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Data released on March 26, 2018

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

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 RIS BibTeX Text

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.

Contact Submitter

Additional information:

https://github.com/RenLabBioinformatics/m6ASNP

http://m6asnp.renlab.org

Keywords:

n6-methyladenosine (m6a) variant annotation variant effect prediction random forest 

Genomic, Software

http://gigadb.org/images/data/cropped/100428.jpg

Funding:

  • Funding body - National Key Research and Development Program
  • Award ID - 2017YFA0106700
  • Comment - Roles and mechanisms of m6A methylation of lncRNA in the maintenance and differentiation of pluripotent stem cells
  • Awardee - Z Zuo
  • Funding body - National Natural Science Foundation of China
  • Award ID - 31771462
  • Comment - Construction and application of a comprehensive toolkit for the analysis of RNA methylation high-throughput data at single-nucleotide resolution
  • Awardee - J Ren
  • Funding body - National Natural Science Foundation of China
  • Award ID - 81772614
  • Comment - Molecular mechanism of m6A methyltransferase METTL3 in promoting proliferation and metastasis of colorectal cancer
  • Awardee - Z Zuo
  • Funding body - National Natural Science Foundation of China
  • Award ID - 31471252
  • Comment - Systematic study of SUMO regulations using biomolecular fluorescence complementation(BiFC)
  • Awardee - J Ren
  • Funding body - National Natural Science Foundation of China
  • Award ID - U1611261
  • Comment - The hybrid platform for biomedical bigdata applications on Tianhe-2
  • Awardee - Z Zuo
  • Funding body - National Natural Science Foundation of China
  • Award ID - 31500813
  • Comment - The mechanisms of fullerene nanomaterials modulation of CaMKII activity and functions through generation of reactive oxygen species
  • Awardee - Y Miao
  • Funding body - China Postdoctoral Science Foundation
  • Award ID - 2017M622864
  • Comment - Construction and application of a comprehensive platform for the analysis of allele-specific m6A sites
  • Awardee - Y Xie
  • Funding body - Fundamental Research Funds for the Central Universities
  • Award ID - No. 17lgpy106
  • Comment - The study of the mechanisms of fullerene in regulating learning and memory through reactive oxygen species
  • Awardee - Y Miao
  • Funding body - Guangdong Natural Science Foundation
  • Award ID - 2014TQ01R387
  • Comment - Guangdong High-level Personnel of Special Support Program
  • Awardee - J Ren
  • Funding body - Guangdong Natural Science Foundation
  • Award ID - 2014A030313181
  • Comment - Systematic study of SUMO regulation in Homo sapiens
  • Awardee - J Ren
  • Funding body - Guangdong Natural Science Foundation
  • Award ID - 2017A030313134
  • Comment - The mechanisms of fullerene C60 in modulating learning and memory
  • Awardee - Y Miao

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File NameSample IDData TypeFile FormatSizeRelease Date 
GitHub archivearchive3.07 MB2018-03-22
Tabular DataCSV516.08 KB2018-03-22
Tabular DataCSV592.21 KB2018-03-22
Tabular DataCSV253.66 KB2018-03-22
Tabular DataCSV835 KB2018-03-22
ReadmeTEXT2.49 KB2018-03-22
SoftwareUNKNOWN7.55 MB2018-03-22
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