Database Commons

a catalog of biological databases

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

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General information

URL: http://rmvar.renlab.org
Full name:
Description: Database of functional variants involved in RNA modifications
Year founded: 2018
Last update:
Version:
Accessibility:
Manual:
Accessible
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Country/Region: China
Data type:
RNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: Sun Yat-Sen University
Address:
City: Guangzhou
Province/State: Guangdong
Country/Region: China
Contact name (PI/Team): Jian Ren
Contact email (PI/Helpdesk): renjian.sysu@gmail.com

Publications

33021671
RMVar: an updated database of functional variants involved in RNA modifications. [PMID: 33021671]
Xiaotong Luo, Huiqin Li, Jiaqi Liang, Qi Zhao, Yubin Xie, Jian Ren, Zhixiang Zuo

Distinguishing the few disease-related variants from a massive number of passenger variants is a major challenge. Variants affecting RNA modifications that play critical roles in many aspects of RNA metabolism have recently been linked to many human diseases, such as cancers. Evaluating the effect of genetic variants on RNA modifications will provide a new perspective for understanding the pathogenic mechanism of human diseases. Previously, we developed a database called 'm6AVar' to host variants associated with m6A, one of the most prevalent RNA modifications in eukaryotes. To host all RNA modification (RM)-associated variants, here we present an updated version of m6AVar renamed RMVar (http://rmvar.renlab.org). In this update, RMVar contains 1 678 126 RM-associated variants for 9 kinds of RNA modifications, namely m6A, m6Am, m1A, pseudouridine, m5C, m5U, 2'-O-Me, A-to-I and m7G, at three confidence levels. Moreover, RBP binding regions, miRNA targets, splicing events and circRNAs were integrated to assist investigations of the effects of RM-associated variants on posttranscriptional regulation. In addition, disease-related information was integrated from ClinVar and other genome-wide association studies (GWAS) to investigate the relationship between RM-associated variants and diseases. We expect that RMVar may boost further functional studies on genetic variants affecting RNA modifications.

Nucleic Acids Res. 2020:() | 2 Citations (from Europe PMC, 2021-06-12)
29036329
m6AVar: a database of functional variants involved in m6A modification. [PMID: 29036329]
Zheng Y, Nie P, Peng D, He Z, Liu M, Xie Y, Miao Y, Zuo Z, Ren J.

Identifying disease-causing variants among a large number of single nucleotide variants (SNVs) is still a major challenge. Recently, N6-methyladenosine (m6A) has become a research hotspot because of its critical roles in many fundamental biological processes and a variety of diseases. Therefore, it is important to evaluate the effect of variants on m6A modification, in order to gain a better understanding of them. Here, we report m6AVar (http://m6avar.renlab.org), a comprehensive database of m6A-associated variants that potentially influence m6A modification, which will help to interpret variants by m6A function. The m6A-associated variants were derived from three different m6A sources including miCLIP/PA-m6A-seq experiments (high confidence), MeRIP-Seq experiments (medium confidence) and transcriptome-wide predictions (low confidence). Currently, m6AVar contains 16 132 high, 71 321 medium and 326 915 low confidence level m6A-associated variants. We also integrated the RBP-binding regions, miRNA-targets and splicing sites associated with variants to help users investigate the effect of m6A-associated variants on post-transcriptional regulation. Because it integrates the data from genome-wide association studies (GWAS) and ClinVar, m6AVar is also a useful resource for investigating the relationship between the m6A-associated variants and disease. Overall, m6AVar will serve as a useful resource for annotating variants and identifying disease-causing variants.

Nucleic Acids Res. 2018:46(D1) | 47 Citations (from Europe PMC, 2021-06-12)

Ranking

All databases:
527/4987 (89.453%)
Modification:
24/225 (89.778%)
Genotype phenotype and variation:
65/700 (90.857%)
527
Total Rank
49
Citations
16.333
z-index

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Record metadata

Created on: 2020-09-06
Curated by:
Chang Liu [2020-11-10]
Dong Zou [2020-09-06]