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

45

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