List of long non-coding RNA databases

Short description: None

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

## Long non-coding RNA databases

Name  | Description | References

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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. 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. 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. Bibcode: 2020NatSD...7..326S.
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" (in en). Database 2023. doi:10.1093/database/baad009. ISSN 1758-0463. PMID 36869839.

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