DNMIVD: DNA methylation interactive visualization database
DNMIVD: DNA methylation interactive visualization database
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DNMIVD：DNA 甲基化交互式可视化数据库
DOI：
10.1093/nar/gkz830
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发表时间：
2020-01-08
影响因子：
14.9
通讯作者：
Shi, Tieliu
中科院分区：
文献类型：
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作者：
Ding, Wubin;Chen, Jiwei;Shi, Tieliu
异常DNA甲基化在癌症进展中起重要作用。然而，目前还没有资源能够全面提供基于DNA甲基化的诊断和预后模型、表达甲基化数量性状位点（emQTL）、途径活性甲基化数量性状位点（pathway- meqtl）、差异变量和差异甲基化CpGs、生存分析以及不同癌症的功能表观遗传模块。这些为研究人员从癌症的不同方面探索DNA甲基化谱提供了有价值的信息。为此，我们构建了一个用户友好的DNA甲基化交互式可视化数据库（DNMIVD），该数据库全面提供了以下重要资源：(1)癌症基因组图谱（TCGA）中基于DNA甲基化的多种癌症类型的诊断和预后模型；（ii）不同癌症的meQTL、emQTL和pathway-meQTL；（iii）整合TCGA肿瘤DNA甲基化和基因表达数据，构建基于蛋白-蛋白相互作用（PPI）和共现互异（COME）网络的功能表观遗传模块（FEM）；（iv）差异可变和差异甲基化的CpGs和差异甲基化的基因以及相关的增强子信息；(v)基因启动子甲基化与相应基因表达的相关性；（vi）患者生存相关的CpGs与不同终点的基因。DNMIVD可在http://www.unimd.org/dnmivd/免费获得。我们相信DNMIVD可以促进各种癌症的研究。
Aberrant DNA methylation plays an important role in cancer progression. However, no resource has been available that comprehensively provides DNA methylation-based diagnostic and prognostic models, expression-methylation quantitative trait loci (emQTL), pathway activity-methylation quantitative trait loci (pathway-meQTL), differentially variable and differentially methylated CpGs, and survival analysis, as well as functional epigenetic modules for different cancers. These provide valuable information for researchers to explore DNA methylation profiles from different aspects in cancer. To this end, we constructed a user-friendly database named DNA Methylation Interactive Visualization Database (DNMIVD), which comprehensively provides the following important resources: (i) diagnostic and prognostic models based on DNA methylation for multiple cancer types of The Cancer Genome Atlas (TCGA); (ii) meQTL, emQTL and pathway-meQTL for diverse cancers; (iii) Functional Epigenetic Modules (FEM) constructed from Protein-Protein Interactions (PPI) and Co-Occurrence and Mutual Exclusive (COME) network by integrating DNA methylation and gene expression data of TCGA cancers; (iv) differentially variable and differentially methylated CpGs and differentially methylated genes as well as related enhancer information; (v) correlations between methylation of gene promoter and corresponding gene expression and (vi) patient survival-associated CpGs and genes with different endpoints. DNMIVD is freely available at http://www.unimd.org/dnmivd/. We believe that DNMIVD can facilitate research of diverse cancers.