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List of long non-coding RNA databases

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This is a list of long noncoding RNA databases, which provide information about lncRNAs.

Long non-coding RNA databases

Name Description References
deepBase Identification, expression, evolution and function of long non-coding RNAs (LncRNAs), small RNAs and circular RNAs from deep-sequencing data
LNCipedia A comprehensive compendium of human long non-coding RNAs.
lncRNAdb The Reference Database For Functional Long Noncoding RNAs.
LncRNAWiki A wiki-based, publicly editable and open-content platform for community curation of human long non-coding RNAs (lncRNAs)
LncBook A comprehensive collection of 270,044 human lncRNAs and systematic curation of lncRNAs’ annotation by multi-omics data integration, function annotation and disease association
MONOCLdb The MOuse NOnCode Lung database provides the annotations and expression profiles of mouse long non-coding RNAs (lncRNAs) involved in influenza and SARS-CoV infections.
NONCODE An integrated knowledge database dedicated to ncRNAs, especially lncRNAs
lncRNome A comprehensive searchable biologically oriented knowledgebase for long noncoding RNAs in Humans.
NRED A database of long noncoding RNA expression.
C-It-Loci A tool to explore and to compare the expression profiles of conserved loci among various tissues in three organisms

MiTranscriptome A catalog of human long poly-adenylated RNA transcripts derived from computational analysis of high-throughput RNA-Seq data from over 6,500 samples, spanning diverse cancer and tissue types
slncky Evolution Browser This site contains alignments and evolutionary metrics of conserved lncRNAs.
Cancer LncRNA Census (CLC) Database of long-noncoding RNAs causally implicated in cancer through in vivo, in vitro and other evidence.
BIGTranscriptome High-confidence of coding and noncoding transcriptomes assembled with hundreds of pseudo-stranded and stranded RNA-seq datasets.
lncRNAKB A knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA
lncHUB2 Functional predictions of human and mouse long non-coding RNAs based on lncRNA-gene co-expression correlations.

References

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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)
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
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