Introduction to the Plant Metabolic Network: Data and Tools for Analysis and Discovery

1. Introduction to the Plant Metabolic Network: Data and Tools forAnalysisand Discovery katedreher biocurator / plant molecular biologist The Carnegie Institution for Science Stanford, CA

2. Plants provide crucial benefits to humanity and the ecosystem A better understanding of plant metabolism may contribute to: More nutritious foods More pest-resistant plants More stress-tolerant crops Higher photosynthetic capacity and higher yield in agricultural and biofuel crops . . . many more applications Free access to high quality, curated data promotes beneficial research on plant metabolism • These efforts benefit from access to high quality plant metabolism data

3. PMN provides data and analysis tools: www.plantcyc.org

4. Support research, breeding, and education Transform published results into data-rich metabolic pathways Capture information on Enzymes, Reactions, and Compounds Create and deploy improved methods for predicting enzyme function and metabolic capacity using plant genome sequences Provide public resources: PlantCyc AraCyc 16 additional species-specific databases Facilitate data analysis The Plant Metabolic Network has multiple goals www.plantcyc.org

5. SoyBase Numerous collaborators contribute to the Plant Metabolic Network • SRI International – BioCyc project • Provide Pathway Tools Software • Maintain and update MetaCyc • Other collaborators / contributors include: • MaizeGDB • GoFORSYS • SoyBase • Sol Genomics Network (SGN) / Boyce Thompson Institute • Cosmoss • Gramene • PlantMetabolomics group • . . . and more Community Submissions Editorial Board

6. 17 PMN species are phylogenetically and "functionally" diverse • Major crops • Model species • Legume • Woody and herbaceous species • Annuals and perennials • C3 and C4 species Eudicots Cereals Basal land plants Green alga

7. PlantCyc provides access to important pathways not found in species-specific databases • PlantCyc contains over 1000 pathways and information from over 400 plant species 1050 pathways 476 pathways (average)

8. PlantCyc provides access to numerous specialized metabolic pathways • Many PlantCyc-specific metabolic pathways produce or break-down specialized ("secondary") metabolites • Many of the enzymes in these pathways have experimental evidence Caffeine biosynthesis I (Caffeaarabica) Raspberry ketone biosynthesis (Rubusidaeus) Morphine biosynthesis (Papaversomniferum) Taxol biosynthesis (cancer drug) (Taxusbrevifolia) Vicianinbioactivation (defense compound) (Vicia sativa) Alliin degradation (garlic odor) (Allium sativum)

9. The PMN developed a new method to predict enzyme functions • A high-confidence Reference Protein Sequence Database was built • RPSD 2.0contains 34,269 enzymes and 82,216 non-enzymes • The Ensemble Enzyme Prediction Pipeline (E2P2) uses the RPSD to predict functions based on protein sequence • It assigns protein functions using standard EC (Enzyme Commission) numbers AND using specific reaction IDs • Many reactions are not associated with full EC numbers but are associated with specific reaction IDs • E2P2 can predict a higher number of enzyme functions • E2P2 may help to fine-tune predictions among large enzyme families

10. Evidence codes enhance transparency • Evidence codes clearly define when enzymes are assigned to reactions based on computational or experimental evidence • Users can check references for computational prediction methods and original experiments in journal articles

11. A simple search connects you to a wealth of information AT3G16785

12. Quickly move between genes, enzymes, reactions, compounds, and pathways

13. Pathways may look deceptively simple at first glance

14. The PMN provides valuable pathway context information Evidence Codes Upstream pathway Regulation Pathway Enzyme Gene Compound Reaction

15. Curated summaries provide background information, cite papers, and link to other PMN pages

16. Different search tools help meet the needs of many usersfrom high school biology students to bioinformaticians • Quick Search • Detailed search menus for for Compounds, Pathways, and Enzymes • Advanced Search (queryable with BioVelo language) • BLAST against PMN-specific enzyme sets • Comparative analysis • JavaCyc and PerlCyc • Complete downloadable files - Biopax and other file formats • Groups - for custom dataset building

17. "Groups" facilitate data retrieval, enrichment, and sharing

18. Transform your search results into a rich data set

19. Work with groups

20. Different properties and transformations are available for enzymes, reactions, pathways, and compounds

21. Groups can be downloaded and shared

22. Omics datasets can be displayed on a metabolic map

23. A simple tab-delimited text file should IDs/names and data value(s) ID (Gene ID) (enzyme name) (compound name) etc. Numerical data: (Relative values) (Absolutelevels)

24. Results can be examined at different levels andconnect to relevant pages

25. Additional analysis tools and resources are available

26. The PMN actively interacts with its users • We answer questions! • curator@plantcyc.org • We make suggested corrections! • We make public presentations and meet with individuals • Booth 200 • Poster 07029 • Email • We ask for your help • We thank you publicly CHOCOLATE !! (Theobroma cacao)

27. The PMN is working on additional enhancements • Continue to improve our enzyme annotation pipeline • Increase coverage of secondary metabolism • Add transcription factors that affect enzyme expression • Predict plant metabolic pathways for additional species

28. Plant metabolic NETWORKING • Please use our data • Please use our tools • Please help us to improve our databases! • Please contact us if we can be of any help! curator@plantcyc.org www.plantcyc.org

29. PMN Acknowledgements Curator: - katedreher Post-docs: • - Lee Chae • - Ricardo NiloPoyanco • - Chuan Wang • Interns • - Caryn Johansen • Tech Team Members: • - Bob Muller (Manager) • - Larry Ploetz (Sys. Admin) • - Shanker Singh • - Bill Nelson • Rhee Lab Members: • - FlaviaBossi • - Jue Fan • - Hye-in Nam • - TaehyongKim • - MengXu Peifen Zhang (Director and curator) Sue Rhee (PI) • Collaborators: • SRI • - Peter Karp • - Ron Caspi • - HartmutFoerster • - Suzanne Paley • - SRI Tech Team • MaizeGDB • - Mary Schaeffer • - Lisa Harper • - Jack Gardiner • - TanerSen • ChlamyCyc • - Patrick May • - Dirk Walther • - Lukas Mueller (SGN) • - Gramene and MedicCyc PMN Alumni: • - A. S. Karthikeyan (curator) • - Christophe Tissier (curator) • - HartmutFoerster(curator) • - Eva Huala (co-PI) • - Tam Tran (intern) • - VarunDwaraka(intern) • - Damian Priamurskiy(intern) • - Ricardo Leitao(intern) • - Michael Ahn(intern) • - PurvaKaria (intern) • - AnuradhaPujar(SGN curator) • Tech Team Alumni • - Anjo Chi • - Cynthia Lee • - Tom Meyer • - Vanessa Kirkup • - Chris Wilks • - Raymond Chetty DOE

30. Thank you!! Peifen Zhang (Director) • Please use our data • Please use our tools Sue Rhee (PI) We're here to help . . . Booth 200 Poster 7029 curator@plantcyc.org www.plantcyc.org