Proccessed and Input Data for the Pipelines of the Project "Multiomics and quantitative modelling disentangle diet, host, and microbiota contributions to the host metabolome" ----------------------------------------------------------------------------------------------------- Contents: ----------------------------------------------------------------------------------------------------- Folder /ProcessedData/metabolomics/ contains processed metabolomics data from the project: /metabolomics/metabolites_allions_combined_norm_intensity.csv - file containing normalized intensities of ions detected across tissues with six measurement methods. /metabolomics/metabolites_allions_combined_formulas_with_metabolite_filters_spatial100clusters_with_mean.csv - file containing metabolite attribution to spatial clusters and mean intensity values across tissues and conditions. Other files are described in README_ProcessedData.md. ----------------------------------------------------------------------------------------------------- Folder /ProcessedData/sequencing/ contains raw and normalized counts of metagenomics and metatransriptomics data mapped to bacterial genomes. Folder /ProccessedData/util/ contains files used for data preprocessing and attribution to chemical classes and pathways. Folder /ProcessedData/example_output/ contains example output of the pipelines: /output/model_results_SMOOTH_raw_2LIcoefHost1LIcoefbact_allions.csv - file containing estimated model parameters (intestinal flux and metabolic flux values) for the forward problem for metabolomics measurements in the GIT. /output/model_results_SMOOTH_normbyabsmax_reciprocal_problem_allions.csv - file containing estimated model parameters for the reverse problem (metabolite intensities) for the parameters estimated with the forward problem. /output/model_results_SMOOTH_normbyabsmax_2LIcoefHost1LIcoefbact_allions.csv - file containing estimated model parameters (intestinal flux and metabolic flux values) for the forward problem for metabolomics measurements in the GIT, normalized by absolute maximum value. /output/model_results_SMOOTH_normbyabsmax_ONLYMETCOEF_2LIcoefHost1LIcoefbact_allions.csv - file containing estimated model parameters (only metabolic flux values) for the forward problem for metabolomics measurements in the GIT, normalized by absolute maximum value. /output/table_hierarchical_clustering_groups.csv - file containing attribution of the annotated metabolites to groups according to hierarchical clustering of the normalized model parameters. /output/cgo_clustergrams_of_model_coefficients.mat - matlab object containing clustergram of the normalized model parameters and manually derived sub-clustergrams corresponding to different largest parameter values. Description of other files is provided in the file README_ProcessedData.md. ----------------------------------------------------------------------------------------------------- Folder /InputData/ contains HMDB and KEGG tables used for metabolite annotations and chemical group analysis. Folder InputData_KEGGreaction_path contains matlab files with metabolite-metabolite paths calculated from KEGG reaction-pair information (Each matrix contains a subset of paths). These files are used by the script workflow_extract_keggECpathes_for_SPpairs_final.m. Folder InputData_metabolomics_data contains raw metabolomics data from six methods (three LC columns: C08, C18 and HILIC, and positive and negative acquisition modes) and file tissue_weights.txt with tissue weight information used for normalization. Folder InputData_sequencing_data contains folders ballgown_DNA and ballgown_RNA with results of metagenomic and metatranscriptomic data analysis (raw counts, GetMM normalized counts, EdgeR and DeSeq2 analysis). Description of folders is provided in the file readme_InputData.md. -----------------------------------------------------------------------------------------------------