List of long non-coding RNA databases explained

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

Long non-coding RNA databases

NameDescription References
deepBaseIdentification, expression, evolution and function of long non-coding RNAs (LncRNAs), small RNAs and circular RNAs from deep-sequencing data [3]
LNCipediaA comprehensive compendium of human long non-coding RNAs. [4] [5]
lncRNAdbThe Reference Database For Functional Long Noncoding RNAs. [6]
LncRNAWikiA wiki-based, publicly editable and open-content platform for community curation of human long non-coding RNAs (lncRNAs) [7]
LncBookA comprehensive collection of 270,044 human lncRNAs and systematic curation of lncRNAs’ annotation by multi-omics data integration, function annotation and disease association [8]
MONOCLdbThe 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]
NONCODEAn integrated knowledge database dedicated to ncRNAs, especially lncRNAs [10]
lncRNomeA comprehensive searchable biologically oriented knowledgebase for long noncoding RNAs in Humans.
NREDA database of long noncoding RNA expression. [11]
C-It-LociA tool to explore and to compare the expression profiles of conserved loci among various tissues in three organisms [12]
MiTranscriptomeA 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 BrowserThis 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]
BIGTranscriptomeHigh-confidence of coding and noncoding transcriptomes assembled with hundreds of pseudo-stranded and stranded RNA-seq datasets. [16]
lncRNAKBA knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA[17]

Notes and References

  1. Rinn . J. L. . Chang . H. Y. . 10.1146/annurev-biochem-051410-092902 . Genome Regulation by Long Noncoding RNAs . Annual Review of Biochemistry. 81 . 145–166 . 2012 . 22663078 . 3858397 .
  2. Martin . L. . Chang . H. Y. . 10.1172/JCI60020 . Uncovering the role of genomic "dark matter" in human disease . Journal of Clinical Investigation. 122 . 5 . 1589–1595 . 2012 . 22546862 . 3336981 .
  3. Zheng . LL . Li . JH . Wu . J . Sun . WJ . Liu . S . Wang . ZL . Zhou . H . Yang . JH . Qu . LH . deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data. . Nucleic Acids Research . 4 January 2016 . 44 . D1 . D196–202 . 10.1093/nar/gkv1273 . 26590255. 4702900 .
  4. Volders . P. -J. . Helsens . K. . Wang . X. . Menten . B. . Martens . L. . Gevaert . K. . Vandesompele . J. . Mestdagh . P. . LNCipedia: A database for annotated human lncRNA transcript sequences and structures . 10.1093/nar/gks915 . Nucleic Acids Research. 2012 . 23042674 . 3531107. 41 . Database issue . D246–D251.
  5. 25378313. 2015. Volders. P. J.. An update on LNCipedia: A database for annotated human lncRNA sequences. Nucleic Acids Research. 43. Database issue. D174–180. Verheggen. K. Menschaert. G. Vandepoele. K. Martens. L. Vandesompele. J. Mestdagh. P. 10.1093/nar/gku1060 . 4383901.
  6. Amaral . P. P. . Clark . M. B. . Gascoigne . D. K. . Dinger . M. E. . Mattick . J. S. . LncRNAdb: A reference database for long noncoding RNAs . 10.1093/nar/gkq1138 . Nucleic Acids Research . 39 . Database issue . D146–D151 . 3013714 . 2010 . 21112873.
  7. Ma . Lina . Li . Ang . Zou . Dong . Xu . Xingjian . Xia . Lin . Yu . Jun . Bajic . Vladimir B. . Zhang . Zhang . LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs . 10.1093/nar/gku1167 . Nucleic Acids Research . 43 . Database issue . D187–D92 . 4383965 . 2015 . 25399417.
  8. Ma . Lina . Cao . Jiabao . Liu . Lin . Du . Qiang . Li . Zhao . Zou . Dong . Bajic . Vladimir B. . Zhang . Zhang . LncBook: a curated knowledgebase of human long non-coding RNAs . 10.1093/nar/gky960 . Nucleic Acids Research . 47 . Database issue . D128–D134 . 6323930 . 2019 . 30329098.
  9. Josset L, Tchitchek N, Gralinski LE, Ferris MT, Eisfeld AJ, Green RR . etal. 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 . 2014 . 11 . 7 . 875–90 . 24922324 . 10.4161/rna.29442 . 4179962 .
  10. Bu . D. . Yu . K. . Sun . S. . Xie . C. . Skogerbø . G. . Miao . R. . Xiao . H. . Liao . Q. . Luo . H. . 10.1093/nar/gkr1175 . Zhao . G. . Zhao . H. . Liu . Z. . Liu . C. . Chen . R. . Zhao . Y. . NONCODE v3.0: Integrative annotation of long noncoding RNAs . Nucleic Acids Research . 40 . Database issue . D210–D215 . 2011 . 22135294 . 3245065 .
  11. Dinger . M. E. . Pang . K. C. . Mercer . T. R. . Crowe . M. L. . Grimmond . S. M. . Mattick . J. S. . 10.1093/nar/gkn617 . NRED: A database of long noncoding RNA expression . Nucleic Acids Research . 37 . Database issue . D122–D126 . 2009 . 18829717 . 2686506 .
  12. Weirick . T. . David . J.. Stefanie . D. . Uchida . S. . C-It-Loci: a knowledge database for tissue-enriched loci . 10.1093/bioinformatics/btv410 . Bioinformatics. 2015 . 26163692 . 31 . 21 . 3537–3543. free.
  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. 10.1038/ng.3192. 1546-1718. 4417758. 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. 10.1186/s13059-016-0880-9. 1474-760X. 4739325. 26838501 . free .
  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. en. 3. 1 . 56 . 10.1038/s42003-019-0741-7 . 32024996 . 7002399. free.
  16. You. Bo-Hyun. Yoon. Sang-Ho. Nam. Jin-Wu. 2017-06-01. High-confidence coding and noncoding transcriptome maps. Genome Research. en. 27. 6. 1050–1062. 10.1101/gr.214288.116. 1088-9051. 28396519. free. 5453319.
  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 . . 7 . 1 . 326 . 326 . 10.1038/s41597-020-00659-z . free . 33020484 . 7536183. 2020NatSD...7..326S .

This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "List of long non-coding RNA databases".

Except where otherwise indicated, Everything.Explained.Today is © Copyright 2009-2024, A B Cryer, All Rights Reserved. Cookie policy.