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Associated diseases

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MEXPRESS specifications

Information


Unique identifier OMICS_16286
Name MEXPRESS
Interface Web user interface
Restrictions to use None
Input data A gene symbol or Ensembl id, a cancer type.
Output data The corresponding expression, DNA methylation and clinical data, as well as the relationship between these data sets.
Programming languages Javascript, PHP, R, Shell (Bash)
Computer skills Basic
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Alexander Koch <>

Information


Unique identifier OMICS_16286
Name MEXPRESS
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data A gene symbol or Ensembl id, a cancer type.
Output data The corresponding expression, DNA methylation and clinical data, as well as the relationship between these data sets.
Operating system Unix/Linux
Programming languages Javascript, PHP, R, Shell (Bash)
Database management system MySQL
License MIT License
Computer skills Medium
Stability Stable
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Alexander Koch <>

Publication for MEXPRESS

library_books

MEXPRESS: visualizing expression, DNA methylation and clinical TCGA data.

2015 BMC Genomics
PMCID: 4549898
PMID: 26306699
DOI: 10.1186/s12864-015-1847-z

MEXPRESS in pipeline

2017
PMCID: 5431893
PMID: 28500316
DOI: 10.1038/s41598-017-01856-4

[…] for the identified smoking-related oncogenes. the rna expression data are log-transformed before being utilized for statistical analysis and data visualization. by using the web-based tool of mexpress, which has two main functions of pearson correlation and the non-parametric wilcoxon rank-sum test, we determined whether methylation probes were correlated with the extent of expression […]


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MEXPRESS in publications

 (8)
PMCID: 5431893
PMID: 28500316
DOI: 10.1038/s41598-017-01856-4

[…] for the identified smoking-related oncogenes. the rna expression data are log-transformed before being utilized for statistical analysis and data visualization. by using the web-based tool of mexpress, which has two main functions of pearson correlation and the non-parametric wilcoxon rank-sum test, we determined whether methylation probes were correlated with the extent of expression […]

PMCID: 5522326
PMID: 28467815
DOI: 10.18632/oncotarget.17107

[…] observed a predominant overlap with the dna hypermethylation signature of luminal bc as compared to tnbc patients (figure ). subsequent analysis of invasive bc patient samples (n = 871) by means of mexpress software revealed significant correlations between dna methylation levels of the verified cpg motifs and the her2, esr and pr status of bc patients (table ) []. in this respect, wa induced […]

PMCID: 5368932
PMID: 28347288
DOI: 10.1186/s12885-017-3224-6

[…] from tcga database (additional file : fig. s1, p < 0.001)., the tcga data about abcg2 in kidney clear cell cancer are available on the scientific website http://www.oncolnc.org, and http://mexpress.be/. there are significant differences of mrna levels of abcg2 between normal kidney tissue and tumor (p = <0.0001), and at various stages (p = 0.024). comparison of mrna levels of abcg2 […]

PMCID: 5346320
PMID: 27530686
DOI: 10.5483/BMBRep.2016.49.11.145

[…] with prognosis of patients. because typical molecular biologists would not have good background on statistics that is necessary to run survival analysis, it would be useful tool for them., mexpress (http://mexpress.be/) provides easy-to-use data visualization tool of the tcga data including mrna expression, dna methylation, and clinical data (). in addition, it also provide […]

PMCID: 5349929
PMID: 27845902
DOI: 10.18632/oncotarget.13275

[…] (log rank p=0.093). uqcrc1 was not associated with overall survival (log rank p=0.608)., in order to identify potential possible causes for uqcrfs1 and uqcrc1 downregulation, we used the mexpress software [] to evaluate the relevance of dna cpg island hypermethylation on gene expression levels in the cancer genome atlas dataset []. dna methylation levels of the uqcrfs1 and uqcrc […]


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MEXPRESS institution(s)
Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium; Laboratory of Cancer Epigenetics, Université Libre de Bruxelles, Brussels, Belgium; Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
MEXPRESS funding source(s)
Supported by grants from the Vlaamse Liga tegen Kanker (VLK) and the Fonds de la Recherche Scientifique (FNRS).

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