Plant Metabolic Pathways
RiceCyc# ver 3.3  Oryza sativa japonica Strain: Nipponbare Browse | Summary | More info |
AraCyc* ver 10.0  Arabidopsis thaliana Strain: Columbia Browse | Summary | More info |
EcoCyc* ver 17.0  Escherichia coli Strain: K-12 MG1655 Browse | Summary | More info |
SorghumCyc# ver 1.1  Sorghum bicolor Strain: BTx623 Browse | Summary | More info |
MedicCyc* ver 1.0.1  Medicago truncatula, Barrelclover Unavailable Browse | Summary | More info |
MetaCyc* ver 17.0  Reference Pathway Database Strain: not applicable Browse | Summary | More info |
MaizeCyc# ver 2.1  Zea mays Strain: B73 Browse | Summary | More info |
PoplarCyc* ver 5.0  Populus trichocarpa (and other Populus species and hybrids) Strain: n/a Browse | Summary | More info |
PlantCyc* ver 7.0  Plant Metabolic Pathway Database Strain: not applicable Browse | Summary | More info |
BrachyCyc# ver 2.0  Brachypodium distachyon Strain: Bd21 Browse | Summary | More info |
PotatoCyc* ver 1.0.1  Solanum tuberosum, Potato Strain: n/a Browse | Summary | More info |
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VitisCyc+ ver 1.1  Vitis vinifera, Grape Strain: n/a Browse | Summary | More info |
CoffeaCyc* ver 1.1.1  Coffea canephora, Coffee Strain: n/a Browse | Summary | More info |
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EucalyptusCyc+ ver 1.7  Eucalyptus grandis, Eucaplyptus Strain: n/a Browse | Summary | More info |
LycoCyc* ver 2.0.1  Solanum lycopersicum, Tomato Strain: n/a Browse | Summary | More info |
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FragariaCyc+ ver 2.0  Fragaria vesca, Strawberry Strain: n/a Browse | Summary | More info |
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*Mirror database.
#Curated and developed by the Gramene database. +Developed by the Naithani and Jaiswal Labs. |
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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. |
Quicklink for selected rice pathways
Useful external links
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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
- Arabidopsis thaliana pathways were imported from AraCyc
- PlantCyc pathways were imported from PlantCyc
- Esherichia. coli pathways were imported from EcoCyc
- 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
Pathway databases were created using the Pathway Tools software developed by Peter D. Karp and coworkers in the Bioinformatics Research Group at SRI International.
We host mirrors of several species specific plant pathways imported from their original project sites: