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

Reactome

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 Hierarchical view of pathways and reactions Detailed information about participating molecules

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

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

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

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

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