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RiceCyc home and Biochemical pathways

About pathways The Pathway Tools is a web-based tool for viewing gene annotations mapped to various biochemical pathways in plants, rice (Oryza sativa) and Arabidopsis thaliana and bacteria E. coli. The pathways for rice (RiceCyc) were curated by Gramene. The rice genes and their annotation used in this analyses were based on release 4 of the TIGR's-assembly of Oryza sativa japonica cv.Nipponbare genome sequenced by IRGSP. Your favorite rice pathways Auxin metabolism Brassinosteroid metabolsm Cytokinin metabolism Gibberellin metabolism Ethylene biosynthesis from methionine Jasmonic acid biosynthesis Salicylic acid biosynthesis Photosynthesis Respiration TCA cycle Secondary metabolic pathways Starch biosynthesis Pentose phosphate pathways ALL pathways In order to promote exciting new discoveries on biochemical pathways in rice, the current version of RiceCyc has undergone a round of curation that has removed data unlikely to be relevant to Rice. We maintain a list of pathways that have been deleted. Since the functions of many of the rice genes are either provided by homology and HMM based predictions or unknown, many of the pathways might be incomplete or may contain errors. The manual curation of pathways is an ongoing process at Gramene and we welcome feedback from the research community. If you notice any problems or errors on the pathways, please send a message to Gramene curators or by clicking the 'Feedback' button at the bottom of the pathway tools display page. The Pathway Tools  is a bioinformatics software system for pathway analysis of genomes, and for creating Pathway/Genome Databases (PGDBs). It was developed by Peter D. Karp and coworkers at the Bioinformatics Research Group at SRI International. The RiceCyc pathways were created using the Pathway Tools' PathoLogic module. This tool generates an initial set of pathways by comparing annotations of genes and gene models against the reference pathway database MetaCyc. The computationally generated pathways are subjected to manual curation based on published literature. When necessary, species-specific biochemical pathways are added. Arabidopsis thaliana and E. coli pathways were imported from AraCyc and EcoCyc project sites.

Pathways in Gramene Species Source Overview# Summary Pathway comparison RICE Oryza sativa japonica cv. Nipponbare Gramene,  RiceCyc 1.3 Arabidopsis E.coli ARABIDOPSIS * Arabidopsis thaliana strain Columbia TAIR, AraCyc 3.5 Rice E.coli E. COLI * Escherichia coli strain K-12 MG1655 SRI, EcoCyc 10.5 Rice Arabidopsis * Not curated by Gramene.    # click on icons to vist the overview Useful links to pathway tools Compare data sets from the three species for reactions, pathways, compounds and proteins Map your microrray expression, proteomics, metabolomics and other datasets on Pathway overview diagrams Details on pathway visualization [Help document] Learn how to use the tool Still have questions, consult the frequently asked questions section Want your own copy of the RiceCyc? Download from our ftp archive. For Arabidopsis and E. coli pathways please visit AraCyc and EcoCyc project sites. Download Useful external links KEGG pathways IUBMB Enzyme nomenclature Brenda enzyme database ENZYME at Expasy BioCyc KEGG rice pathways Rice oligonucleotide array project Cellular Expression Profiling of Rice