We present MaREA4Galaxy, a user-friendly tool that allows a user to characterize and to graphically compare groups of samples with different transcriptional regulation of metabolism, as estimated from cross-sectional RNA-seq data. The tool is available as plug-in for the widely-used Galaxy platform for comparative genomics and bioinformatics analyses. MaREA4Galaxy combines three modules. The Expression2RAS module, which, for each reaction of a specified set, computes a Reaction Activity Score (RAS) as a function of the expression level of genes encoding for the associated enzyme. The MaREA (Metabolic Reaction Enrichment Analysis) module that allows to highlight significant differences in reaction activities between specified groups of samples. The Clustering module which employs the RAS computed before as a metric for unsupervised clustering of samples into distinct metabolic subgroups; the Clustering tool provides different clustering techniques and implements standard methods to evaluate the goodness of the results.

Damiani, C., Rovida, L., Maspero, D., Sala, I., Rosato, L., Di Filippo, M., et al. (2020). MaREA4Galaxy: metabolic reaction enrichment analysis and visualization of RNA-seq data using Galaxy. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 18, 993-999 [10.1016/j.csbj.2020.04.008].

MaREA4Galaxy: metabolic reaction enrichment analysis and visualization of RNA-seq data using Galaxy

Damiani, C
Primo
;
Rovida, L;Maspero, D;Di Filippo, M;Pescini, D;Graudenzi, A;Antoniotti, M
Penultimo
;
Mauri, G
Ultimo
2020

Abstract

We present MaREA4Galaxy, a user-friendly tool that allows a user to characterize and to graphically compare groups of samples with different transcriptional regulation of metabolism, as estimated from cross-sectional RNA-seq data. The tool is available as plug-in for the widely-used Galaxy platform for comparative genomics and bioinformatics analyses. MaREA4Galaxy combines three modules. The Expression2RAS module, which, for each reaction of a specified set, computes a Reaction Activity Score (RAS) as a function of the expression level of genes encoding for the associated enzyme. The MaREA (Metabolic Reaction Enrichment Analysis) module that allows to highlight significant differences in reaction activities between specified groups of samples. The Clustering module which employs the RAS computed before as a metric for unsupervised clustering of samples into distinct metabolic subgroups; the Clustering tool provides different clustering techniques and implements standard methods to evaluate the goodness of the results.
Articolo in rivista - Articolo scientifico
RNA-seq; Metabolism; Galaxy; Sample stratification; TCGA
English
17-apr-2020
2020
18
993
999
open
Damiani, C., Rovida, L., Maspero, D., Sala, I., Rosato, L., Di Filippo, M., et al. (2020). MaREA4Galaxy: metabolic reaction enrichment analysis and visualization of RNA-seq data using Galaxy. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 18, 993-999 [10.1016/j.csbj.2020.04.008].
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/269031
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