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Plant Metabolic Pathways

Pathways section in the Gramene databases is home for the RiceCyc and the SorghumCyc, the pathway databases for rice and Sorghum respectively. It also provides mirrors of pathway databases from Arabidopsis, tomato, potato, pepper, coffee, Medicago, E. coli and the MetaCyc reference database. 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 Search, Browse and Other Options

Click on the species specific links such as search to start searches by typing the keyword; 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 2.0.1  Oryza sativa japonica Strain: Nipponbare Search | Browse | Summary |  More info	AraCyc* ver 4.1.1  Arabidopsis thaliana Strain: Columbia Search | Browse | Summary |  More info	EcoCyc* ver 11.5   Escherichia coli Strain: K-12 MG1655 Search | Browse | Summary |  More info
SorghumCyc ver 1.0 beta  Sorghum bicolor Strain: BTx623 Search | Browse | Summary |  More info	MedicCyc* ver 1.0.1.1  Medicago truncatula, Barrelclover Strain: n/a Search | Browse | Summary |  More info	MetaCyc* ver 11.5  Reference Pathway Database Strain: not applicable Search | Browse | Summary |  More info
	LycoCyc* ver 1.0.1.1  Solanum lycopersicum, Tomato Strain: n/a Search | Browse | Summary |  More info
	CapCyc* ver 1.0.1.1  Capsicum anuum, Pepper Strain: n/a Search | Browse | Summary |  More info
	PotatoCyc* ver 1.0.1.1  Solanum tuberosum, Potato Strain: n/a Search | Browse | Summary |  More info
	CoffeaCyc* ver 1.0.1.1  Coffea canephora, Coffee Strain: n/a Search | Browse | Summary |  More info
* Mirror database. Not curated by the Gramene database. Click on more info link for details.

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 exaple 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

Auxin metabolism Brassinosteroid metabolsm Cytokinin metabolism Ethylene biosynthesis from methionine Gibberellin metabolism

Jasmonic acid biosynthesis Salicylic acid biosynthesis Pentose phosphate pathways Photosynthesis Respiration

Secondary metabolic pathways Starch biosynthesis TCA cycle ALL pathways

Download

• Download RiceCyc and SorghumCyc 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 and Sorghum pathways were created by Gramene database using the Pathway Tools developed by Peter D. Karp and coworkers at the Bioinformatics Research Group at SRI International.

We host mirrors of sevaral species specific plant pathways imported from their original project sites:

• Arabidopsis thaliana pathways were imported from AraCyc
• Esherichia. coli pathways were imported from EcoCyc
• Capsicum anuum, Coffea canephora, Solanum lycopersicum, and Solanum tuberosum pathways were imported from Sol Genomics Network
• Medicago truncatula pathways were imported from the The SR Noble foundation
• MetaCyc pathways were imported as integral part of the Pathway Tools provided by the SRI International

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