kate dreher biocurator / plant molecular biologist The Carnegie Institution for Science Stanford, CA Introduction to the Plant Metabolic Network: Data and Tools for Analysis and Discovery

Free access to high quality, curated data promotes beneficial research on plant metabolism  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  These efforts benefit from access to high quality plant metabolism data

PMN provides data and analysis tools:

The Plant Metabolic Network has multiple goals  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

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 SoyBase Editorial Board Community Submissions

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

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 1050 pathways 476 pathways (average) 476 pathways (average)

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 (Caffea arabica) Morphine biosynthesis (Papaver somniferum) Taxol biosynthesis (cancer drug) (Taxus brevifolia) Raspberry ketone biosynthesis (Rubus idaeus) Vicianin bioactivation (defense compound) (Vicia sativa) Alliin degradation (garlic odor) (Allium sativum)

The PMN developed a new method to predict enzyme functions  A high-confidence Reference Protein Sequence Database was built RPSD 2.0 contains 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

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

A simple search connects you to a wealth of information AT3G16785

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

Pathways may look deceptively simple at first glance

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

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

Different search tools help meet the needs of many users from 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

"Groups" facilitate data retrieval, enrichment, and sharing

Transform your search results into a rich data set

Work with groups

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

Groups can be downloaded and shared

Omics datasets can be displayed on a metabolic map

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

Results can be examined at different levels and connect to relevant pages

Additional analysis tools and resources are available

The PMN actively interacts with its users  We answer questions!  We make suggested corrections!  We make public presentations and meet with individuals Booth 200 Poster  We ask for your help  We thank you publicly CHOCOLATE !! (Theobroma cacao)

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

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!

PMN Acknowledgements Curator: - kate dreher Post-docs: - Lee Chae - Ricardo Nilo Poyanco - Chuan Wang Interns - Caryn Johansen Tech Team Members: - Bob Muller (Manager) - Larry Ploetz (Sys. Admin) - Shanker Singh - Bill Nelson Rhee Lab Members: - Flavia Bossi - Jue Fan - Hye-in Nam - Taehyong Kim - Meng Xu Peifen Zhang (Director and curator) Sue Rhee (PI) Collaborators: SRI - Peter Karp - Ron Caspi - Hartmut Foerster - Suzanne Paley - SRI Tech Team MaizeGDB - Mary Schaeffer - Lisa Harper - Jack Gardiner - Taner Sen ChlamyCyc - Patrick May - Dirk Walther - Lukas Mueller (SGN) - Gramene and MedicCyc DOE PMN Alumni: - A. S. Karthikeyan (curator) - Christophe Tissier (curator) - Hartmut Foerster (curator) - Eva Huala (co-PI) - Tam Tran (intern) - Varun Dwaraka (intern) - Damian Priamurskiy (intern) - Ricardo Leitao (intern) - Michael Ahn (intern) - Purva Karia (intern) - Anuradha Pujar (SGN curator) Tech Team Alumni - Anjo Chi - Cynthia Lee - Tom Meyer - Vanessa Kirkup - Chris Wilks - Raymond Chetty

 Please use our data  Please use our tools  Sue Rhee (PI) Peifen Zhang (Director) We're here to help... Booth 200 Poster 7029 Booth 200 Poster 7029 Thank you!!