MaREA4Galaxy: Metabolic reaction enrichment analysis and visualization of RNA-seq data within Galaxy.
Galaxy
Metabolism
RNA-seq
Sample stratification
TCGA
Journal
Computational and structural biotechnology journal
ISSN: 2001-0370
Titre abrégé: Comput Struct Biotechnol J
Pays: Netherlands
ID NLM: 101585369
Informations de publication
Date de publication:
2020
2020
Historique:
received:
18
10
2019
revised:
20
03
2020
accepted:
08
04
2020
entrez:
7
5
2020
pubmed:
7
5
2020
medline:
7
5
2020
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 32373287
doi: 10.1016/j.csbj.2020.04.008
pii: S2001-0370(19)30465-9
pmc: PMC7191582
doi:
Types de publication
Journal Article
Langues
eng
Pagination
993-999Informations de copyright
© 2020 The Authors.
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