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Intralab Workshop Reactome CMAP Chang-Feng Quo June 29th, 2006 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 – The European Bioinformatics Institute – The Gene Ontology Consortium 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 Features Home • Reaction map – color-coded by verification methods • Reactions – categorized by functions and species • Search option – text input Data model / Schema Hierarchical view of database objects Detailed attributes of classes Search / Extended search Highlighted pathways and reactions Detailed information about participating molecules Hierarchical view of pathways and reactions Pathfinder 2-fold search for pathways that link input / output compounds Results highlighted in reaction map List compound identifiers Skypainter Discover highly correlated pathways / reactions given list of compound identifiers Downloads / Editorial calendar Download and manage local versions Planned releases by date and topic Reactome demo http://www.reactome.org 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 Cancer Molecular Analysis Project http://cmap.nci.nih.gov/ http://tr.nci.nih.gov/cmap Background • Prototype system – access and link • molecular profiles • molecular targets • targeted agents • clinical data • Integrated with caBIO • NIH, NCI, NCICB 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 Features 1 2 5 3 4 Molecular profiles • Formats – Chromosomal • SAGE • EST • UCSC – 2D array • NCI60 • SAGE Molecular targets Pictorial annotation of significant deviations of target expression Targeted agents Search for agents to retrieve relevant clinical trial information Clinical trials Cancer Molecular Analysis Project http://cmap.nci.nih.gov/ http://tr.nci.nih.gov/cmap 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 Comparison • Cellular / molecular basis • Cellular / molecular basis • Cross-references • Clinical trial data available • Strong visual pathway presentation • Clinical researchers, physicians, pharmaceutical companies
