1. Intralab Workshop - Reactome CMAP Chang-Feng Quo June 29 th, 2006

2. Reactome http://www.reactome.org

3. Background Curated resource of core pathways and reactions in human biology Free on-line resource; open-source software Collaboration among –Cold Spring Harbor Laboratory –The European Bioinformatics Institute –The Gene Ontology Consortium

4. Data sources Cross-referenced with –PubMed –GO –UniProt –ENSEMBL –Entrez Gene –KEGG gene –OMIM 21 non-human species –e.g. mouse, rat, chicken, fugu fish, worms, fly, yeast, E.coli

5. Features

6. Home Reaction map –color-coded by verification methods Reactions –categorized by functions and species Search option –text input

7. Data model / Schema Hierarchical view of database objects Detailed attributes of classes

8. Search / Extended search Highlighted pathways and reactions Hierarchical view of pathways and reactions Detailed information about participating molecules

9. Pathfinder 2-fold search for pathways that link input / output compounds Results highlighted in reaction map List compound identifiers

10. Skypainter Discover highly correlated pathways / reactions given list of compound identifiers

11. Downloads / Editorial calendar Download and manage local versions Planned releases by date and topic

12. Reactome demo http://www.reactome.org http://www.reactome.org

13. Feature summary Data model / Schema –consists of pathways, reactions, entities Search / Extended search –links to external references Pathfinder –finds pathways linked with input/output compounds Skypainter –identifies significant events linked with genes Downloads –manage local versions Editorial calendar –lists planned updates, curation information

14. Cancer Molecular Analysis Project http://cmap.nci.nih.gov/ http://tr.nci.nih.gov/cmap

15. Background Prototype system –access and link molecular profiles molecular targets targeted agents clinical data Integrated with caBIO NIH, NCI, NCICB

16. Key concepts Context** –Tissue, histology type, histology subtype Target** –Protein (at present), complex or antigen –Functional classification: pathways, ontology –Not directly linked to context Anomaly –Deviation in structure or expression of target Profile** –Set of anomalies from NCI 60 cell lines (at present) Agent** –Linked to targets, contexts (at present) and profiles Trial** –Linked to context and agents; not directly to targets

17. Features 1 23 45

18. Molecular profiles Formats –Chromosomal SAGE EST UCSC –2D array NCI60 SAGE

19. Molecular targets Pictorial annotation of significant deviations of target expression

20. Targeted agents Search for agents to retrieve relevant clinical trial information

21. Clinical trials

22. Cancer Molecular Analysis Project http://cmap.nci.nih.gov/ http://tr.nci.nih.gov/cmap http://cmap.nci.nih.gov/ http://tr.nci.nih.gov/cmap

23. Feature summary Context –defines tissue and histology types Molecular profiles –displays expression ratios spatially in chromosomal and 2D array formats Molecular targets –organizes gene targets based on: ontology (GO) pathways (BioCARTA) CMAP annotated pathways Targeted agents –found in CTEP, CMAP trials Clinical trials

24. Comparison Cellular / molecular basis Cross-references Strong visual pathway presentation Cellular / molecular basis Clinical trial data available Clinical researchers, physicians, pharmaceutical companies