lncRNASNP Edit

Citations: 83

z-index: 20.75

Basic information
Short name lncRNASNP
Full name
Description LncRNASNP is a database providing comprehensive resources of single nucleotide polymorphisms (SNPs) in human/mouse lncRNAs.
URL http://bioinfo.life.hust.edu.cn/lncRNASNP/
Year founded 2014
Last update & version 2017-12-01 v2.0
Accessibility Accessible
Contact information

The contact information is provided to facilitate update of database information, and it is curated based on the contact details in the database or the related publications. To ensure effective contact with database constructors, we give priority to the contact details in the database.

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
Data information
Data object
Data type
Database category
Major organism
Keyword
Publications
  • lncRNASNP2: an updated database of functional SNPs and mutations in human and mouse lncRNAs. [PMID: 29077939]
    Ya-Ru Miao, Wei Liu, Qiong Zhang, An-Yuan Guo

    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)

    9 Citations (from Europe PMC, 2019-07-27)

  • lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse. [PMID: 25332392]
    Jing Gong, Wei Liu, Jiayou Zhang, Xiaoping Miao, An-Yuan Guo

    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)

    74 Citations (from Europe PMC, 2019-08-03)

Rank

  • Ranking in all databases: No. 341
  • Ranking in category/categories:
    • Genotype phenotype and variation: No. 44
    • Interaction: No. 43
The box plots depict Z-index distribution for all databases in Database Commons and for specific database category/categories. The red line indicates log2(Z-index) of lncRNASNP.

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Record metadata

  • Created on: 2015-06-20
    • ***ina@***c.cn [2018-06-06]
    • ***d@***c.cn [2018-03-05]
    • ***hunlei@***c.cn [2016-04-17]
    • ***hunlei@***c.cn [2016-04-01]
    • ***hunlei@***c.cn [2015-11-20]
    • ***hunlei@***c.cn [2015-06-29]

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