EnteroPathway is a manually curated database applicable for human gut microbiome analyses. It contains three types of data: (1) Compounds, (2) Modules, and (3) Reactions, which are incorporated in a biochemical pathway map.
Users are fully encouraged to map their own microbiome metagenomic data onto the EnteroPathway map to visualize their data entities in a knowledge based biochemical network representation.
EnteroPathway data are either extracted from the Kyoto Encyclopedia of Genes and Genomes (KEGG) or newly collected from scientific literature by our curators. The data collection process focused on biochemical reactions carried out by the human gut microbiomes. The data entries are incorporated in a network representation, or a biochemical pathway map.
Users may mouse-over the nodes and the edges in the pathway map to see the entry IDs and more detailed information including full description of the entries and links to the KEGG database.
Circles kkrepresent chemical compounds (e.g. C00010), which are connected one another with edges, which represent biochemical reactions (e.g. R02794). Edges may contain enzyme data whose entries are identified by KEGG ortholog IDs (e.g. K01822). These representations compose a series of reactions referred to as modules (e.g. M00103) represented by rectangles. Modules are hierarchically categorized in biological functions (e.g. “Steroid metabolism”) represented in distinct colors.
|Date type||Number of entries||Example|
Kendall's compound B;
Reichstein's substance H
corticosterone => 11beta-OH-3alpha,
|Reactions||3370||R02794||Cholate:CoA ligase (AMP-forming)
ATP + Cholic acid + CoA <=> AMP + Diphosphate + Choloyl-CoA
•Note for compound_list data
CXXXXX : compounds are extracted from KEGG database.
EPCXXXX : compounds are newly defined in EnteroPathway.
•Note for module_list data
MXXXXX : modules are extracted from KEGG database.
EPMXXXX : modules are newly defined in EnteroPathway.
•Note for reaction_list data
RXXXXX : reactions are extracted from KEGG database.
EPRXXXX : reactions are newly defined in EnteroPathway.
Modules are classified into three large categories; “Secretion metabolism”, “Drug metabolism”, and “Food metabolism”. The large categories are divided into a number of small categories to hierarchically classify in terms of biochemical reactions.
Users may download our (1) compounds, (2) modules, and (3) reactions data in tab-delimitated files.