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List of long non-coding RNA databases
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<h2 id="long-non-coding-rna-databases">Long non-coding RNA databases</h2> <table><tbody><tr><th>Name</th><th>Description</th><th>References</th></tr><tr><td><a href="http://rna.sysu.edu.cn/deepBase/">deepBase</a></td><td>Identification, expression, evolution and function of <a href="/facts/Long_non-coding_RNA/FHyAb6hP">long non-coding RNAs</a> (LncRNAs), small RNAs and circular RNAs from deep-sequencing data</td><td><a class="footnote-ref" id="fnref:3" href="#fn:3"><sup>3</sup></a></td></tr><tr><td><a href="http://www.lncipedia.org">LNCipedia</a></td><td>A comprehensive compendium of <a href="/facts/Human/rlcTENsr">human</a> long non-coding RNAs.</td><td><a class="footnote-ref" id="fnref:4" href="#fn:4"><sup>4</sup></a><a class="footnote-ref" id="fnref:5" href="#fn:5"><sup>5</sup></a></td></tr><tr><td><a href="http://lncrnadb.com/">lncRNAdb</a></td><td>The Reference Database For Functional Long Noncoding RNAs.</td><td><a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a></td></tr><tr><td><a href="http://lncrna.big.ac.cn/">LncRNAWiki</a></td><td>A wiki-based, publicly editable and open-content platform for community curation of human long non-coding RNAs (lncRNAs)</td><td><a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a></td></tr><tr><td><a href="http://bigd.big.ac.cn/lncbook">LncBook</a></td><td>A comprehensive collection of 270,044 human lncRNAs and systematic curation of lncRNAs’ annotation by multi-omics data integration, function annotation and disease association</td><td><a class="footnote-ref" id="fnref:8" href="#fn:8"><sup>8</sup></a></td></tr><tr><td><a href="http://www.monocldb.org">MONOCLdb</a></td><td>The MOuse NOnCode Lung database provides the annotations and expression profiles of mouse long non-coding RNAs (lncRNAs) involved in <a href="/facts/Influenza/nWuFzh6L">influenza</a> and <a href="/facts/SARS-CoV/jXYCe6w5">SARS-CoV</a> infections.</td><td><a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a></td></tr><tr><td><a href="http://www.noncode.org">NONCODE</a></td><td>An integrated knowledge database dedicated to ncRNAs, especially lncRNAs</td><td><a class="footnote-ref" id="fnref:10" href="#fn:10"><sup>10</sup></a></td></tr><tr><td><a href="http://genome.igib.res.in/lncRNome/">lncRNome</a></td><td>A comprehensive searchable biologically oriented knowledgebase for long noncoding RNAs in Humans.</td><td></td></tr><tr><td><a href="https://web.archive.org/web/20121128024842/http://nred.matticklab.com/cgi-bin/ncrnadb.pl">NRED</a></td><td>A database of long noncoding RNA expression.</td><td><a class="footnote-ref" id="fnref:11" href="#fn:11"><sup>11</sup></a></td></tr><tr><td><a href="http://c-it-loci.uni-frankfurt.de">C-It-Loci</a></td><td>A tool to explore and to compare the expression profiles of conserved loci among various tissues in three organisms</td><td><p><a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a></p></td></tr><tr><td><a href="http://mitranscriptome.org/">MiTranscriptome</a></td><td>A catalog of human long poly-adenylated RNA transcripts derived from computational analysis of high-throughput <a href="/facts/RNA/HxPeNfNj">RNA</a>-Seq data from over 6,500 samples, spanning diverse <a href="/facts/Cancer/PVW6n1D0">cancer</a> and <a href="/facts/Tissue_(biology)/H7CpML7A">tissue</a> types</td><td><a class="footnote-ref" id="fnref:13" href="#fn:13"><sup>13</sup></a></td></tr><tr><td><a href="https://garberwiki.umassmed.edu/slncky/"><i>slncky</i> Evolution Browser</a></td><td>This site contains alignments and evolutionary metrics of conserved lncRNAs.</td><td><a class="footnote-ref" id="fnref:14" href="#fn:14"><sup>14</sup></a></td></tr><tr><td><a href="https://www.gold-lab.org/clc">Cancer LncRNA Census (CLC)</a></td><td>Database of long-noncoding RNAs causally implicated in cancer through <i>in vivo</i>, <i>in vitro</i> and other evidence.</td><td><a class="footnote-ref" id="fnref:15" href="#fn:15"><sup>15</sup></a></td></tr><tr><td><a href="http://big.hanyang.ac.kr/CAFE">BIGTranscriptome</a></td><td>High-confidence of coding and noncoding transcriptomes assembled with hundreds of pseudo-stranded and stranded RNA-seq datasets.