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The HMDB facilitates human metabolomics research, including the identification and characterization of human metabolites using NMR spectroscopy, GC-MS spectrometry and LC/MS spectrometry. To aid in this discovery process, the HMDB contains three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology / biochemistry data (Fig ...
Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates, and products of cell metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind", the study of their small-molecule metabolite ...
The Human Metabolome Database (HMDB) is a freely available, open-access database containing detailed data on more than 40,000 metabolites that have already been identified or are likely to be found in the human body. The HMDB contains three kinds of information: Chemical information, Clinical information and; Biochemical information.
For input, MetPA expects either a list of compound names (identified as statistically significant or significant perturbed) or a metabolite concentration table with phenotypic labels (i.e. sick vs. healthy). The list of compounds can include common names, HMDB IDs or KEGG IDs with one compound per row. Compound concentration tables must have ...
The HMDB has over 7900 human metabolites and roughly 7200 associated DNA and protein sequences, that are linked to these metabolite entries. While DrugBank includes information on 6707 drugs and 4228 non-redundant drug targets, enzymes, transporters, and carriers, T3DB houses over 2900 common toxins and environmental pollutants.
Metabolite Set Enrichment Analysis (MSEA) is a method designed to help metabolomics researchers identify and interpret patterns of metabolite concentration changes in a biologically meaningful way. [1] It is conceptually similar to another widely used tool developed for transcriptomics called Gene Set Enrichment Analysis or GSEA. [2]
SMPDB is part of a suite of metabolomics databases that also includes Human Metabolome Database, DrugBank, and the Toxin and Toxin-Target Database (T3DB). While DrugBank includes information on 7000 drugs and >4200 non-redundant drug targets, enzymes, transporters, and carriers, HMDB houses over 40,000 small molecule metabolites found in the ...
The Serum Metabolome database is a free web database about small molecule metabolites found in human serum and their concentration values. The database includes chemical data, clinical data and molecular/biochemistry data from literature and experiment.