kate dreher biocurator / plant molecular biologist the carnegie institution for science stanford, ca...
TRANSCRIPT
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: www.plantcyc.org
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
www.plantcyc.org
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 BoardCommunity
Submissions
17 PMN species are phylogenetically and "functionally" diverse
Database Species Pathways* Enzymes Reactions CompoundsPlantCyc 8.0 400+ 1050 188798 5332 4410AraCyc 11.5 Arabidopsis thaliana 597 9041 3490 2613
CassavaCyc 3.0 Manihot esculenta 491 10007 3058 2232ChineseCabbageCyc 1.0 Brassica rapa (+ spp.) 499 10976 3104 2270
GrapeCyc 3.0 Vitis vinifera 479 7572 3015 2229PapayaCyc 2.0 Carica papaya 481 5714 2999 2220PoplarCyc 6.0 Populus trichocarpa (+ spp.) 505 20822 3124 2295
SoyCyc 4.0 Glycine max 520 20317 3105 2273BarleyCyc 1.0 Hordeum vulgare 465 7572 2901 2135
BrachypodiumCyc 1.0 Brachypodium distachyon 473 8802 2915 2128CornCyc 3.5 Zea mays 484 13979 2821 2160OryzaCyc 1.0 Oryza sativa (+ spp.) 482 15677 3000 2226
SetariaCyc 1.0 Setaria italica 477 10214 2942 2145SorghumBicolorCyc 1.0 Sorghum bicolor 480 8630 2939 2141
SwitchgrassCyc 1.0 Panicum virgatum 479 17319 2985 2184MossCyc 2.0 Physcomitrella patens 416 7805 2713 1901
SelaginellaCyc 2.0 Selaginella moellendorffii 421 6462 2737 1987ChlamyCyc 3.5 Chlamydomonas reinhardtii 349 3330 2263 1514
Eudicots
Cereals
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
Database Species Pathways* Enzymes Reactions CompoundsPlantCyc 8.0 400+ 1050 188798 5332 4410AraCyc 11.5 Arabidopsis thaliana 597 9041 3490 2613
CassavaCyc 3.0 Manihot esculenta 491 10007 3058 2232ChineseCabbageCyc 1.0 Brassica rapa (+ spp.) 499 10976 3104 2270
GrapeCyc 3.0 Vitis vinifera 479 7572 3015 2229PapayaCyc 2.0 Carica papaya 481 5714 2999 2220PoplarCyc 6.0 Populus trichocarpa (+ spp.) 505 20822 3124 2295
SoyCyc 4.0 Glycine max 520 20317 3105 2273BarleyCyc 1.0 Hordeum vulgare 465 7572 2901 2135
BrachypodiumCyc 1.0 Brachypodium distachyon 473 8802 2915 2128CornCyc 3.5 Zea mays 484 13979 2821 2160OryzaCyc 1.0 Oryza sativa (+ spp.) 482 15677 3000 2226
SetariaCyc 1.0 Setaria italica 477 10214 2942 2145SorghumBicolorCyc 1.0 Sorghum bicolor 480 8630 2939 2141
SwitchgrassCyc 1.0 Panicum virgatum 479 17319 2985 2184MossCyc 2.0 Physcomitrella patens 416 7805 2713 1901
SelaginellaCyc 2.0 Selaginella moellendorffii 421 6462 2737 1987ChlamyCyc 3.5 Chlamydomonas reinhardtii 349 3330 2263 1514
1050pathways
476pathways(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
PathwayEnzyme
Gene
Compound
Evidence Codes
Regulation
Upstreampathway
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 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
"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.
Numerical data:(Relative values)(Absolute levels)
Results can be examined at different levels andconnect 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 07029 Email
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!
www.plantcyc.org
PMN AcknowledgementsCurator:
- 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 MedicCycDOE
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
www.plantcyc.org
Sue Rhee (PI)
Peifen Zhang (Director)
We're here to help . . .
Booth 200
Poster 7029
Thank you!!