</td><td><a class="footnote-ref" id="fnref:16" href="#fn:16"><sup>16</sup></a></td></tr><tr><td><a href="https://osf.io/ru4d2/">lncRNAKB</a></td><td>A knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA</td><td><a class="footnote-ref" id="fnref:17" href="#fn:17"><sup>17</sup></a></td></tr><tr><td><a href="https://maayanlab.cloud/lncHUB2/">lncHUB2</a></td><td>Functional predictions of human and mouse long non-coding RNAs based on lncRNA-gene co-expression correlations.</td><td><a class="footnote-ref" id="fnref:18" href="#fn:18"><sup>18</sup></a></td></tr></tbody></table> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>Rinn, J. L.; Chang, H. Y. (2012). "Genome Regulation by Long Noncoding RNAs". Annual Review of Biochemistry. 81: 145–166. doi:10.1146/annurev-biochem-051410-092902. PMC 3858397. PMID 22663078. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3858397" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3858397</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>Martin, L.; Chang, H. Y. (2012). "Uncovering the role of genomic "dark matter" in human disease". Journal of Clinical Investigation. 122 (5): 1589–1595. doi:10.1172/JCI60020. PMC 3336981. PMID 22546862. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3336981" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3336981</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>Zheng, LL; Li, JH; Wu, J; Sun, WJ; Liu, S; Wang, ZL; Zhou, H; Yang, JH; Qu, LH (4 January 2016). "deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data". Nucleic Acids Research. 44 (D1): D196–202. doi:10.1093/nar/gkv1273. PMC 4702900. PMID 26590255. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702900" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702900</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>Volders, P. -J.; Helsens, K.; Wang, X.; Menten, B.; Martens, L.; Gevaert, K.; Vandesompele, J.; Mestdagh, P. (2012). "LNCipedia: A database for annotated human lncRNA transcript sequences and structures". Nucleic Acids Research. 41 (Database issue): D246 – D251. doi:10.1093/nar/gks915. PMC 3531107. PMID 23042674. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531107" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531107</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>Volders, P. J.; Verheggen, K; Menschaert, G; Vandepoele, K; Martens, L; Vandesompele, J; Mestdagh, P (2015). "An update on LNCipedia: A database for annotated human lncRNA sequences". Nucleic Acids Research. 43 (Database issue): D174–180. doi:10.1093/nar/gku1060. PMC 4383901. PMID 25378313. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383901" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383901</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>Amaral, P. P.; Clark, M. B.; Gascoigne, D. K.; Dinger, M. E.; Mattick, J. S. (2010). "LncRNAdb: A reference database for long noncoding RNAs". Nucleic Acids Research. 39 (Database issue): D146 – D151. doi:10.1093/nar/gkq1138. PMC 3013714. PMID 21112873. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013714" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013714</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>Ma, Lina; Li, Ang; Zou, Dong; Xu, Xingjian; Xia, Lin; Yu, Jun; Bajic, Vladimir B.; Zhang, Zhang (2015). "LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs". Nucleic Acids Research. 43 (Database issue): D187 – D92. doi:10.1093/nar/gku1167. PMC 4383965. PMID 25399417. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383965" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383965</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>Ma, Lina; Cao, Jiabao; Liu, Lin; Du, Qiang; Li, Zhao; Zou, Dong; Bajic, Vladimir B.; Zhang, Zhang (2019). "LncBook: a curated knowledgebase of human long non-coding RNAs". Nucleic Acids Research. 47 (Database issue): D128 – D134. doi:10.1093/nar/gky960. PMC 6323930. PMID 30329098. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323930" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323930</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>Josset L, Tchitchek N, Gralinski LE, Ferris MT, Eisfeld AJ, Green RR; et al. (2014). "Annotation of long non-coding RNAs expressed in collaborative cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts". RNA Biol. 11 (7): 875–90. doi:10.4161/rna.29442. PMC 4179962. PMID 24922324.{{cite journal}}: CS1 maint: multiple names: authors list (link) <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4179962" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4179962</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>Bu, D.; Yu, K.; Sun, S.; Xie, C.; Skogerbø, G.; Miao, R.; Xiao, H.; Liao, Q.; Luo, H.; Zhao, G.; Zhao, H.; Liu, Z.; Liu, C.; Chen, R.; Zhao, Y. (2011). "NONCODE v3.0: Integrative annotation of long noncoding RNAs". Nucleic Acids Research. 