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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
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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