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m6ASNP：一种通过 m6A 功能注释遗传变异的工具。

m6ASNP: a tool for annotating genetic variants by m6A function.

机构信息

Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China.

State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.

出版信息

Gigascience. 2018 May 1;7(5). doi: 10.1093/gigascience/giy035.

DOI:10.1093/gigascience/giy035
PMID:29617790
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6007280/
Abstract

BACKGROUND

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.

FINDINGS

In this study, we present a user-friendly web server called "m6ASNP" that is dedicated to the identification of genetic variants that target 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 that surround the site. In m6ASNP, genetic variants in a standard variant call format (VCF) are accepted as the input data, and the output includes an interactive table that contains the genetic variants annotated by m6A function. In addition, statistical diagrams and a genome browser are provided to visualize the characteristics and to annotate the genetic variants.

CONCLUSIONS

We believe that m6ASNP is a very 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 [60].

摘要

背景

大规模基因组测序项目已经确定了许多与各种疾病相关的遗传变异。这些项目的主要目标之一是对这些遗传变异进行特征描述，以深入了解它们在疾病中的功能和作用。N6-甲基腺苷（m6A）是真核生物中最丰富的 RNA 修饰之一。最近的研究表明，异常的 m6A 修饰与许多疾病有关。

发现

在这项研究中，我们提出了一个用户友好的网络服务器，称为“m6ASNP”，专门用于鉴定靶向 m6A 修饰位点的遗传变异。m6ASNP 中实现了随机森林模型，以预测 m6A 位点的甲基化状态是否会被位点周围的变异所改变。在 m6ASNP 中，标准变异调用格式（VCF）中的遗传变异被接受为输入数据，输出包括一个交互式表格，其中包含 m6A 功能注释的遗传变异。此外，还提供了统计图表和基因组浏览器，以可视化特征并注释遗传变异。

结论

我们相信 m6ASNP 是一个非常方便的工具，可以用于促进进一步研究遗传变异的功能。网络服务器“m6ASNP”是用 JAVA 和 PHP 实现的，并可在[60]免费获得。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa0a/6007280/4bb60b9e3271/giy035fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa0a/6007280/1449af8da55c/giy035fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa0a/6007280/17412b34285f/giy035fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa0a/6007280/4bb60b9e3271/giy035fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa0a/6007280/1449af8da55c/giy035fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa0a/6007280/17412b34285f/giy035fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa0a/6007280/4bb60b9e3271/giy035fig3.jpg

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