Reactome: A Curated Reactome: A Curated Database of Human Database of Human Biological PathwaysBiological Pathways
Lincoln SteinInfectious Disease Ontologies
CSHL 2007
My Screen Found Lots of My Screen Found Lots of Genes: Now What?Genes: Now What?
Fuzzy Hairball?Fuzzy Hairball?
Long List of GO Terms?Long List of GO Terms?
Boehringer-Mannheim, ca 1970
Fauré et al Bioinformatics 22 (14): e124 (2002)
Reactome A computable representation of human
pathways and reactions. Uses a “chemical” reaction model to represent
causality. Molecules identified explicitly – including small
molecules, proteins, complexes, post-translational modifications, compartments.
Exportable as SBML, BioPax, PDF and MySQL dumps.
Open Source Authored & curated by experts in the
field.
Home Page
A Pathway Page
A Reaction Page
Reaction Details
Where the Data Comes From
1) Recruit bench scientists to write modules.2) Authors use a software tool to describe
their pathway.1) All molecules must be identified explicitly.
2) All assertions backed up by literature references.
3) Curators work with authors to ensure consistency and completeness.
4) Module checked by peer review & software before publication.
Author Tool
SkyPainter – Overrepresentation Analysis
Increasing Coverage Add non-Reactome data sets to create a
“corona” of less reliable data around each pathway.
Corona connected to pathway components by probable functional interaction links.
Enhanced Skypainter
Reactome & Infectious Disease
Via collaboration with Richard Scheuermann, have created an influenza lifecycle module. 64 reactions, 338 molecules Modeling issues:
Is the virion a molecular complex? A compartment? A cell?
When is it OK for the proteins of two species to interact?
We’d encourage other groups to do this for more pathogens.
Physiology vs Pathophysiology
Reactome databases Normal physiological pathways Pathophysiological pathways
Non-Reactome databases specialized for infecious disease Ontology dbs WIKIs Pathogen metagenome databases etc
Pathophysiology<->PhysiologyPathogen-specific database
Reactome Database
Credits
Cold Spring Harbor Laboratory
European Bioinformatics Institute
Gene Ontology Consortium
Lincoln SteinPeter D'EustachioGopal GopinathraoLisa MatthewsMarc GillespieGuanming Wu
Ewan BirneyImre VastrikBernardo de BonoEsther SchmidtBijay JassalDavid Croft
Suzanna Lewis
NHGRI Grant # R01 HG002639and a subcontract from the NIGMS-funded Cell Migration Consortium
Richard Scheuermann & Co.