MEXPRESS: visualizing expression, DNA methylation and clinical TCGA data.
MEXPRESS: visualizing expression, DNA methylation and clinical TCGA data.
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DOI：
10.1186/s12864-015-1847-z
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发表时间：
2015-08-26
期刊：
影响因子：
4.4
通讯作者：
Van Criekinge W
中科院分区：
文献类型：
--
作者：
Koch A;De Meyer T;Jeschke J;Van Criekinge W
近年来，越来越多的基因组和临床癌症数据已经通过大规模的合作项目，如癌症基因组图谱（TCGA）。然而，只要这些数据集难以访问和解释，它们对研究界的主要部分基本上是无用的，它们的科学潜力将无法充分实现。为了解决这些问题，我们开发了MEXPRESS，这是一种简单易用的网络工具，用于在单基因水平上整合和可视化表达、DNA甲基化和临床TCGA数据（http：mexpress.be）。与现有的工具相比，MEXPRESS允许研究人员快速可视化和解释不同的TCGA数据集及其与单个基因的关系，如前列腺癌中GSTP 1所示。我们还使用MEXPRESS来揭示乳腺癌亚型之间PAM 50标记基因MLPH的DNA甲基化状态的差异，以及这些差异如何与MPLH的表达相关。我们已经创建了一个用户友好的工具，用于TCGA数据的可视化和解释，为临床研究人员提供了一种简单的方法来评估TCGA数据，以确定他们感兴趣的基因或候选生物标志物。本文的在线版本（doi：10.1186/s12864-015-1847-z）包含补充材料，可供授权用户使用。
In recent years, increasing amounts of genomic and clinical cancer data have become publically available through large-scale collaborative projects such as The Cancer Genome Atlas (TCGA). However, as long as these datasets are difficult to access and interpret, they are essentially useless for a major part of the research community and their scientific potential will not be fully realized. To address these issues we developed MEXPRESS, a straightforward and easy-to-use web tool for the integration and visualization of the expression, DNA methylation and clinical TCGA data on a single-gene level (http://mexpress.be). In comparison to existing tools, MEXPRESS allows researchers to quickly visualize and interpret the different TCGA datasets and their relationships for a single gene, as demonstrated for GSTP1 in prostate adenocarcinoma. We also used MEXPRESS to reveal the differences in the DNA methylation status of the PAM50 marker gene MLPH between the breast cancer subtypes and how these differences were linked to the expression of MPLH. We have created a user-friendly tool for the visualization and interpretation of TCGA data, offering clinical researchers a simple way to evaluate the TCGA data for their genes or candidate biomarkers of interest. The online version of this article (doi:10.1186/s12864-015-1847-z) contains supplementary material, which is available to authorized users.