This repository contains metabolic maps for the Human-GEM (Human1) and are served by Metabolic Atlas.
Two types of map have been produced:
Correspond to a compartment in the model. Note that the Cytosol has been divided into 5 separate maps, and the Inner mitochondrial membrane compartment is included on the Mitochondria map. We do not provide maps for Boundary and Extracellular compartments, as reactions on thoses maps are largely disconnected and uninformative.
Each map corresponds to a subsystem as it is annotated in the model. Some subsystem maps are still under construction:
Arachidonic acid metabolism, Beta oxidation of even-chain fatty acids (peroxisomal), Chondroitin / heparan sulfate biosynthesis, Chondroitin sulfate degradation, Estrogen metabolism, Fatty acid biosynthesis, Fatty acid oxidation, Folate metabolism, Formation and hydrolysis of cholesterol esters, Glycine, serine and threonine metabolism, Glycosphingolipid biosynthesis-lacto and neolacto series, Glycosphingolipid metabolism, Heparan sulfate degradation, Keratan sulfate biosynthesis, Linoleate metabolism, Metabolism of xenobiotics by cytochrome P450, Peptide metabolism, Prostaglandin biosynthesis, Protein assembly, Protein degradation, Retinol metabolism, Valine, leucine, and isoleucine metabolism, Vitamin E metabolism.
A few subsystem maps are not planned for construction because they contain artificial reactions, are highly disconnected, or are very small, and thus a map would be uninformative:
Artificial reactions, Beta oxidation of odd-chain fatty acids (peroxisomal), Carnitine shuttle (cytosolic), Carnitine shuttle (endoplasmic reticular), Carnitine shuttle (mitochondrial), Carnitine shuttle (peroxisomal), CoA catabolism, Exchange/demand reactions, Miscellaneous, Nitrogen metabolism, Pool reactions, R group synthesis, Transport reactions.
Custom maps or combination maps of multiple subsystems are planned, but are still under development.
SVG: Scalable Vector Graphics, ideal for web browsers; these maps are displayed on Metabolic Atlas but do not contain metabolic network information and thus are only used for visualization.
SBML: Systems Biology Markup Language extended to incorporate graphical information. While SBML files may be used for metabolic analysis or flux visualization, SBML maps exported using Omix have not been used or tested for such purposes.
SBGN: Systems Biology Graphical Notation files. They have not been used for any analyses.
All three formats were exported from maps made using Omix, using the built-in Omix plugins (SBML, SBGN) or a custom plugin (SVG).
Some metabolic reactions are excluded from the maps. Only Transport/Exchange reactions associated with enzymes have been added (mostly disconnected) on compartment maps. Subsystem maps do not currently include any transport reactions (those belonging to the Transport reactions subsystem).
Subsystem maps are synced with version 1.3.0 of the Human-GEM model, but compartment maps are synced with version 1.0.5.
This repository is administered by Pierre Cholley (@pecholleyc), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology.