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The Plant Metabolic Network: PlantCyc, AraCyc, and NEW Metabolic Pathway Databases for Plant Research

The Plant Metabolic Network (PMN) is an online resource that provides data and tools for plant research. Visit www.plantcyc.org for information on enzymes, compounds, and biochemical pathways in over 300 plant species.

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The Plant Metabolic Network: PlantCyc, AraCyc, and NEW Metabolic Pathway Databases for Plant Research

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  1. The Plant Metabolic Network: PlantCyc, AraCyc, and NEW Metabolic Pathway Databases for Plant Research *K. Dreher, P. Zhang, L. Chae, R.A. Nilo Poyanco, D. Priamurskiy, T. Tran, R. Muller, L. Ploetz, S. Singh, and S.Y. Rhee www.plantcyc.org www.plantcyc.org The Carnegie Institution for Science, Department of Plant Biology, Stanford, CA How can I use the PMN in my research? What is the Plant Metabolic Network? Identify metabolic functions of uncharacterized plant proteins The Plant Metabolic Network (PMN) is an online resource that provides data and tools to help enhance your research! Please come visit us at www.plantcyc.orgto connect to experimentally verified and computationally predicted information about enzymes, compounds, and biochemical pathways in over 300 plant species Vitamin E biosynthesis >A very interesting protein MKATLAPPSSLISLPRHKVSSLRSPSLLLQSQRPSSALMTTTASRGSVAVTAAATSSAEALREGIAEFYNETSGLWEEIWGD What can I find in the PMN? Examine data using the Metabolic Overview Lots of information – including 4 NEW DATABASES Latest release: PMN 6.0 March 2012 New databases! Overlay quantitative data: Zoom to learn more details: Examine isozymes: * The term "enzyme" refers to both monomers and complexes found in the databases. Important pathways for over 300 plant species • Caffeine biosynthesis (Coffea arabica) • Glucosinolate biosynthesis (Arabidopsis thaliana) • Kauralexin biosynthesis (Zea mays) • Sorbitol degradation (Malus x domestica) • Resveratrol biosynthesis (Vitis vinifera) • Photosynthesis • Gibberellin biosynthesis • Starch degradation • Fatty Acid beta-oxidation • Urea cycle Secondary metabolism Primary metabolism • Identify metabolic changes due to : • Different tissues • Different developmental stages • Different genotypes • Different stresses • . . . and many other conditions Highlight list of items Navigate to specific items Analysis tools and software Software: Pathway Tools v. 15.5 (SRI International) Display data on pathway Desktop version Connect to: Enter a list of differentially expressed enzymes or compounds • Numerous basic and advanced searching and browsing options • Omics data visualization interface • PMN-specific BLAST datasets • Data management and sharing capabilities • Comparative analysis tools • Desktop software and downloadable database files • Flux balance analysis module (using desktop software) View Omics Data on Pathway Pages • Phytozome • UniProt • BRENDA • ChEBI • PubChem • KEGG • Knapsack • TAIR • MetaCyc Generate a stable url / bookmark: Generate and upload a text file CPD-468 CPD-8250 CPD-8234 CPD-8243 ALPHA-GLUCOSE CPD-490 ALPHA-GLUCOSE-16-BISPHOSPHATE • Data can also be plotted using bar and line graphs • Pathways can be modified, connected, or created by users to enhance the analysis Who makes the PMN possible? What’s coming next at the PMN? Funding and support provided by: PMN grants: DBI-0640769 and IOS-1026003 (NSF) • New databases for: • --Chlamydomonas reinhardtii -- Selaginella moellendorffii • --Physcomitrella patens -- Carica papaya • Enhanced computationally predicted and experimentally supported coverage of metabolism in all PMN databases • Upgraded Pathway Tools 16.0 software with login and data storage capabilities PMN team members: PI: Dr. Sue Rhee, Director and Lead Curator: Dr. PeifenZhang Post-docs: Dr. Lee Chaeand Dr. Ricardo Nilo Interns: Damian Priamurskiy, Tam Tran, Caryn Johansen External collaborators: SRI International: Ron Caspi, Peter Karp, Carol Fulcher, Suzanne Paley, Pathway Tools support team, et al; Sol Genomics Network: Lukas Mueller, Hartmut Foerster, et al ; MaizeGDB: Mary Schaeffer, Lisa Harper, Jack Gardiner, Taner Sen, Gramene: Pankaj Jaiswal, et al; MedicCyc: Lloyd Sumner, Ewa Urbanczyk-Wochniak; Questions?? New or updated data?? Please contact us at: SGN Many thanks to: TAIR / Rhee Lab: Flavia Bossi, Hyein Nam, MengXu, Taehyong Kim, Varun Dwaraka, Caryn Johansen, A. S. Karthikeyan, Michael Ahn, Kun He, Ricardo Leitao, Tom Walk, Eva Huala, Tanya Berardini, Dave Swarbreck, Debbie Alexander, Rajkumar Sasidharan, Philippe Lamesch, Donghui Li, et al curator@plantcyc.org

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