The Plant Metabolic Network: PlantCyc, AraCyc, and

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.org to
connect to experimentally verified and computationally predicted
Vitamin E
biosynthesis
>A very interesting protein
MKATLAPPSSLISLPRHKVSSLRSPSLL
LQSQRPSSALMTTTASRGSVAVTAAAT
SSAEALREGIAEFYNETSGLWEEIWGD
information about enzymes, compounds, and biochemical pathways
in over 300 plant species
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!
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
Identify metabolic changes due to :
• Different tissues
• Different developmental stages
• Different genotypes
• Different stresses
• . . . and many other conditions
Enter a list of differentially expressed
enzymes or compounds
Navigate to specific items
Generate a stable url / bookmark:
CPD-468
CPD-8250
CPD-8234
CPD-8243
ALPHA-GLUCOSE
CPD-490
ALPHA-GLUCOSE-16-BISPHOSPHATE
* The term "enzyme" refers to both monomers and complexes found in the databases.
Important pathways for over 300 plant species
Overlay quantitative data:
Zoom to learn more details:
Examine isozymes:
• Caffeine biosynthesis (Coffea arabica)
• Gibberellin biosynthesis
• Starch degradation
• Fatty Acid beta-oxidation
Secondary
metabolism
• Photosynthesis
Primary
metabolism
Highlight list of items
• Glucosinolate biosynthesis (Arabidopsis thaliana)
• Kauralexin biosynthesis (Zea mays)
• Sorbitol degradation (Malus x domestica)
• Resveratrol biosynthesis (Vitis vinifera)
• Urea cycle
Analysis tools and software
Software: Pathway Tools v. 15.5 (SRI International)
Display data on pathway
Desktop version
• Numerous basic and advanced searching and browsing options
View Omics Data on Pathway Pages
Connect to:
• Phytozome
Generate and upload a text file
• UniProt
• Omics data visualization interface
• BRENDA
• ChEBI
• PMN-specific BLAST datasets
• PubChem
• KEGG
• Data management and sharing capabilities
• Comparative analysis tools
• Knapsack
•
Data can also be plotted using bar and line graphs
•
Pathways can be modified, connected, or created
by users to enhance the analysis
• TAIR
• MetaCyc
• Desktop software and downloadable database files
• Flux balance analysis module (using desktop software)
What’s coming next at the PMN?
Who makes the PMN possible?
Funding and support provided by:
PMN grants: DBI-0640769 and IOS-1026003 (NSF)
• New databases for:
--Chlamydomonas reinhardtii
--Physcomitrella patens
-- Selaginella moellendorffii
-- Carica papaya
• Enhanced computationally predicted and experimentally supported coverage of
metabolism in all PMN databases
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:
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;
• Upgraded Pathway Tools 16.0 software with login and data storage capabilities
Questions?? New or updated data??
Please contact us at:
[email protected]
SGN
Many thanks to:
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