Presentation on theme: "Kate Dreher AraCyc, TAIR, PMN Carnegie Institution for Science"— Presentation transcript:
1 Kate Dreher AraCyc, TAIR, PMN Carnegie Institution for Science AraCyc and the OMICS Viewer: Making sense of metabolism in your favorite biological processKate DreherAraCyc, TAIR, PMNCarnegie Institution for Science
2 Everyone is studying metabolism Many biological processes connect to metabolismDrought tolerance – changes in osmolyte concentrationsHormone signaling – biosynthesis and degradation of hormonesPhotosynthesis – chlorophyll production and ROS scavengingTranslation – amino acid biosynthesis and riboswitchingPlant defense – phytoalexin synthesisYour favorite process . . .AraCyc can help you find these connections!Arabidopsis Metabolic EnCyclopediaDatabase of metabolic pathways found in Arabidopsis(TAIR)(Plant Metabolic Network)
3 AraCyc 4.5 (released June 2008) Pathways288Compounds1956Reactions1723Genes(in pathways)1914Citations2279How can you connect these to your research efforts?
4 OMICS Viewer to the rescue . . . Overlay experimental data on a metabolic mapTranscript data (for enzymes)Proteomic data (for enzymes)Metabolomic dataUse multiple data sourcesYour dataPublicly available dataGene Expression OmnibusNASC Proteomics DatabaseNSF2010 MetabolomicsMany more . . .Generate new testable hypotheses about your favoritegenemetabolitebiological processetc.
5 Addressing common research conundrums . . . My (single/double/triple/quadruple) mutant has “no phenotype”!!!!Compare transcript levels / protein levels / metabolite levels in wild-type and mutant plants using the OMICS viewerLook for “hidden” perturbations in metabolismI have a mutant with a defect in (biological process) but I don’t know the mechanismUse the OMICS viewer to compare data from WT and mutant plantsDownload publicly available data sets related to the biological processScan for affected areas of metabolismI just did a microarray experiment and a bunch of metabolic enzymes popped up . . .Use the OMICS Viewer to quickly identify metabolic pathways that are up- or down-regulatedAnd many more . . .
6 OMICS Viewer Overviewrelated pathways aregrouped together
7 OMICS Viewer Overview COMPOUNDS (icons) TRANSCRIPTS or PROTEINS (lines)
8 Viewing gene/protein families Expression levels forindividual genes/proteinscan be displayedCaution:Only the highest expression level is shown using the single line on the diagramChanges in the levels of homologs are hidden in the low resolution map
9 Getting more information Clicking on a pathway brings you to a pathway detail page
10 AraCyc Pathway pagesAll items can be clicked on to obtain more informationEvidence CodeCompoundReactionPathwayGeneEnzyme+ Additional curated information
13 OMICS Viewer in actionMultiple data sets can be entered using the same input fileAn animation can show changes in data sets:wild type /mutant a / mutant b / mutant c / . . .time points 0, 1, 2, 3, . . .compound concentration x, y, z, . . .Suberin BiosynthesisWild typemutant Amutant B
14 OMICS Viewer data inputs Input filetab-delimited text filepre-analyzed / cleaned dataIdentifiers in first columnGenesAGI locus codes (e.g. At2g46990)EnzymesEnzyme name (e.g. arogenate dehydrogenase)EC number (e.g )CompoundsCompound nameData in additional column(s)absolute or relative valuesSample file and tutorial available at website
17 OMICS Viewer data upload Select speciesUpload data fileEnter appropriate parametersGO!
18 lysine biosynthesis pathway New ideas to pursue . . .Wild typeThe transcript levelsof several enzymes in thelysine biosynthesis pathwayare reduced ~4-fold!Mutant with“no phenotype”Mutant witha metabolicphenotypeNew hypotheses and experiments
19 Eva Huala (Director and Co-PI) AcknowledgementsAraCyc, the PMN, and TAIRSue Rhee (PI and Co-PI)Eva Huala (Director and Co-PI)Current Curators:- Peifen Zhang (Director and lead curator- metabolism)- Tanya Berardini (lead curator – functional annotation)- David Swarbreck (lead curator – structural annotation)- Debbie Alexander (curator)- A. S. Karthikeyan (curator)- Donghui Li (curator)Recent Past Contributors:- Christophe Tissier (curator)- Hartmut Foerster (curator)Tech Team Members:- Bob Muller (Manager)- Larry Ploetz (Sys. Administrator)- Raymond Chetty- Anjo Chi- Vanessa Kirkup- Cynthia Lee- Tom Meyer- Shanker Singh- Chris WilksMetabolic Pathway Software:- Peter Karp and SRI group (NIH)
20 Need more help? If you have any questions or want a live demo . . . Come to the Curation Booth – Booth #1Open throughout the conference!banner by Philippe LameschPlease stop by during a poster session
21 Thank you . . . www.arabidopsis.org email@example.com