1. 1 AraCyc Metabolic Pathway Annotation

2. 2 AraCyc – An overview  AraCyc is a metabolic pathway database for Arabidopsis thaliana;  Computational prediction by PathoLogic software using MetaCyc as the reference database (Peter Karp, SRI);  Predicted pathways were then manually validated; ongoing manual curation.

3. 3 Recent AraCyc releases AraCyc 2.1 Apr 2005 AraCyc 2.5 Oct 2005 AraCyc 2.6 May 2006 AraCyc 3.5 Feb 2007 Total pathways 221197228262 New-373551 Updated-0437 Deleted-61612 Pathways manually reviewed with literature evidence 71 (32%)170 (86%)201 (88%)233 (89%)

4. 4 Upcoming AraCyc 4.0  New pathways, updated pathways  Gene function annotation updated according to TAIR7 genome release  Significant changes of the assignment of genes to reactions/pathways

5. 5 Outline  Search and browse AraCyc  Arabidopsis Metabolic map  OmicsViewer

6. 6

7. 7 Search AraCyc Browse pathways, enzymes, genes, compounds Metabolic Map ‘Bird’s eye’ view of the Arabidopsis metabolic network OMICS Viewer Paint data from high-throughput experiments on the metabolic map Data submission AraCyc Tutorials

8. 8

9. 9 A pathway example: sucrose biosynthesis

10. 10 A pathway example: sucrose biosynthesis Beta-D-glucose-6-phosphate Enzyme: phosphoglucomutase Evidence: Inferred by a human based on computational evidence [Kofler00], Inferred from direct assay [Periappura00] Gene: PGM Alpha-D-glucose-1-phosphate = alpha-D-glucose-6-phosphate

11. 11

12. 12 Evidence codes

13. 13 Evidence based on an Author Statement Computational evidence Experimental evidence Evidence codes

14. 14 Evidence in pathways

15. 15 Evidence for enzymatic activities

16. 16

17. 17 AraCyc: Metabolic Map Compound: L-histidine Pathway: histidine biosynthesis

18. 18 AraCyc: Metabolic Map Biosynthesis: Amino acids Biosynthetic Catabolic un-assigned Plant hormone biosynthesis

19. 19 OmicsViewer: evaluating data in metabolic context Microarray expression data: low temperature regulatory circuits and gene regulons in higher plants (Michael Tomashow group).

20. 20 Compound: dihydrozeatin Pathway: cytokinins 9-N-glucoside biosynthesis Compound: xanthoxin Pathway: abscisic acid biosythesis

21. 21 OMICS Viewer Data types accepted by OmicsViewer Experiment/ Data Value assigned to OmicsViewer output Microarray Expression Genes (enzymes) Colored reaction lines Proteomics Proteins (enzymes) Colored reaction lines Metabolomics Metabolites (compounds) Colored compounds

22. 22

23. 23 Access Omics Viewer

24. 24 0 1 2 3 4

25. 25 Data value 0 1 2 3 4

26. 26

27. 27 0 1 2 3 4 Result A: single page for a single time point

28. 28 0 1 2 3 4 Result B: animation (two time points)

29. 29 0 1 2 3 4 Result C: single page (ratio of two time points: 2 /3 )

30. 30 0 1 2 3 4 Result D: animation (three pages: : 2 /1, 3 /1, 4 /2 )

31. 31

32. 32