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.[1][2]

Long non-coding RNA databases[edit]

Name Description References
deepBase Identification, expression, evolution and function of long non-coding RNAs (LncRNAs), small RNAs and circular RNAs from deep-sequencing data [3]
LNCipedia A comprehensive compendium of human long non-coding RNAs. [4][5]
lncRNAdb The Reference Database For Functional Long Noncoding RNAs. [6]
LncRNAWiki A wiki-based, publicly editable and open-content platform for community curation of human long non-coding RNAs (lncRNAs) [7]
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 [8]
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 [9]
lncRNome A comprehensive searchable biologically oriented knowledgebase for long noncoding RNAs in Humans.
NRED A database of long noncoding RNA expression. [10]
C-It-Loci A tool to explore and to compare the expression profiles of conserved loci among various tissues in three organisms

[11]

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 [12]
slncky Evolution Browser This site contains alignments and evolutionary metrics of conserved lncRNAs. [13]
Cancer LncRNA Census (CLC) Database of long-noncoding RNAs causally implicated in cancer through in vivo, in vitro and other evidence. [14]

References[edit]

  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): D174–80. 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. ^ 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.
  10. ^ 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.
  11. ^ 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.
  12. ^ 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.
  13. ^ 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.
  14. ^ Carlevaro-Fita, Joana; Lanzós, Andrés; Feuerbach, Lars; Hong, Chen; Mas-Ponte, David; Skou Pedersen, Jakob; Johnson, Rory (2017-08-25). "Unique genomic features and deeply-conserved functions of long non-coding RNAs in the Cancer LncRNA Census (CLC)". bioRxiv: 152769. doi:10.1101/152769.