Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database information

lncRNASNP

General information

Description: LncRNASNP is a database providing comprehensive resources of single nucleotide polymorphisms (SNPs) in human/mouse lncRNAs.
Year founded: 2014
Last update: 2017-12-01
Version: v2.0
Accessibility:
Manual:
Accessible
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Country/Region: China
Data type:
RNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: Huazhong University of Science and Technology
Address: Wuhan,Hubei 430030,PR China
City: Wuhan
Province/State: Hubei
Country/Region: China
Contact name (PI/Team): An-Yuan Guo
Contact email (PI/Helpdesk): guoay@mail.hust.edu.cn

Record metadata

Created on: 2015-06-20
Curated by:
Lina Ma [2018-06-06]
Dong Zou [2018-03-05]
Chunlei Yu [2016-04-17]
Chunlei Yu [2016-04-01]
Chunlei Yu [2015-11-20]
Chunlei Yu [2015-06-29]

Ranking

All databases:
351/4656 (92.483%)
Genotype phenotype and variation:
49/628 (92.357%)
Interaction:
46/691 (93.488%)
351
Total Rank
111
Citations
22.2
z-index

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Not Rated
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Word cloud

Publications

29077939
lncRNASNP2: an updated database of functional SNPs and mutations in human and mouse lncRNAs. [PMID: 29077939]
Miao YR, Liu W, Zhang Q, Guo AY.

Long non-coding RNAs (lncRNAs) are emerging as important regulators in different biological processes through various ways. Because the related data, especially mutations in cancers, increased sharply, we updated the lncRNASNP to version 2 (http://bioinfo.life.hust.edu.cn/lncRNASNP2). lncRNASNP2 provides comprehensive information of SNPs and mutations in lncRNAs, as well as their impacts on lncRNA structure and function. lncRNASNP2 contains 7260238 SNPs on 141353 human lncRNA transcripts and 3921448 SNPs on 117405 mouse lncRNA transcripts. Besides the SNP information in the first version, the following new features were developed to improve the lncRNASNP2. (i) noncoding variants from COSMIC cancer data (859534) in lncRNAs and their effects on lncRNA structure and function; (ii) TCGA cancer mutations (315234) in lncRNAs and their impacts; (iii) lncRNA expression profiling of 20 cancer types in both tumor and its adjacent samples; (iv) expanded lncRNA-associated diseases; (v) optimized the results about lncRNAs structure change induced by variants; (vi) reduced false positives in miRNA and lncRNA interaction results. Furthermore, we developed online tools for users to analyze new variants in lncRNA. We aim to maintain the lncRNASNP as a useful resource for lncRNAs and their variants.

Nucleic Acids Res. 2018:46(D1) | 27 Citations (from Europe PMC, 2020-08-08)
25332392
lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse. [PMID: 25332392]
Gong J, Liu W, Zhang J, Miao X, Guo AY.

Long non-coding RNAs (lncRNAs) play key roles in various cellular contexts and diseases by diverse mechanisms. With the rapid growth of identified lncRNAs and disease-associated single nucleotide polymorphisms (SNPs), there is a great demand to study SNPs in lncRNAs. Aiming to provide a useful resource about lncRNA SNPs, we systematically identified SNPs in lncRNAs and analyzed their potential impacts on lncRNA structure and function. In total, we identified 495,729 and 777,095 SNPs in more than 30,000 lncRNA transcripts in human and mouse, respectively. A large number of SNPs were predicted with the potential to impact on the miRNA-lncRNA interaction. The experimental evidence and conservation of miRNA-lncRNA interaction, as well as miRNA expressions from TCGA were also integrated to prioritize the miRNA-lncRNA interactions and SNPs on the binding sites. Furthermore, by mapping SNPs to GWAS results, we found that 142 human lncRNA SNPs are GWAS tagSNPs and 197,827 lncRNA SNPs are in the GWAS linkage disequilibrium regions. All these data for human and mouse lncRNAs were imported into lncRNASNP database (http://bioinfo.life.hust.edu.cn/lncRNASNP/), which includes two sub-databases lncRNASNP-human and lncRNASNP-mouse. The lncRNASNP database has a user-friendly interface for searching and browsing through the SNP, lncRNA and miRNA sections. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2015:43(Database issue) | 85 Citations (from Europe PMC, 2020-08-15)