Putting the Plant Metabolic Network Pathway Databases to Work: Going Offline to Gain New Capabilities
Metabolic databases such as The Plant Metabolic Network/MetaCyc and KEGG PATHWAY are publicly accessible resources providing organism-specific information on reactions and metabolites. KEGG PATHWAY depicts metabolic networks as wired, electronic circuit-like maps, whereas the MetaCyc family of databases uses a canonical textbook-like representation. The first MetaCyc-based database for a plant species was AraCyc, which describes metabolism in the model plant Arabidopsis. This database was created over 10 years ago and has since then undergone extensive manual curation to reflect updated information on enzymes and pathways in Arabidopsis. This chapter describes accessing and using AraCyc and its underlying Pathway Tools software. Specifically, methods for (1) navigating Pathway Tools, (2) visualizing omics data and superimposing the data on a metabolic pathway map, and (3) creating pathways and pathway components are discussed.
Key wordsPlant metabolism Omics data analysis Biochemical pathway databases
The author would like to thank George Dreher for testing the protocols and improving the manuscript as well as Peifen Zhang, Sue Rhee, the members of the Rhee lab, and all of the members of the Pathways Tools/MetaCyc group. This work was funded by the US National Science Foundation (awards NSF DBI-0640769 and IOS-1026003).
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