kate dreher The Carnegie Institution for Science Stanford, CA (CIMMYT, Mexico)

1.  Introduction to the Plant Metabolic Network: 18 Databases and Omics-Level Tools for Analysis and Discovery katedreher The Carnegie Institution for Science Stanford, CA (CIMMYT, Mexico)

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 New pharmaceutical sources . . . 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

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

5. SoyBase Plant Metabolic Network collaborators • SRI International – BioCyc project • Provide Pathway Tools Software • Maintain and update MetaCyc • Other collaborators / contributors include: • MaizeGDB • GoFORSYS • TAIR • SoyBase • Sol Genomics Network (SGN) / Boyce Thompson Institute • Gramene • MedicCyc / Nobel Foundation • 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 477 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. Species-specific databases require predictions Pathway/Genome Database (PoplarCyc) E2P2 Pathways Annotated Genome e.g. Populustrichocarpa Reactions PathoLogic Software compounds Gene products Reference Pathway Database (MetaCyc) genes

10. The PMN predicts enzyme functions from sequenced proteomes To improve enzyme functional predictions: • 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 • E2P2 can predict reactions that are not fully defined in the EC system by incorporating MetaCyc reaction IDs

11. Pathway predictions are refined through a SAVI pipeline Pathway/Genome Database (PoplarCyc) E2P2 Pathways Annotated Genome e.g. Populustrichocarpa Reactions PathoLogic Software compounds Gene products Reference Pathway Database (MetaCyc) genes SAVI Validated – Publicly Released Pathway/Genome Database (PoplarCyc)

12. SAVI pipeline • Decision rules and criteria for each pathway are generated by curators • The Semi-automated validation / incorporation pipeline uses the rules to: • Identify pathways with curated experimental evidence* • Bring in “Ubiquitous Plant Pathways” that were not predicted • Calvin cycle, glycolysis, etc. • Remove predicted non-plant / non-PMN pathways • Glycogen biosynthesis (non-plant) • Proteolysis (not small molecule metabolism) • Check key reactions and expected phylogenetic range to automatically assess many other predicted pathways • Highlight pathways that require manual validation

13. Expert input welcome!! • To submit data, report an error, volunteer to validate, or ask a question • Send an e-mail: curator@plantcyc.org • Use our feedback form: • Meet with me at the end of the workshop • Schedule an individual meeting with me at PAG

14. Community gratitude • We thank you publicly! • Together, we can make valuable, high quality databases

15. The PMN databases provide data and tools for analysis • Information, curated summaries, high quality predictions, and experimentally supported information about: • Pathways • Enzymes • Reactions • Compounds • Tools • General and specific searches • Comparative analysis tools • BLAST against enzymes in the PMN or the RPSD

16. OMICs-level data analysis

17. Data analysis with the Metabolic Map / Omics Viewer gene IDs relative expression levels at different timepoints • Display experimental data on a metabolic map • Data types: • Genes - transcriptomics • Enzymes – proteomics • Reactions - fluxomics • Compounds – metabolomics • Data inputs: • Single or multiple values for each object • Absolute or relative values

18. Visualizing quantitative data

19. Visualizing quantitative data input file data columns type of data relative or absolute scale color gradient data display options

20. Easily identify altered pathways

21. Navigate to items of interest on the metabolic map

23. Working with Groups • Opportunities • Create custom data sets • Explore experimental results • Perform enrichment analyses • Share data • Requires free registration

26. Generate custom datasets

27. Create groups from searches

29. export to Excel modify content paint on map compare to other groups share with others

30. Plant metabolic NETWORKING • Please use our data • Please use our tools • Please come explore our new species databases coming in 2014 • Please help us to improve our databases! • Please contact us if we can be of any help! curator@plantcyc.org www.plantcyc.org

31. PMN Acknowledgements • 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) • - Rex Nelson (Soybase) • - Gramene and MedicCyc Curator: - katedreher Post-docs: • - Lee Chae • - Ricardo NiloPoyanco • - Chuan Wang • Interns • - Ashley Joseph • Tech Team Members: • Bob Muller • Garret Huntress • Rhee Lab Members: • - FlaviaBossi • - Hye-in Nam • - TaehyongKim • - MengXu • Jim Guo • Jue Fan • Caryn Johansen Peifen Zhang (Director and curator) Sue Rhee (PI) 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 • Larry Ploetz • Shanker Singh • Bill Nelson • - Vanessa Kirkup • - Chris Wilks • - Raymond Chetty

32. Peifen Zhang (Director) • Please use our data • Please use our tools Sue Rhee (PI) We're here to help . . . curator@plantcyc.org www.plantcyc.org