40 (Database issue): D210 – D215. doi:10.1093/nar/gkr1175. PMC 3245065. PMID 22135294. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245065" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245065</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> <li id="fn:11"><p>Dinger, M. E.; Pang, K. C.; Mercer, T. R.; Crowe, M. L.; Grimmond, S. M.; Mattick, J. S. (2009). "NRED: A database of long noncoding RNA expression". Nucleic Acids Research. 37 (Database issue): D122 – D126. doi:10.1093/nar/gkn617. PMC 2686506. PMID 18829717. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686506" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686506</a> <a href="#fnref:11" class="footnote-back-ref">↩</a></p></li> <li id="fn:12"><p>Weirick, T.; David, J.; Stefanie, D.; Uchida, S. (2015). "C-It-Loci: a knowledge database for tissue-enriched loci". Bioinformatics. 31 (21): 3537–3543. doi:10.1093/bioinformatics/btv410. PMID 26163692. <a href="https://doi.org/10.1093%2Fbioinformatics%2Fbtv410" target="_blank">https://doi.org/10.1093%2Fbioinformatics%2Fbtv410</a> <a href="#fnref:12" class="footnote-back-ref">↩</a></p></li> <li id="fn:13"><p>Iyer, Matthew K.; Niknafs, Yashar S.; Malik, Rohit; Singhal, Udit; Sahu, Anirban; Hosono, Yasuyuki; Barrette, Terrence R.; Prensner, John R.; Evans, Joseph R. (March 2015). "The landscape of long noncoding RNAs in the human transcriptome". Nature Genetics. 47 (3): 199–208. doi:10.1038/ng.3192. ISSN 1546-1718. PMC 4417758. PMID 25599403. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417758" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417758</a> <a href="#fnref:13" class="footnote-back-ref">↩</a></p></li> <li id="fn:14"><p>Chen, Jenny; Shishkin, Alexander A.; Zhu, Xiaopeng; Kadri, Sabah; Maza, Itay; Guttman, Mitchell; Hanna, Jacob H.; Regev, Aviv; Garber, Manuel (2016-02-02). "Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs". Genome Biology. 17: 19. doi:10.1186/s13059-016-0880-9. ISSN 1474-760X. PMC 4739325. PMID 26838501. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4739325" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4739325</a> <a href="#fnref:14" class="footnote-back-ref">↩</a></p></li> <li id="fn:15"><p>Carlevaro-Fita, Joana; Lanzós, Andrés; Feuerbach, Lars; Hong, Chen; Mas-Ponte, David; Skou Pedersen, Jakob; Johnson, Rory (2020). "Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis". Communications Biology. 3 (1): 56. doi:10.1038/s42003-019-0741-7. PMC 7002399. PMID 32024996. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7002399" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7002399</a> <a href="#fnref:15" class="footnote-back-ref">↩</a></p></li> <li id="fn:16"><p>You, Bo-Hyun; Yoon, Sang-Ho; Nam, Jin-Wu (2017-06-01). "High-confidence coding and noncoding transcriptome maps". Genome Research. 27 (6): 1050–1062. doi:10.1101/gr.214288.116. ISSN 1088-9051. PMC 5453319. PMID 28396519. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5453319" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5453319</a> <a href="#fnref:16" class="footnote-back-ref">↩</a></p></li> <li id="fn:17"><p>Seifuddin, Fayaz; Singh, Komudi; Suresh, Abhilash; Judy, Jennifer T.; Chen, Yun-Ching; Chaitankar, Vijender; Tunc, Ilker; Ruan, Xiangbo; Ping, Li; Chen, Yi; Cao, Haiming; Lee, Richard S.; Goes, Fernando S.; Zandi, Peter P.; Jafri, M. Saleet; Pirooznia, Mehdi (2020-10-05). "lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA". Scientific Data. 7 (1) 326: 326. Bibcode:2020NatSD...7..326S. doi:10.1038/s41597-020-00659-z. PMC 7536183. PMID 33020484. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7536183" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7536183</a> <a href="#fnref:17" class="footnote-back-ref">↩</a></p></li> <li id="fn:18"><p>Marino, Giacomo B; Wojciechowicz, Megan L; Clarke, Daniel J B; Kuleshov, Maxim V; Xie, Zhuorui; Jeon, Minji; Lachmann, Alexander; Ma’ayan, Avi (2023-03-04). "lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs". Database. 2023. doi:10.1093/database/baad009. ISSN 1758-0463. PMC 9985331. PMID 36869839. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9985331" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9985331</a> <a href="#fnref:18" class="footnote-back-ref">↩</a></p></li> </ol>