School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China.
Guangzhou Institute of Respiratory health, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 510120, China.
Nucleic Acids Res. 2022 Jan 7;50(D1):D1208-D1215. doi: 10.1093/nar/gkab1088.
DNA methylation has a growing potential for use as a biomarker because of its involvement in disease. DNA methylation data have also substantially grown in volume during the past 5 years. To facilitate access to these fragmented data, we proposed DiseaseMeth version 3.0 based on DiseaseMeth version 2.0, in which the number of diseases including increased from 88 to 162 and High-throughput profiles samples increased from 32 701 to 49 949. Experimentally confirmed associations added 448 pairs obtained by manual literature mining from 1472 papers in PubMed. The search, analyze and tools sections were updated to increase performance. In particular, the FunctionSearch now provides for the functional enrichment of genes from localized GO and KEGG annotation. We have also developed a unified analysis pipeline for identifying differentially DNA methylated genes (DMGs) from the original data stored in the database. 22 718 DMGs were found in 99 diseases. These DMGs offer application in disease evaluation using two self-developed online tools, Methylation Disease Correlation and Cancer Prognosis & Co-Methylation. All query results can be downloaded and can also be displayed through a box plot, heatmap or network module according to whichever search section is used. DiseaseMeth version 3.0 is freely available at http://diseasemeth.edbc.org/.
由于 DNA 甲基化在疾病中的作用，它作为生物标志物的潜力越来越大。在过去的 5 年中，DNA 甲基化数据的数量也大幅增加。为了方便访问这些碎片化的数据，我们在 DiseaseMeth 版本 2.0 的基础上提出了 DiseaseMeth 版本 3.0，其中包括的疾病数量从 88 种增加到 162 种，高通量分析样本从 32701 种增加到 49949 种。通过从 PubMed 中的 1472 篇论文中手动文献挖掘，新增了 448 对经实验证实的关联。搜索、分析和工具部分进行了更新，以提高性能。特别是，FunctionSearch 现在可以对来自局部化 GO 和 KEGG 注释的基因进行功能富集分析。我们还开发了一个统一的分析管道，用于从数据库中存储的原始数据中识别差异 DNA 甲基化基因（DMGs）。在 99 种疾病中发现了 22718 个 DMGs。这些 DMGs 可以通过两个自主开发的在线工具，即甲基化疾病相关性和癌症预后与共甲基化，用于疾病评估。所有查询结果都可以下载，并且可以根据使用的搜索部分通过箱线图、热图或网络图模块显示。DiseaseMeth 版本 3.0 可在 http://diseasemeth.edbc.org/ 免费获得。
