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

NameDescriptionReferences
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]
lncHUB2 Functional predictions of human and mouse long non-coding RNAs based on lncRNA-gene co-expression correlations. [18]

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 baad009. doi:10.1093/database/baad009. ISSN   1758-0463. PMC   9985331 . PMID   36869839.
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