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
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
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 3
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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
• Cross-references
• Strong visual pathway presentation
• Cellular / molecular basis
• Clinical trial data available
• Clinical researchers, physicians, pharmaceutical companies
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