Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 47 (W1), W561-W565

MEXPRESS Update 2019

Affiliations

MEXPRESS Update 2019

Alexander Koch et al. Nucleic Acids Res.

Abstract

The recent growth in the number of publicly available cancer omics databases has been accompanied by the development of various tools that allow researchers to visually explore these data. In 2015, we built MEXPRESS, an online tool for the integration and visualization of gene expression, DNA methylation and clinical data from The Cancer Genome Atlas (TCGA), a large collection of publicly available multi-omics cancer data. MEXPRESS addresses the need for an easy-to-use, interactive application that allows researchers to identify dysregulated genes and their clinical relevance in cancer. Furthermore, while other tools typically do not support integrated visualization of expression and DNA methylation data in combination with the precise genomic location of the methylation, MEXPRESS is unique in how it depicts these diverse data types together. Motivated by the large number of users MEXPRESS has managed to attract over the past 3 years and the recent migration of all TCGA data to a new data portal, we developed a new version of MEXPRESS (https://mexpress.be). It contains the latest TCGA data, additional types of omics and clinical data and extra functionality, allowing users to explore mechanisms of gene dysregulation beyond expression and DNA methylation.

Figures

Figure 1.
Figure 1.
MEXPRESS visualization of the TCGA data for GSTP1 in prostate adenocarcinoma. (A) The default view, in which the samples are sorted by their GSTP1 expression levels and the samples without expression data were removed. The figure and the statistics on the right hand side show how GSTP1 expression and promoter DNA methylation are negatively correlated. (B) The summary view, a novel feature of MEXPRESS, in which the samples have been divided into two groups based on their GSTP1 expression level. The horizontal lines at each probe location indicate the median percentage of methylation (β value), whereas the vertical lines mark the range between the 25th and the 75th percentile.
Figure 2.
Figure 2.
MEXPRESS visualization of the TCGA data for CDKN2A in lung squamous cell carcinoma. This figure shows the complex interplay between gene expression, copy number, DNA methylation and somatic mutations, highlighting the value of the data types that have been added in the new version of MEXPRESS.

Similar articles

See all similar articles

Cited by 5 articles

References

    1. Ciriello G., Miller M.L., Aksoy B.A., Senbabaoglu Y., Schultz N., Sander C. Emerging landscape of oncogenic signatures across human cancers. Nat. Genet. 2013; 45:1127–1133. - PMC - PubMed
    1. Sanchez-Vega F., Mina M., Armenia J., Chatila W.K., Luna A., La K.C., Dimitriadoy S., Liu D.L., Kantheti H.S., Saghafinia S. et al. . Oncogenic signaling pathways in the cancer genome atlas. Cell. 2018; 173:321–337. - PMC - PubMed
    1. Gao J., Aksoy B.A., Dogrusoz U., Dresdner G., Gross B., Sumer S.O., Sun Y., Jacobsen A., Sinha R., Larsson E. et al. . Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci. Signal. 2013; 6:l1. - PMC - PubMed
    1. Diez-Villanueva A., Mallona I., Peinado M.A. Wanderer, an interactive viewer to explore DNA methylation and gene expression data in human cancer. Epigenetics Chromatin. 2015; 8:22. - PMC - PubMed
    1. Koch A., De Meyer T., Jeschke J., Van Criekinge W. MEXPRESS: visualizing expression, DNA methylation and clinical TCGA data. BMC Genomics. 2015; 16:636. - PMC - PubMed
Feedback