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| Plant Reactome (beta)
Plant Metabolic Pathways
The pathways section in the Gramene databases is home for RiceCyc, MaizeCyc, BrachyCyc and SorghumCyc, the pathway databases for rice, maize, Bracypodium, and sorghum, respectively. In the past, we have provided mirrors of pathway databases from Arabidopsis, tomato, potato, pepper, coffee, Medicago, E. coli, and the MetaCyc and PlantCyc reference databases, and might reinstate them again upon software upgrade that supports the most current version at the original sources, e.g., Plant Metabolic Network (PMN) and the SolGenomics Network (SGN). In addition to search and browse functions, the database allows users to find genes mapped to respective reactions and pathways and draw inetrspecific comparison between the pathways.Pathways Browse and Other Options
Click on the species specific links such as browse to go through the list of pathways; summary to get a summarized overview. Click on the more info link to learn more details on the respective pathway database.
RiceCyc ver 3.2
Oryza sativa japonica
Strain: Nipponbare
Browse | Summary | More info
SorghumCyc ver 1.1 
Sorghum bicolor
Strain: BTx623
Browse | Summary | More info
MaizeCyc ver 2.0.2 
Zea mays
Strain: B73
Browse | Summary | More info
BrachyCyc ver 2.0 
Brachypodium distachyon
Strain: Bd21
Browse | Summary | More info
Other Tools
Omics Viewer: Upload and view the realtime mappings of your datasets from microrray expression, proteomics, metabolomics on Pathway overview diagram Comparative analysis: Compare data sets from two or more species for reactions, pathways, compounds, proteins, transporters and/or transcription units Help
Help Presents an overview on how to use the pathway database and lists explanations of field names. Tutorial More in-depth than the help pages, use the tutorial for an example of using the database, see how it integrates other datasets, and get tips to increase your data search efficiency. FAQ Frequently Asked Questions - see what questions users have asked, and get the developers answers. Release Notes For more information about the most recent release. Quicklink for selected rice pathways
Download
- Downloads from our ftp archive.
- For other species, please follow the links from the Acknowledgements
Useful external links
KEGG pathways
KEGG rice pathways
IUBMB Enzyme nomenclature
Brenda enzyme database
BioCyc
ENZYME at Expasy
Reactome
Cellular Expression Profiling of Rice
Rice oligonucleotide array project
Feedback
Since the functions of many of the rice genes are either provided by homology and HMM based predictions, many of the pathways might be incomplete or may contain errors. The manual curation of pathways is an ongoing process at Gramene. If you notice any problems or errors on the pathways or would like to nominate a pathway for inclusion, please send a message to Gramene users on the Gramene list-serve or by clicking the ' Feedback' button at the bottom of the pathway tools display page.
Acknowledgements
RiceCyc, SorghumCyc, MaizeCyc and BrachyCyc pathway databases were created using the Pathway Tools software developed by Peter D. Karp and coworkers in the Bioinformatics Research Group at SRI International.
