List of long non-coding RNA databases

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

References

^ 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.
^ 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.
^ 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.
^ 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.
^ 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.
^ 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.
^ 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.
^ 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.
^ 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)
^ 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.
^ 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.
^ 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.
^ 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.
^ 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.
^ 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.
^ 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.
^ 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.
^ 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.

[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.

[pmid24922324-9] 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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