Biology: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

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. [9]
NONCODE An integrated knowledge database dedicated to ncRNAs, especially lncRNAs [10]
lncRNome A comprehensive searchable biologically oriented knowledgebase for long noncoding RNAs in Humans.
NRED A database of long noncoding RNA expression. [11]
C-It-Loci A tool to explore and to compare the expression profiles of conserved loci among various tissues in three organisms

[12]

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 [13]
slncky Evolution Browser This site contains alignments and evolutionary metrics of conserved lncRNAs. [14]
Cancer LncRNA Census (CLC) Database of long-noncoding RNAs causally implicated in cancer through in vivo, in vitro and other evidence. [15]
BIGTranscriptome High-confidence of coding and noncoding transcriptomes assembled with hundreds of pseudo-stranded and stranded RNA-seq datasets. [16]
lncRNAKB A knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA [17]

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. 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. PMID 22546862. 
  3. ↑ Zheng, LL; Li, JH; Wu, J; Sun, WJ; Liu, S; Wang, ZL; Zhou, H; Yang, JH et al. (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. 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. 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. 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. 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. 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. PMID 30329098. 
  9. ↑ Josset L, Tchitchek N, Gralinski LE, Ferris MT, Eisfeld AJ, Green RR (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. PMID 24922324. 
  10. ↑ Bu, D.; Yu, K.; Sun, S.; Xie, C.; Skogerbø, G.; Miao, R.; Xiao, H.; Liao, Q. et al. (2011). "NONCODE v3.0: Integrative annotation of long noncoding RNAs". Nucleic Acids Research 40 (Database issue): D210–D215. doi:10.1093/nar/gkr1175. 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. 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. et al. (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. PMID 25599403. 
  14. ↑ Chen, Jenny; Shishkin, Alexander A.; Zhu, Xiaopeng; Kadri, Sabah; Maza, Itay; Guttman, Mitchell; Hanna, Jacob H.; Regev, Aviv et al. (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. 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" (in en). Communications Biology 3 (1): 56. doi:10.1038/s42003-019-0741-7. PMID 32024996. 
  16. ↑ You, Bo-Hyun; Yoon, Sang-Ho; Nam, Jin-Wu (2017-06-01). "High-confidence coding and noncoding transcriptome maps" (in en). Genome Research 27 (6): 1050–1062. doi:10.1101/gr.214288.116. ISSN 1088-9051. PMID 28396519. 
  17. ↑ Seifuddin, Fayaz; Singh, Komudi; Suresh, Abhilash; Judy, Jennifer T.; Chen, Yun-Ching; Chaitankar, Vijender; Tunc, Ilker; Ruan, Xiangbo et al. (2020-10-05). "lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA". Scientific Data 7 (1): 326. doi:10.1038/s41597-020-00659-z. PMID 33020484. 



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