the plant metabolic network: plantcyc, aracyc, and new metabolic pathway databases for plant...
TRANSCRIPT
The Plant Metabolic Network: PlantCyc, AraCyc, andNEW 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 to
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 proteinMKATLAPPSSLISLPRHKVSSLRSPSLLLQSQRPSSALMTTTASRGSVAVTAAATSSAEALREGIAEFYNETSGLWEEIWGD
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
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-468CPD-8250CPD-8234CPD-8243ALPHA-GLUCOSECPD-490ALPHA-GLUCOSE-16-BISPHOSPHATE
Enter a list of differentially expressed enzymes or compounds
Highlight list of items Navigate 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
Pathways Enzymes * Reactions Compounds
PlantCyc 6.0 898 27652 3421 3334
AraCyc 9.0 502 7100 3320 3210
PoplarCyc 4.0 354 8691 2220 1596
CassavaCyc 1.0 323 7178 2103 1524
CornCyc 1.0 341 10519 2156 1731
GrapeCyc 1.0 330 5338 2101 1540
SoyCyc 2.0 412 13094 2528 1987
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;
Prim
ary
met
abol
ism
Sec
onda
ry m
etab
olis
m
www.plantcyc.org www.plantcyc.org
What’s coming next at the PMN?
• Phytozome
• UniProt
• BRENDA
• ChEBI
• PubChem
• KEGG
• Knapsack
• TAIR
• MetaCyc
Display data on pathwayDesktop 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