LnCeVar: a comprehensive database of genomic variations that disturb ceRNA network regulation
LnCeVar: a comprehensive database of genomic variations that disturb ceRNA network regulation
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LnCeVar：干扰 ceRNA 网络调控的基因组变异综合数据库
DOI：
10.1093/nar/gkz887
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发表时间：
2020-01-08
影响因子：
14.9
通讯作者：
Li, Xia
中科院分区：
文献类型：
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作者：
Wang, Peng;Li, Xin;Li, Xia
LnCeVar(http://www.bio-bigdata.net/LnCeVar/))是一个全面的数据库，旨在提供干扰LncRNA相关竞争内源RNA(CENA)网络调控的基因组变异，这些调控来自已发表的文献和高通量数据集。LnCeVar从数千个样本和细胞系中挑选了119 501个Cerna变异事件，包括：(I)2000多个实验支持的循环、耐药和与预后相关的lncRNA生物标记物；(Ii)11 418个体细胞突变-来自TCGA和COSMIC的Cerna事件；(Iii)来自TCGA的112 674个CNV-Cerna事件；(Iv)来自1000个基因组计划的67 066个SNP-Cerna事件。LnCeVar提供了用户友好的搜索和浏览界面。此外，作为数据库的重要补充，还开发了几个灵活的工具来协助检索和分析数据。LnCeVar-BLAST接口是用户按感兴趣的序列搜索ceRNA的便捷方式。LnCeVar-Function是一个用于执行功能丰富分析的工具。LnCeVar-Hallmark识别变异的失调癌症特征-Cerna事件。LnCeVar-Survival执行Cox回归分析并生成Variance-Cerna事件的生存曲线。LnCeVar-Network识别并创建失调变异的可视化-Cerna网络。总的来说，LnCeVar将成为研究个性化基因组变异的功能和机制的重要资源，这些变异扰乱了CENA网络在人类疾病中的调控。
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 in vestigatingthe functions and mechanisms of personalized genomic variations that disturb ceRNA network regulation in human diseases.