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

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

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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

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9 A pathway example: sucrose biosynthesis

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

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12 Evidence codes

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

14 Evidence in pathways

15 Evidence for enzymatic activities

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

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

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

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

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

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23 Access Omics Viewer

25 Data value

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Result A: single page for a single time point

Result B: animation (two time points)

Result C: single page (ratio of two time points: 2 /3 )

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

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