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 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.org towww.plantcyc.org connect to experimentally verified and computationally predicted information about enzymes, compounds, and biochemical pathways in over 300 plant species What is the Plant Metabolic Network? What can I find in the PMN? How can I use the PMN in my research? >A very interesting protein MKATLAPPSSLISLPRHKVSSLRSPSLL LQSQRPSSALMTTTASRGSVAVTAAAT SSAEALREGIAEFYNETSGLWEEIWGD Vitamin E biosynthesis * The term "enzyme" refers to both monomers and complexes found in the databases. 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 curator@plantcyc.org Questions?? New or updated data?? Please contact us at: Examine data using the Metabolic Overview Identify metabolic functions of uncharacterized plant proteins Software: Pathway Tools v. 15.5 (SRI International) 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) Analysis tools and software Photosynthesis Gibberellin biosynthesis Starch degradation Fatty Acid beta-oxidation Urea cycle Overlay quantitative data:Examine isozymes:Zoom to learn more details: Connect to: Identify metabolic changes due to : Different tissues Different developmental stages Different genotypes Different stresses... and many other conditions CPD-468 CPD-8250 CPD-8234 CPD-8243 ALPHA-GLUCOSE CPD-490 ALPHA-GLUCOSE-16-BISPHOSPHATE Enter a list of differentially expressed enzymes or compounds Highlight list of itemsNavigate to specific items Generate a stable url / bookmark: The Carnegie Institution for Science, Department of Plant Biology, Stanford, CA Lots of information – including 4 NEW DATABASES Important pathways for over 300 plant species New databases! Latest release: PMN 6.0 March 2012 Caffeine biosynthesis (Coffea arabica) Glucosinolate biosynthesis (Arabidopsis thaliana) Kauralexin biosynthesis (Zea mays) Sorbitol degradation (Malus x domestica) Resveratrol biosynthesis (Vitis vinifera) Funding and support provided by: TAIR / Rhee Lab: Flavia Bossi, Hyein Nam, Meng Xu, 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 PMN grants: DBI-0640769 and IOS-1026003 (NSF) Many thanks to: Who makes the PMN possible? PMN team members: PI: Dr. Sue Rhee, Director and Lead Curator: Dr. Peifen Zhang Post-docs: Dr. Lee Chae and Dr. Ricardo Nilo Interns: Damian Priamurskiy, Tam Tran, Caryn Johansen External collaborators: SGN 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; Primary metabolism Secondary metabolism www.plantcyc.org What’s coming next at the PMN? Phytozome UniProt BRENDA ChEBI PubChem KEGG Knapsack TAIR MetaCyc Display data on pathway Desktop version Generate and upload a text file View Omics Data on Pathway Pages Data can also be plotted using bar and line graphs Pathways can be modified, connected, or created by users to enhance the analysis