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. 2015 Aug 26;16(1):636.
doi: 10.1186/s12864-015-1847-z.

MEXPRESS: visualizing expression, DNA methylation and clinical TCGA data

Alexander Koch  1   2 , Tim De Meyer  3 , Jana Jeschke  4 , Wim Van Criekinge  5
Affiliations

MEXPRESS: visualizing expression, DNA methylation and clinical TCGA data

Alexander Koch et al. BMC Genomics. .

Abstract

Background: 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 ).

Results: 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.

Conclusions: 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.

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Figures

Fig. 1
Fig. 1
Visualization of the TCGA data for GSTP1 in prostate adenocarcinoma using MEXPRESS. a In the default MEXPRESS plot, the samples are ordered by their expression value. This view shows how GSTP1 expression and promoter methylation are negatively correlated, which is confirmed by the Pearson correlation coefficients on the right. It also indicates that normal samples tend to have higher GSTP1 expression than tumor samples. b When reordered by sample type, the differences in expression and methylation between normal and tumor samples become even more apparent
Fig. 2
Fig. 2
MEXPRESS view of the TCGA data for MLPH in breast invasive carcinoma. The samples are ordered by breast cancer subtype, revealing clear differences in expression and methylation, as well as HER2, estrogen and progesterone receptor status, between the different subtypes
See this image and copyright information in PMC

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