Reactome

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Database Organization

In Reactome, human biological processes are annotated by breaking them down into series of molecular events. Like classical chemistry reactions each Reactome event has input physical entities (substrates) which interact, possibly facilitated by enzymes or other molecular catalysts, to generate output physical entities (products).

Reactions include the classical chemical interconversions of intermediary metabolism, binding events, complex formation, transport events that direct molecules between cellular compartments, and events such as the activation of a protein by cleavage of one or more of its peptide bonds. Individual events can be grouped together into pathways.

Physical entities can be small molecules like glucose or ATP, or large molecules like DNA, RNA, and proteins, encoded directly or indirectly in the human genome. Physical entities are cross-referenced to relevant external databases, such as UniProt for proteins and ChEBI for small molecules. Localization of molecules to subcellular compartments is a key feature of the regulation of human biological processes, so molecules in the Reactome database are associated with specific locations. Thus in Reactome instances of the same chemical entity in different locations (e.g., extracellular glucose and cytosolic glucose) are treated as distinct chemical entities.

The Gene Ontology controlled vocabularies are used to describe the subcellular locations of molecules and reactions, molecular functions, and the larger biological processes that a specific reaction is part of.

Database Content

The Reactome data set currently includes information about a diverse set of domains of molecular and cellular biology:

• Apoptosis
• Cell cycle checkpoints
• Cell cycle, mitotic
• DNA repair
• DNA replication
• Electron transport chain
• Gene expression (mRNA transcription and processing)
• Hemostasis
• HIV infection
• Influenza infection
• Insulin receptor mediated signaling
• Integration of pathways of energy metabolism
• Lipid metabolism
• Metabolism of amino acids and related nitrogen-containing molecules
• Metabolism of glucose and other sugars
• mRNA processing
• Notch signaling
• Nucleotide metabolism
• Oxidative decarboxylation of pyruvate and TCA cycle
• Post-translational modification of proteins
• Transcription (RNA synthesis)
• Translation (protein synthesis)
• Xenobiotic metabolism

A calendar of annotation projects currently underway is also available

Tools

The database can be browsed and searched as an on-line textbook. An on-line users' guide is available. Users can also download the current data set or individual pathways and reactions in a variety of formats including PDF, BioPAX, and SBML.

Other databases that represent human biological processes as molecular pathways include Panther Pathways, KEGG (the Kyoto Encyclopedia of Genes and Genomes), and HumanCyc. Each has its own distinct style and coverage of human biology.