further, ClinicLSNP will serve as a useful resource for cancer specific lncRNA variants and their related information. The database is freely accessible and available at
http://dibresources.jcbose.ac.in/zhumur/lncrbase2/
.</description><subject>Animals</subject><subject>Biochemistry & Molecular Biology</subject><subject>Breast Neoplasms - genetics</subject><subject>Breast Neoplasms - metabolism</subject><subject>Breast Neoplasms - pathology</subject><subject>Caenorhabditis elegans - genetics</subject><subject>Caenorhabditis elegans - metabolism</subject><subject>Cattle</subject><subject>Chickens - genetics</subject><subject>Chickens - metabolism</subject><subject>clinicLSNP</subject><subject>Databases, Nucleic Acid</subject><subject>Drosophila melanogaster - genetics</subject><subject>Drosophila melanogaster - metabolism</subject><subject>Female</subject><subject>female cancer</subject><subject>Genome</subject><subject>Humans</subject><subject>Life Sciences & Biomedicine</subject><subject>lncrbase</subject><subject>lncRNA variant</subject><subject>Long non-coding RNA</subject><subject>Male</subject><subject>Mice</subject><subject>MicroRNAs - classification</subject><subject>MicroRNAs - genetics</subject><subject>MicroRNAs - metabolism</subject><subject>Molecular Sequence Annotation</subject><subject>Ovarian Neoplasms - genetics</subject><subject>Ovarian Neoplasms - metabolism</subject><subject>Ovarian Neoplasms - pathology</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Rats</subject><subject>Research Paper</subject><subject>RNA, Long Noncoding - classification</subject><subject>RNA, Long Noncoding - genetics</subject><subject>RNA, Long Noncoding - metabolism</subject><subject>RNA, Small Interfering - classification</subject><subject>RNA, Small Interfering - genetics</subject><subject>RNA, Small Interfering - metabolism</subject><subject>Science & Technology</subject><subject>sORFs</subject><subject>Species Specificity</subject><subject>sub-cellular localization</subject><subject>Uterine Cervical Neoplasms - genetics</subject><subject>Uterine Cervical Neoplasms - metabolism</subject><subject>Uterine Cervical Neoplasms - pathology</subject><subject>Zebrafish - genetics</subject><subject>Zebrafish - metabolism</subject><issn>1547-6286</issn><issn>1555-8584</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>HGBXW</sourceid><sourceid>EIF</sourceid><recordid>eNqNkUtv1DAURiMEoqXwE0BeIqEMfsSJwwJRIl7SqCBeW8uxb6ZGiR1sp1WX_HMczXQEG8TKlu_57rV9iuIxwRuCBX5OeNXUVNQbimk-Eoxx2t4pTgnnvBRcVHfXfdWUK3RSPIjxB8asFi2_X5wwRghtMD0tfm2d_vxaRUDfN_QFUg4ts1EJDAoQ_RI0oMEHNC1jsnEGbSGiMUcuzmOGDepG66zefrn4hC59TNbt0A4cJKvRlQpWuRSRdcfI2ksrpyGgWSULufywuDeoMcKjw3pWfHv75mv3vtx-fPehO9-WuqpFKinv60aZWveGknx1LuoWBqaMMKBAadprNoheG0YM5Ho9mIEMfd9C3xJSK3ZWvNz3nZd-AqPz7KBGOQc7qXAjvbLy74qzl3Lnr6SgVdU0ODd4emgQ_M8FYpKTjRrGUTnwS5S04lywirAV5XtUBx9jgOE4hmC56pO3-uSqTx705dyTP-94TN36ysCzPXANvR9i1pH_8ohhjLP4WjCSd5hkWvw_3dmUjXjX-cWlHH21j1qXnU3q2ofRyKRuRh-GkA3aKNm_H_Mb_WDNtA</recordid><startdate>20210803</startdate><enddate>20210803</enddate><creator>Das, Troyee</creator><creator>Deb, Aritra</creator><creator>Parida, Sibun</creator><creator>Mondal, Sudip</creator><creator>Khatua, Sunirmal</creator><creator>Ghosh, Zhumur</creator><general>Taylor & Francis</general><scope>BLEPL</scope><scope>DTL</scope><scope>HGBXW</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/0000-0002-0624-9718</orcidid></search><sort><creationdate>20210803</creationdate><title>LncRBase V.2: an updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients</title><author>Das, Troyee ; Deb, Aritra ; Parida, Sibun ; Mondal, Sudip ; Khatua, Sunirmal ; Ghosh, Zhumur</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c468t-25b67ad6cbd217025869ef3ad8deaeac2bc3f8bcd31de7026fdf1fbb9eb9116a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Animals</topic><topic>Biochemistry & Molecular Biology</topic><topic>Breast Neoplasms - genetics</topic><topic>Breast Neoplasms - metabolism</topic><topic>Breast Neoplasms - pathology</topic><topic>Caenorhabditis elegans - genetics</topic><topic>Caenorhabditis elegans - metabolism</topic><topic>Cattle</topic><topic>Chickens - genetics</topic><topic>Chickens - metabolism</topic><topic>clinicLSNP</topic><topic>Databases, Nucleic Acid</topic><topic>Drosophila melanogaster - genetics</topic><topic>Drosophila melanogaster - metabolism</topic><topic>Female</topic><topic>female cancer</topic><topic>Genome</topic><topic>Humans</topic><topic>Life Sciences & Biomedicine</topic><topic>lncrbase</topic><topic>lncRNA variant</topic><topic>Long non-coding RNA</topic><topic>Male</topic><topic>Mice</topic><topic>MicroRNAs - classification</topic><topic>MicroRNAs - genetics</topic><topic>MicroRNAs - metabolism</topic><topic>Molecular Sequence Annotation</topic><topic>Ovarian Neoplasms - genetics</topic><topic>Ovarian Neoplasms - metabolism</topic><topic>Ovarian Neoplasms - pathology</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Rats</topic><topic>Research Paper</topic><topic>RNA, Long Noncoding - classification</topic><topic>RNA, Long Noncoding - genetics</topic><topic>RNA, Long Noncoding - metabolism</topic><topic>RNA, Small Interfering - classification</topic><topic>RNA, Small Interfering - genetics</topic><topic>RNA, Small Interfering - metabolism</topic><topic>Science & Technology</topic><topic>sORFs</topic><topic>Species Specificity</topic><topic>sub-cellular localization</topic><topic>Uterine Cervical Neoplasms - genetics</topic><topic>Uterine Cervical Neoplasms - metabolism</topic><topic>Uterine Cervical Neoplasms - pathology</topic><topic>Zebrafish - genetics</topic><topic>Zebrafish - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Das, Troyee</creatorcontrib><creatorcontrib>Deb, Aritra</creatorcontrib><creatorcontrib>Parida, Sibun</creatorcontrib><creatorcontrib>Mondal, Sudip</creatorcontrib><creatorcontrib>Khatua, Sunirmal</creatorcontrib><creatorcontrib>Ghosh, Zhumur</creatorcontrib><collection>Web of Science Core Collection</collection><collection>Science Citation Index Expanded</collection><collection>Web of Science - Science Citation Index Expanded - 2021</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>RNA biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Das, Troyee</au><au>Deb, Aritra</au><au>Parida, Sibun</au><au>Mondal, Sudip</au><au>Khatua, Sunirmal</au><au>Ghosh, Zhumur</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>LncRBase V.2: an updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients</atitle><jtitle>RNA biology</jtitle><stitle>RNA BIOL</stitle><addtitle>RNA Biol</addtitle><date>2021-08-03</date><risdate>2021</risdate><volume>18</volume><issue>8</issue><spage>1136</spage><epage>1151</epage><pages>1136-1151</pages><issn>1547-6286</issn><eissn>1555-8584</eissn><abstract>The recent discovery of long non-coding RNA as a regulatory molecule in the cellular system has altered the concept of the functional aptitude of the genome. Since our publication of the first version of LncRBase in 2014, there has been an enormous increase in the number of annotated lncRNAs of multiple species other than Human and Mouse. LncRBase V.2 hosts information of 549,648 lncRNAs corresponding to six additional species besides Human and Mouse, viz. Rat, Fruitfly, Zebrafish, Chicken, Cow and C.elegans. It provides additional distinct features such as (i) Transcription Factor Binding Site (TFBS) in the lncRNA promoter region, (ii) sub-cellular localization pattern of lncRNAs (iii) lnc-pri-miRNAs (iv) Possible small open reading frames (sORFs) within lncRNA. (v) Manually curated information of interacting target molecules and disease association of lncRNA genes (vi) Distribution of lncRNAs across multiple tissues of all species. Moreover, we have hosted ClinicLSNP within LncRBase V.2. ClinicLSNP has a comprehensive catalogue of lncRNA variants present within breast, ovarian, and cervical cancer inferred from 561 RNA-Seq data corresponding to these cancers. Further, we have checked whether these lncRNA variants overlap with (i)Repeat elements,(ii)CGI, (iii)TFBS within lncRNA loci (iv)SNP localization in trait-associated Linkage Disequilibrium(LD) region, (v)predicted the potentially pathogenic variants and (vi)effect of SNP on lncRNA secondary structure. Overall, LncRBaseV.2 is a user-friendly database to survey, search and retrieve information about multi-species lncRNAs. Further, ClinicLSNP will serve as a useful resource for cancer specific lncRNA variants and their related information. The database is freely accessible and available at
http://dibresources.jcbose.ac.in/zhumur/lncrbase2/
.</abstract><cop>PHILADELPHIA</cop><pub>Taylor & Francis</pub><pmid>33112702</pmid><doi>10.1080/15476286.2020.1833529</doi><tpages>16</tpages><orcidid>https://orcid.org/0000-0002-0624-9718</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Animals Biochemistry & Molecular Biology Breast Neoplasms - genetics Breast Neoplasms - metabolism Breast Neoplasms - pathology Caenorhabditis elegans - genetics Caenorhabditis elegans - metabolism Cattle Chickens - genetics Chickens - metabolism clinicLSNP Databases, Nucleic Acid Drosophila melanogaster - genetics Drosophila melanogaster - metabolism Female female cancer Genome Humans Life Sciences & Biomedicine lncrbase lncRNA variant Long non-coding RNA Male Mice MicroRNAs - classification MicroRNAs - genetics MicroRNAs - metabolism Molecular Sequence Annotation Ovarian Neoplasms - genetics Ovarian Neoplasms - metabolism Ovarian Neoplasms - pathology Polymorphism, Single Nucleotide Rats Research Paper RNA, Long Noncoding - classification RNA, Long Noncoding - genetics RNA, Long Noncoding - metabolism RNA, Small Interfering - classification RNA, Small Interfering - genetics RNA, Small Interfering - metabolism Science & Technology sORFs Species Specificity sub-cellular localization Uterine Cervical Neoplasms - genetics Uterine Cervical Neoplasms - metabolism Uterine Cervical Neoplasms - pathology Zebrafish - genetics Zebrafish - metabolism |
| title | LncRBase V.2: an updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients |
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