DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data.
Bioinformatics
; 40(5)2024 05 02.
Article
em En
| MEDLINE
| ID: mdl-38656970
ABSTRACT
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.
Texto completo:
1
Bases de dados:
MEDLINE
Assunto principal:
Software
/
Metabolômica
/
Marcação por Isótopo
Limite:
Humans
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2024
Tipo de documento:
Article
País de afiliação:
França