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AraCyc Metabolic Pathway Annotation

AraCyc Metabolic Pathway Annotation. 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);.

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AraCyc Metabolic Pathway Annotation

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  1. AraCyc Metabolic Pathway Annotation

  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. Recent AraCyc releases

  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. Outline • Search and browse AraCyc • Arabidopsis Metabolic map • OmicsViewer

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

  7. A pathway example: sucrose biosynthesis

  8. 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

  9. Evidence codes

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

  11. Evidence in pathways

  12. Evidence for enzymatic activities

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

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

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

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

  17. OMICS Viewer • Data types accepted by OmicsViewer

  18. Access Omics Viewer

  19. 0 1 2 3 4

  20. Data value 0 1 2 3 4

  21. 0 1 2 3 4 Result A: single page for a single time point

  22. 0 1 2 3 4 Result B: animation (two time points)

  23. 0 1 2 3 4 Result C: single page (ratio of two time points: 2 /3)

  24. 0 1 2 3 4 Result D: animation (three pages: : 2 /1, 3 /1, 4 /2)

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