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基因组变异对于ceRNA调控影响数据库:LnCeVar

LnCeVar: a comprehensive database of genomic variations that disturb ceRNA network regulation11.501Nucleic Acids Res . 2020 Jan 8;48(D1):D111-D117. doi: 10.1093/nar/gkz887.

Abstract

LnCeVar (http://www.bio-bigdata.net/LnCeVar/) is a comprehensive database that aims to provide genomic variations that disturb lncRNA-associated competing endogenous RNA (ceRNA) network regulation curated from the published literature and high-throughput data sets. LnCeVar curated 119 501 variation-ceRNA events from thousands of samples and cell lines, including: (i) more than 2000 experimentally supported circulating, drug-resistant and prognosis-related lncRNA biomarkers; (ii) 11 418 somatic mutation-ceRNA events from TCGA and COSMIC; (iii) 112 674 CNV-ceRNA events from TCGA; (iv) 67 066 SNP-ceRNA events from the 1000 Genomes Project. LnCeVar provides a user-friendly searching and browsing interface. In addition, as an important supplement of the database, several flexible tools have been developed to aid retrieval and analysis of the data. The LnCeVar-BLAST interface is a convenient way for users to search ceRNAs by interesting sequences. LnCeVar-Function is a tool for performing functional enrichment analysis. LnCeVar-Hallmark identifies dysregulated cancer hallmarks of variation-ceRNA events. LnCeVar-Survival performs COX regression analyses and produces survival curves for variation-ceRNA events. LnCeVar-Network identifies and creates a visualization of dysregulated variation-ceRNA networks. Collectively, LnCeVar will serve as an important resource for investigating the functions and mechanisms of personalized genomic variations that disturb ceRNA network regulation in human diseases.

ceRNA作为一个成熟的基因间调控假说，一直受到广泛关注。小编今天就给大家介绍一个特别的数据库：基因组变异对于ceRNA调控影响的数据库LnCeVar(http://www.bio-bigdata.net/LnCeVar/index.jsp)。

LnCeVar从成千上万的样本和细胞系中识别了ceRNA事件，包括：

实验支持的循环、耐药和预后相关的lncRNA生物标志物；
来自TCGA和COSMIC的体细胞突变-ceRNA事件；
来自TCGA的CNV–ceRNA事件；
千人基因组计划中的SNP-ceRNA事件。

LnCeVar工作流程如下：

感兴趣RNA的搜索界面；
感兴趣RNA的浏览和人体图的界面；
通过搜索和浏览感兴趣RNA得到的数据表；
感兴趣RNA–变异–ceRNA事件的基本信息和miRNA结合状态；
功能分析，包括GO和KEGG富集分析；
基于相关生物学过程的感兴趣RNA的hallmark分析；
受基因组变异干扰的所有可能的与感兴趣RNA相关的ceRNA相互作用的网络图；
与感兴趣RNA相关的ceRNA的生存分析和生存曲线；
不同样品和人群中感兴趣RNA的基因组变异分布；
感兴趣RNA和相关ceRNA的聚类图；
LnCeVar–BLAST的自定义序列搜索和LnCeVar–Browser的基因组搜索。

接下来我们就来看看LnCeVar的使用方法和结果展示吧！

首先，在首页搜索框直接搜索感兴趣的lncRNA/miRNA/mRNA/癌症等信息，以NEAT1为例，LnCeVar会给出该lncRNA按照基因组变异分类的整体概述结果，包括基于TCGA和Cosmic数据库中与突变相关的ceRNA结果，基于千人基因组计划获得的SNP有关的数据结果，基于TCGA数据库拷贝数变异相关的ceRNA结果，基于实验验证的突变或标志物。