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Bioinformatics Group Department of Co... 1 Galaxy Europe University of Freiburg ... 1 Medical Pharmacology Department Borde... 1 RECETOX Faculty of Science Masaryk Un... 1 University of Bordeaux Bordeaux Bioin... 1 University of Bordeaux CNRS IBGC UMR ... 1 University of Bordeaux INSERM BPH U12... 1
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Bioinformatics Group Department of Co... 1 Galaxy Europe University of Freiburg ... 1 Medical Pharmacology Department Borde... 1 RECETOX Faculty of Science Masaryk Un... 1 University of Bordeaux Bordeaux Bioin... 1 University of Bordeaux CNRS IBGC UMR ... 1 University of Bordeaux INSERM BPH U12... 1
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PubMed
38656970
PubMed Central
PMC11109473
DOI
10.1093/bioinformatics/btae282
PII: 7657698
Knihovny.cz E-zdroje
MOTIVATION: Many diseases, such as cancer, are characterized by an alteration of cellular metabolism allowing cells to adapt to changes in the microenvironment. Stable isotope-resolved metabolomics (SIRM) and downstream data analyses are widely used techniques for unraveling cells' metabolic activity to understand the altered functioning of metabolic pathways in the diseased state. While a number of bioinformatic solutions exist for the differential analysis of SIRM data, there is currently no available resource providing a comprehensive toolbox. RESULTS: In this work, we present DIMet, a one-stop comprehensive tool for differential analysis of targeted tracer data. DIMet accepts metabolite total abundances, isotopologue contributions, and isotopic mean enrichment, and supports differential comparison (pairwise and multi-group), time-series analyses, and labeling profile comparison. Moreover, it integrates transcriptomics and targeted metabolomics data through network-based metabolograms. We illustrate the use of DIMet in real SIRM datasets obtained from Glioblastoma P3 cell-line samples. DIMet is open-source, and is readily available for routine downstream analysis of isotope-labeled targeted metabolomics data, as it can be used both in the command line interface or as a complete toolkit in the public Galaxy Europe and Workfow4Metabolomics web platforms. AVAILABILITY AND IMPLEMENTATION: DIMet is freely available at https://github.com/cbib/DIMet, and through https://usegalaxy.eu and https://workflow4metabolomics.usegalaxy.fr. All the datasets are available at Zenodo https://zenodo.org/records/10925786.
- MeSH
- glioblastom metabolismus MeSH
- izotopové značení * metody MeSH
- lidé MeSH
- metabolomika * metody MeSH
- nádorové buněčné linie MeSH
- software * MeSH
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