Lnc2Cancer: a Manually Curated Database of Experimentally Supported LncRNAs Associated with Various Human Cancers

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2015 Oct 21

PMID 26481356

Citations 166

Authors

Shangwei Ning

Jizhou Zhang

Peng Wang

Hui Zhi

Jianjian Wang

Yue Liu

Yue Gao

Maoni Guo

Ming Yue

Lihua Wang

Xia Li

Affiliations

Soon will be listed here.

Abstract

Lnc2Cancer (http://www.bio-bigdata.net/lnc2cancer) is a manually curated database of cancer-associated long non-coding RNAs (lncRNAs) with experimental support that aims to provide a high-quality and integrated resource for exploring lncRNA deregulation in various human cancers. LncRNAs represent a large category of functional RNA molecules that play a significant role in human cancers. A curated collection and summary of deregulated lncRNAs in cancer is essential to thoroughly understand the mechanisms and functions of lncRNAs. Here, we developed the Lnc2Cancer database, which contains 1057 manually curated associations between 531 lncRNAs and 86 human cancers. Each association includes lncRNA and cancer name, the lncRNA expression pattern, experimental techniques, a brief functional description, the original reference and additional annotation information. Lnc2Cancer provides a user-friendly interface to conveniently browse, retrieve and download data. Lnc2Cancer also offers a submission page for researchers to submit newly validated lncRNA-cancer associations. With the rapidly increasing interest in lncRNAs, Lnc2Cancer will significantly improve our understanding of lncRNA deregulation in cancer and has the potential to be a timely and valuable resource.

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References

Volders P, Verheggen K, Menschaert G, Vandepoele K, Martens L, Vandesompele J . An update on LNCipedia: a database for annotated human lncRNA sequences. Nucleic Acids Res. 2014; 43(Database issue):D174-80. PMC: 4383901. DOI: 10.1093/nar/gku1060. View

Forbes S, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H . COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res. 2014; 43(Database issue):D805-11. PMC: 4383913. DOI: 10.1093/nar/gku1075. View

Du Z, Fei T, Verhaak R, Su Z, Zhang Y, Brown M . Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat Struct Mol Biol. 2013; 20(7):908-13. PMC: 3702647. DOI: 10.1038/nsmb.2591. View

Kim H, Lee D, Yim G, Nam E, Kim S, Kim S . Long non-coding RNA HOTAIR is associated with human cervical cancer progression. Int J Oncol. 2014; 46(2):521-30. PMC: 4277242. DOI: 10.3892/ijo.2014.2758. View

Yuan J, Yang F, Wang F, Ma J, Guo Y, Tao Q . A long noncoding RNA activated by TGF-β promotes the invasion-metastasis cascade in hepatocellular carcinoma. Cancer Cell. 2014; 25(5):666-81. DOI: 10.1016/j.ccr.2014.03.010. View

Batista P, Chang H . Long noncoding RNAs: cellular address codes in development and disease. Cell. 2013; 152(6):1298-307. PMC: 3651923. DOI: 10.1016/j.cell.2013.02.012. View

Li Y, Qiu C, Tu J, Geng B, Yang J, Jiang T . HMDD v2.0: a database for experimentally supported human microRNA and disease associations. Nucleic Acids Res. 2013; 42(Database issue):D1070-4. PMC: 3964961. DOI: 10.1093/nar/gkt1023. View

Pelaez N, Carthew R . Biological robustness and the role of microRNAs: a network perspective. Curr Top Dev Biol. 2012; 99:237-55. PMC: 3746555. DOI: 10.1016/B978-0-12-387038-4.00009-4. View

Ma L, Li A, Zou D, Xu X, Xia L, Yu J . LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs. Nucleic Acids Res. 2014; 43(Database issue):D187-92. PMC: 4383965. DOI: 10.1093/nar/gku1167. View

10.

Flintoft L . Non-coding RNA: Structure and function for lncRNAs. Nat Rev Genet. 2013; 14(9):598. DOI: 10.1038/nrg3561. View

11.

Xiang J, Yin Q, Chen T, Zhang Y, Zhang X, Wu Z . Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus. Cell Res. 2014; 24(5):513-31. PMC: 4011346. DOI: 10.1038/cr.2014.35. View

12.

Paraskevopoulou M, Georgakilas G, Kostoulas N, Reczko M, Maragkakis M, Dalamagas T . DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. Nucleic Acids Res. 2012; 41(Database issue):D239-45. PMC: 3531175. DOI: 10.1093/nar/gks1246. View

13.

Prensner J, Iyer M, Sahu A, Asangani I, Cao Q, Patel L . The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex. Nat Genet. 2013; 45(11):1392-8. PMC: 3812362. DOI: 10.1038/ng.2771. View

14.

Yang J, Li J, Jiang S, Zhou H, Qu L . ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic Acids Res. 2012; 41(Database issue):D177-87. PMC: 3531181. DOI: 10.1093/nar/gks1060. View

15.

Jiang Q, Ma R, Wang J, Wu X, Jin S, Peng J . LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data. BMC Genomics. 2015; 16 Suppl 3:S2. PMC: 4331805. DOI: 10.1186/1471-2164-16-S3-S2. View

16.

Hsu S, Tseng Y, Shrestha S, Lin Y, Khaleel A, Chou C . miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res. 2013; 42(Database issue):D78-85. PMC: 3965058. DOI: 10.1093/nar/gkt1266. View

17.

Quek X, Thomson D, Maag J, Bartonicek N, Signal B, Clark M . lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. Nucleic Acids Res. 2014; 43(Database issue):D168-73. PMC: 4384040. DOI: 10.1093/nar/gku988. View

18.

Hanahan D, Weinberg R . Hallmarks of cancer: the next generation. Cell. 2011; 144(5):646-74. DOI: 10.1016/j.cell.2011.02.013. View

19.

Hajjari M, Salavaty A . HOTAIR: an oncogenic long non-coding RNA in different cancers. Cancer Biol Med. 2015; 12(1):1-9. PMC: 4383848. DOI: 10.7497/j.issn.2095-3941.2015.0006. View

20.

Ning S, Zhao Z, Ye J, Wang P, Zhi H, Li R . LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs. BMC Bioinformatics. 2014; 15:152. PMC: 4038069. DOI: 10.1186/1471-2105-15-152. View