Replication Data for: Metabolic modelling links gut microbiota to metabolic perturbations in Parkinson's disease

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Hensen, Tim, 2025, "Replication Data for: Metabolic modelling links gut microbiota to metabolic perturbations in Parkinson's disease", https://doi.org/10.7910/DVN/PUTXL9, Harvard Dataverse, V1, UNF:6:zIVDsrnZgfh0uxplYeyHsA== [fileUNF]
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*** DESCRIPTION *** Input data for replication of paper titled: "Metabolic modelling links gut microbiota to metabolic perturbations in Parkinson's disease". *** CONTENT *** - ApolloAgora2panSpecies: Folder with AGORA2 + APOLLO pan species gut microbe reconstructions. - luo_2024_replicated_PD_mets.xlsx: List of metabolites for which a replicated association with Parkinson's disease (PD) diagnosis was found by Luo et al. (2024, https://doi.org/10.1038/s41531-024-00732-z) - metaboliteChemicalAnnotation.xlsx: Chemical annotations of PD-associated metabolites that mapped onto the blood compartment of WBM version 1.04c. Chemical annotations were taken from Luo et al. (2024, https://doi.org/10.1038/s41531-024-00732-z). - metadata.xlsx: File with sample and patient metadata information. This file was taken and adapted from Wallen et al. (2022, https://doi.org/10.1038/s41467-022-34667-x) - mWBM_SET1-mWBM_SET5: Folder with microbiome personalised WBMs (version 1.04c). - PD_associatedTaxa_subsetPresentSpeciesMARS.xlsx: List of microbial species for which an association with PD diagnosis was found by Wallen et al. (2022, https://doi.org/10.1038/s41467-022-34667-x). - resultFlux: Folder with FBA flux solutions from the generated microbiome personalised WBMs. - resultMARS: Folder with gut microbiome mapping results after metagenomic mapping on the AGORA2+APOLLO pan species resource. (2025-04-24)
Subject Medicine, Health and Life Sciences; Computer and Information Science
Keyword Parkinson's disease
Related Publication Is Cited By: To be added
Notes Is Supplement To: Metabolic modelling links gut microbiota to metabolic perturbations in Parkinson's disease, Tim Hensen, Ines Thiele. *** INSTRUCTIONS FOR REPLICATION OF ANALYSIS *** To replicate the analysis performed by Hensen et al. (2025), please first perform the following steps: 1. Unzip the downloaded files 2. Create a project folder for replication 3. Within the project folder (e.g, "project"), create a folder named "inputs" 4. Move all files to the "project/inputs" 5. Create the following folder structure and populate the "project/inputs" folder as follows: - project - inputs - resultFlux - luo_2024_replicated_PD_mets.xlsx - metadata.xlsx - PD_associatedTaxa_subsetPresentSpeciesMARS.csv - metaboliteChemicalAnnotation.xlsx - models - ApolloAgora2panSpecies - HMmodels The "HMmodels" folder should contain all .mat from mWBM_SET1 to mWBM_SET5 as follows: - HMmodels - muWBM_DC001_male.mat - muWBM_DC003_female.mat - etcetera 6. After setting up the input data, please obtain the scripts from "https://github.com/ThieleLab/CodeBase" and deposit the associated helper functions in "project/functions". 7. At this point, the computational analysis can be replicated.
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ApolloAgora2panSpecies.zip
ZIP Archive - 252.9 MB
Published May 5, 2025
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MD5: 970699acdaafbb5a1e2e631da1e6c37d
Preview "ApolloAgora2panSpecies.zip"
luo_2024_replicated_PD_mets.xlsx
MS Excel Spreadsheet - 15.9 KB
Published May 5, 2025
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MD5: 029985a4e0be154c73a430440bb8a479
metaboliteChemicalAnnotation.xlsx
MS Excel Spreadsheet - 23.7 KB
Published May 5, 2025
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MD5: b20855363bc36abb1da0bc199085061a
metadata.xlsx
MS Excel Spreadsheet - 177.1 KB
Published May 5, 2025
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MD5: 40520175ece66fb1033ef2bc52fcf7b0
PD_associatedTaxa_subsetPresentSpeciesMARS.tab
Tabular Data - 89.8 KB
Published May 5, 2025
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16 Variables, 455 Observations UNF:6:TfDRRl65rlSLQ2wzMB+KUA==
Preview "PD_associatedTaxa_subsetPresentSpeciesMARS.tab" Preview "PD_associatedTaxa_subsetPresentSpeciesMARS.tab"
WBM_stats.xlsx
MS Excel Spreadsheet - 31.8 KB
Published May 5, 2025
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MD5: dd51834186a962c29645b8e3f9b5615b
muWBM_DP165_male.mat
mWBMs_SET1/MATLAB Data - 15.2 MB
Published May 5, 2025
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MD5: 18b24b881443cd268c1333d00ce882c0
muWBM_DP166_male.mat
mWBMs_SET1/MATLAB Data - 13.4 MB
Published May 5, 2025
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MD5: 90b73c940fd5ba204bc2797398d47be3
muWBM_DP167_female.mat
mWBMs_SET1/MATLAB Data - 15.8 MB
Published May 5, 2025
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MD5: 11f74afe8dab0848cac2f09a13be8a75
muWBM_DP169_male.mat
mWBMs_SET1/MATLAB Data - 16.6 MB
Published May 5, 2025
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MD5: 2f201950534f890ce4d7326b804affb3
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