We are analyzing https://link.springer.com/article/10.1186/s12864-015-1847-z.

Title:
MEXPRESS: visualizing expression, DNA methylation and clinical TCGA data | BMC Genomics
Description:
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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Keywords {🔍}

data, cancer, expression, methylation, mexpress, tcga, article, clinical, genome, pubmed, samples, google, scholar, visualization, research, gstp, gene, dna, genomics, tools, breast, tool, browser, cas, subtypes, types, analysis, genomic, datasets, researchers, prostate, differences, figure, open, access, tumor, normal, table, central, atlas, adenocarcinoma, human, promoter, information, biomarkers, correlation, file, view, ucsc, javascript,

Topics {✒️}

crispr/dcas9-based methylation editing tim de meyer large-scale oncogenomics datasets rna-seq-derived expression data glutathione s-transferase pi van de rijn large-scale collaborative projects cancer genome atlas article download pdf comprehensive molecular profiling location-bound genomic data wilcoxon rank-sum test de meyer rna-seq data location-bound genomic features related subjects integrative genomics viewer cancer genome workbench national cancer institute privacy choices/manage cookies breast cancer based human genome browser epigenetic profiles false discovery rate explore genes traditional genome browsers breast invasive carcinoma js javascript library conventional genome browser bmc genomics 16 breast cancer subtypes current biomarker research specific research questions broad research audience human breast tumours tcga research network full access creative commons license rank-sum test author information authors breast cancer subtype breast cancer samples high-throughput technologies multidimensional tcga data cancer epigenetics data mining analysis detailed methylation analysis dna methylation status dna methylation biomarkers circulating tumor dna

Schema {🗺️}

WebPage:
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         headline:MEXPRESS: visualizing expression, DNA methylation and clinical TCGA data
         description: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.
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      headline:MEXPRESS: visualizing expression, DNA methylation and clinical TCGA data
      description: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.
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         Data visualization
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         general
         Microarrays
         Proteomics
         Animal Genetics and Genomics
         Microbial Genetics and Genomics
         Plant Genetics and Genomics
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      affiliation:
            name:Université Libre de Bruxelles
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               type:PostalAddress
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      name:Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
      name:Laboratory of Cancer Epigenetics, Université Libre de Bruxelles, Brussels, Belgium
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