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Intralab Workshop - Reactome CMAP

Chang-Feng Quo June 29 th , 2006. Intralab Workshop - Reactome CMAP. Reactome http://www.reactome.org. Background. Curated resource of core pathways and reactions in human biology Free on-line resource; open-source software Collaboration among Cold Spring Harbor Laboratory

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Intralab Workshop - Reactome CMAP

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

  2. Reactomehttp://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 Detailed information about participating molecules Hierarchical view of pathways and reactions

  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 demohttp://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 Projecthttp://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 2 3 5 4

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

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