DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data
| dc.rights.license | open | en_US |
| hal.structure.identifier | Institut de biochimie et génétique cellulaires [IBGC] | |
| dc.contributor.author | GALVIS, Johanna | |
| hal.structure.identifier | Bordeaux population health [BPH] | |
| dc.contributor.author | GUYON, Joris | |
| hal.structure.identifier | Centre de Bioinformatique de Bordeaux [CBIB] | |
| dc.contributor.author | DARTIGUES, Benjamin | |
| dc.contributor.author | HECHT, Helge | |
| dc.contributor.author | GRÜNING, Björn | |
| hal.structure.identifier | Institut de biochimie et génétique cellulaires [IBGC] | |
| dc.contributor.author | SPECQUE, Florian | |
| dc.contributor.author | SOUEIDAN, Hayssam | |
| hal.structure.identifier | Institut de biochimie et génétique cellulaires [IBGC] | |
| dc.contributor.author | KARKAR, Slim | |
| hal.structure.identifier | Institut de biochimie et génétique cellulaires [IBGC] | |
| dc.contributor.author | DAUBON, Thomas | |
| hal.structure.identifier | Institut de biochimie et génétique cellulaires [IBGC] | |
| dc.contributor.author | NIKOLSKI, Macha | |
| dc.date.accessioned | 2024-10-31T08:57:13Z | |
| dc.date.available | 2024-10-31T08:57:13Z | |
| dc.date.issued | 2024-05-02 | |
| dc.identifier.issn | 1367-4803 | en_US |
| dc.identifier.uri | https://oskar-bordeaux.fr/handle/20.500.12278/203072 | |
| dc.description.abstractEn | 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. | |
| dc.language.iso | EN | en_US |
| dc.rights | Attribution 3.0 United States | * |
| dc.rights.uri | http://creativecommons.org/licenses/by/3.0/us/ | * |
| dc.title.en | DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data | |
| dc.title.alternative | Bioinformatics | en_US |
| dc.type | Article de revue | en_US |
| dc.identifier.doi | 10.1093/bioinformatics/btae282 | en_US |
| dc.subject.hal | Sciences du Vivant [q-bio] | en_US |
| dc.subject.hal | Informatique [cs] | en_US |
| dc.identifier.pubmed | 38656970 | en_US |
| bordeaux.journal | Bioinformatics | en_US |
| bordeaux.page | btae282 | en_US |
| bordeaux.volume | 40 | en_US |
| bordeaux.hal.laboratories | Bordeaux Population Health Research Center (BPH) - UMR 1219 | en_US |
| bordeaux.issue | 5 | en_US |
| bordeaux.institution | Université de Bordeaux | en_US |
| bordeaux.institution | INSERM | en_US |
| bordeaux.institution | CNRS | |
| bordeaux.team | AHEAD_BPH | en_US |
| bordeaux.peerReviewed | oui | en_US |
| bordeaux.inpress | non | en_US |
| bordeaux.identifier.funderID | Institut National Du Cancer | en_US |
| bordeaux.identifier.funderID | Horizon 2020 Framework Programme | en_US |
| bordeaux.import.source | hal | |
| hal.identifier | hal-04591269 | |
| hal.version | 1 | |
| hal.popular | non | en_US |
| hal.audience | Internationale | en_US |
| hal.export | false | |
| workflow.import.source | hal | |
| dc.rights.cc | Pas de Licence CC | en_US |
| bordeaux.COinS | ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Bioinformatics&rft.date=2024-05-02&rft.volume=40&rft.issue=5&rft.spage=btae282&rft.epage=btae282&rft.eissn=1367-4803&rft.issn=1367-4803&rft.au=GALVIS,%20Johanna&GUYON,%20Joris&DARTIGUES,%20Benjamin&HECHT,%20Helge&GR%C3%9CNING,%20Bj%C3%B6rn&rft.genre=article |
