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

*** 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.本数据集用于复现题为《代谢建模揭示肠道菌群与帕金森病（Parkinson's disease, PD）代谢紊乱关联》的论文研究。 数据集内容如下： - ApolloAgora2panSpecies：包含AGORA2与APOLLO泛菌种肠道微生物重构模型的文件夹。 - luo_2024_replicated_PD_mets.xlsx：收录经Luo等人（2024，https://doi.org/10.1038/s41531-024-00732-z）复现验证得到的、与PD诊断存在显著关联的代谢物列表。 - metaboliteChemicalAnnotation.xlsx：收录与PD相关代谢物的化学注释信息，此类代谢物已匹配至全血模型（Whole Blood Model, WBM）1.04c版本的血液组分中，注释信息来源于Luo等人（2024，https://doi.org/10.1038/s41531-024-00732-z）。 - metadata.xlsx：收录样本与患者元数据的文件，该文件改编自Wallen等人（2022，https://doi.org/10.1038/s41467-022-34667-x）。 - mWBM_SET1-mWBM_SET5：包含微生物组个性化全血模型（版本1.04c）的文件夹。 - PD_associatedTaxa_subsetPresentSpeciesMARS.xlsx：收录经Wallen等人（2022，https://doi.org/10.1038/s41467-022-34667-x）发现的、与PD诊断存在关联的微生物物种列表。 - resultFlux：包含基于生成的微生物组个性化全血模型得到的通量平衡分析（Flux Balance Analysis, FBA）通量解结果的文件夹。 - resultMARS：包含对AGORA2+APOLLO泛菌种资源进行宏基因组映射后得到的肠道菌群映射结果的文件夹。