Proccessed Data for the Pipelines of the Project "Multiomics and quantitative modelling disentangle diet, host, and microbiota contributions to the host metabolome"

Proccessed and Input Data for the Pipelines of the Project "Multiomics and quantitative modelling disentangle diet, host, and microbiota contributions to the host metabolome"

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Contents:

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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.

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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.

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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.

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