Poster: Genomics Resources

Abs # 955: MetaCyc and AraCyc: Encyclopedia of Metabolic Pathways for Plant Research and Application

Presenter:	Zhang, Peifen , peifenz@acoma.stanford.edu
Authors	Zhang, Peifen  (A)   Mueller, Lukas  (A)   Krieger, Cindy  (B)   Paley, Suzanne  (B)   Karp, Peter  (B)   Rhee, Seung Yon (A)
Affiliations:	(A): Carnegie Institution of Washington (B): SRI international

MetaCyc is a literature curated metabolic pathway database. Its goal is to include all known pathways that are experimentally identified. Pathways are collected from multiple organisms and each pathway is annotated with the species in which it is known to occur. In addition to many ubiquitous pathways and pathways specifically found in microbial organisms, a recent enhancement to the database was made to include important pathways found in plants. In addition to pathway information, reactions are annotated with conventional EC numbers, many compounds are associated with chemical structures and extensive synonym names, and physical and catalytic properties such as subcellular location, substrate specificity, activators and inhibitors are annotated to enzymes. MetaCyc lists extensive literature citations and curator commentaries to the major data types. MetaCyc is freely accessible through the Web (http://biocyc.org/metacyc/), the major data types can be browsed or queried. Among other applications, MetaCyc can be used as a reference source for predicting the metabolic pathway content of a specific organism from its annotated genome. It has been recently applied to the Arabidopsis genome and derived the corresponding Arabidopsis database, AraCyc (http://arabidopsis.org/tools/aracyc/). To generate AraCyc, annotated Arabidopsis enzymes and their coding genes were mapped to the reactions and pathways in MetaCyc. The expression overview feature in AraCyc allows overlaying large-scale Arabidopsis gene expression data on to the pathways. AraCyc and MetaCyc, species-specific and species-nonspecific databases of metabolism, are two resources that can facilitate research in plant metabolism and pathway evolution, and assist in designing agricultural engineering applications.