| Content | |
|---|---|
| Description | Reactome: a database of reactions, pathways and biological processes. |
| Contact | |
| Primary Citation | PMID 21067998 |
| Access | |
| Data format | BioPAX SBML |
| Website | http://www.reactome.org |
| Download URL | http://www.reactome.org/download/index.html |
| Tools | |
| Miscellaneous | |
Reactome is a database of biological pathways.[1][2] There are several Reactomes that concentrate on a specific organism, the largest of these is focused on human biology, but includes pathway steps inferred to exist in humans based on experimental data from model organisms and pathways computationally inferred to exist in other organisms. It is an on-line encyclopedia of core human pathways including DNA replication, transcription, translation, the cell cycle, metabolism, and signaling cascades - and can be browsed to retrieve up-to-date information about a topic of interest, e.g., the molecular details of the signaling cascade set off when the hormone insulin binds to its cell-surface receptor, or used as an analytical tool for the interpretation of large data sets like those generated by DNA microarray analysis. The information in Reactome is provided by expert biologists and entered/maintained by Reactome curators, who are all PhD level biologists. Every pathway step or 'Reaction' is supported by published research literature containing an experiment that supports its existence. All content is peer-reviewed before release on the Reactome website, and periodically updated.
Contents |
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.
The database contains curated annotations that cover a diverse set of topics in molecular and cellular biology. Details of current and future annotation projects can be found in the calendar of annotation projects.
Topics of annotation include;
There are tools on the website for performing pathway over-representation analysis and for overlaying expression data onto Reactome pathways. Both are incorporated into the Skypainter tool, this decides which analysis to run based on the input dataset; if a single column of protein/compound identifiers is used, it runs over-representation analysis, if there are additional columns of numeric values, these are interpreted as expression values (they can in fact be any numeric value, e.g. differential expression values or quantitiative proteomics values) and expression overlay is performed, with each additional column interpreted as a different set, e.g. timepoint or disease progression status. Over-representation results are presented as a list of statistically over-represented pathways (note that the default view only shows the major pathway topics, which may not be the most significant, click on the Open All button to see the subpathways). Expression data is represented as colouring of the reaction arrows on the pathway diagram, 'hot' colours represent high values, if there were multiple columns the display cycles through them.
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 molecular pathway databases