Supporting data for “m6ASNP: a tool for annotating genetic variants by m6A function”

Dataset type: Genomic, Software
Data released on March 26, 2018

Jiang S; Xie Y; He Z; Zhang Y; Zhao Y; Chen L; Zheng Y; Miao Y; Zuo Z; Ren J (2018): Supporting data for “m6ASNP: a tool for annotating genetic variants by m6A function” GigaScience Database. http://dx.doi.org/10.5524/100428

DOI10.5524/100428

Large-scale genome sequencing projects have identified many genetic variants for diverse diseases. A major goal of these projects is to characterize these genetic variants to provide insight into their function and roles in diseases. N6-methyladenosine (m6A) is one of the most abundant RNA modifications in eukaryotes. Recent studies have revealed that aberrant m6A modifications are involved in many diseases. In this study, we present a user-friendly web server called “m6ASNP” that is dedicated to the identification of genetic variants targeting m6A modification sites. A random forest model was implemented in m6ASNP to predict whether the methylation status of an m6A site is altered by the variants surrounding the site. In m6ASNP, genetic variants in a standard VCF format are accepted as the input data, and the output includes an interactive table containing the genetic variants annotated by m6A function. In addition, statistical diagrams and a genome browser are provided to visualize the characteristics and annotate the genetic variants. Altogether, we believe that m6ASNP is a highly convenient tool that can be used to boost further functional studies investigating genetic variants. The web server “m6ASNP” is implemented in JAVA and PHP and is freely available at http://m6asnp.renlab.org.

Additional details

Read the peer-reviewed publication(s):

Jiang, S., Xie, Y., He, Z., Zhang, Y., Zhao, Y., Chen, L., … Ren, J. (2018). m6ASNP: a tool for annotating genetic variants by m6A function. GigaScience, 7(5). doi:10.1093/gigascience/giy035

Additional information:

https://github.com/RenLabBioinformatics/m6ASNP

http://m6asnp.renlab.org





File NameSample IDData TypeFile FormatSizeRelease Date 
ReadmeTEXT2.49 KB2018-03-22
Tabular DataCSV253.66 KB2018-03-22
Tabular DataCSV516.08 KB2018-03-22
Tabular DataCSV592.21 KB2018-03-22
Tabular DataCSV835 KB2018-03-22
GitHub archivearchive3.07 MB2018-03-22
SoftwareUNKNOWN7.55 MB2018-03-22
Displaying 1-7 of 7 File(s).
Funding body Awardee Award ID Comments
National Key Research and Development Program Z Zuo 2017YFA0106700 Roles and mechanisms of m6A methylation of lncRNA in the maintenance and differentiation of pluripotent stem cells
National Natural Science Foundation of China J Ren 31771462 Construction and application of a comprehensive toolkit for the analysis of RNA methylation high-throughput data at single-nucleotide resolution
National Natural Science Foundation of China Z Zuo 81772614 Molecular mechanism of m6A methyltransferase METTL3 in promoting proliferation and metastasis of colorectal cancer
National Natural Science Foundation of China J Ren 31471252 Systematic study of SUMO regulations using biomolecular fluorescence complementation(BiFC)
National Natural Science Foundation of China Z Zuo U1611261 The hybrid platform for biomedical bigdata applications on Tianhe-2
National Natural Science Foundation of China Y Miao 31500813 The mechanisms of fullerene nanomaterials modulation of CaMKII activity and functions through generation of reactive oxygen species
China Postdoctoral Science Foundation Y Xie 2017M622864 Construction and application of a comprehensive platform for the analysis of allele-specific m6A sites
Fundamental Research Funds for the Central Universities Y Miao No. 17lgpy106 The study of the mechanisms of fullerene in regulating learning and memory through reactive oxygen species
Guangdong Natural Science Foundation J Ren 2014TQ01R387 Guangdong High-level Personnel of Special Support Program
Guangdong Natural Science Foundation J Ren 2014A030313181 Systematic study of SUMO regulation in Homo sapiens
Guangdong Natural Science Foundation Y Miao 2017A030313134 The mechanisms of fullerene C60 in modulating learning and memory
Date Action
March 26, 2018 Dataset publish
July 4, 2018 Manuscript Link added : 10.1093/gigascience/giy035