List of long non-coding RNA databases

This article provides a list of long noncoding RNA databases, which provide information about lncRNAs.[1][2]

Long non-coding RNA databases

Name Description type Link References
lncRNABase is designed for decoding miRNA-lncRNA(lncRNAs, pseudogenes, circRNAs) and miRNA-ceRNA interaction networks from 108 CLIP-Seq datasets and provides Pan-Cancer(14 cancer types with >6000 tumor samples) interaction networks of lncRNAs, miRNAs, ceRNAs, mRNAs and RNA-Binding Proteins.. database website [3][4]
ChIPBase ChIPBase is a database for annotating and exploring the expression profiles and the transcriptional regulation of lncRNAs and other ncRNAs. database website [5]
LNCipedia a database for annotated human lncRNA transcript sequences and structures database website [6][7]
lncRNAdb lncRNAdb is a database providing comprehensive annotations of functional long non-coding RNAs (lncRNAs) database website [8]
LncRNAWiki LncRNAWiki is a wiki-based, publicly editable and open-content platform for community curation of human long non-coding RNAs (lncRNAs), viz., a community-curated resource of lncRNA knowledge. database website [9]
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. database website
NONCODE NONCODE provides an integrative annotation of long noncoding RNAs. database website [10]
lncRNome lncRNome is a comprehensive searchable biologically oriented knowledgebase for long noncoding RNAs in Humans. database website
NRED a database of long noncoding RNA expression. database website [11]
C-It-Loci A database of RNA expression and conserved loci for studying lncRNAs across species. database website

[12]

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 3858397Freely accessible. 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 3336981Freely accessible. PMID 22546862.
  3. ↑ Yang, J. -H.; Li, J. -H.; Shao, P.; Zhou, H.; Chen, Y. -Q.; Qu, L. -H. (2010). "StarBase: A database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data". Nucleic Acids Research. 39 (Database issue): D202–D209. doi:10.1093/nar/gkq1056. PMC 3013664Freely accessible. PMID 21037263.
  4. ↑ Li, JH; Liu, S; Zhou, H; Qu, LH; Yang, JH (Jan 1, 2014). "starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data.". Nucleic Acids Research. 42 (1): D92–7. doi:10.1093/nar/gkt1248. PMID 24297251.
  5. ↑ Yang, J. -H.; Li, J. -H.; Jiang, S.; Zhou, H.; Qu, L. -H. (2012). "ChIPBase: A database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data". Nucleic Acids Research. 41 (Database issue): D177–D187. doi:10.1093/nar/gks1060. PMC 3531181Freely accessible. PMID 23161675.
  6. ↑ 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 3531107Freely accessible. PMID 23042674.
  7. ↑ 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. PMID 25378313.
  8. ↑ 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 3013714Freely accessible. PMID 21112873.
  9. ↑ 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 4383965Freely accessible. PMID 25399417.
  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 3245065Freely accessible. 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 2686506Freely accessible. 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.

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