Reactome
Category Cross-Omics>Pathway Knowledge Bases/Databases/Tools
Abstract Reactome is a curated knowledge-base of biological pathways. It is an online bioinformatics database of human biology described in molecular terms.
It is also an on-line encyclopedia of core human pathways - 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 datasets like those generated by DNA microarray analysis.
In addition to curated human events, 'inferred orthologous events' in 22 non-human species including mouse, rat, chicken, puffer fish, worm, fly, yeast, two plants and E.coli are also available.
The information in Reactome is provided by expert biologists and gathered from the published research literature, is peer-reviewed before release on the Reactome website, and is periodically updated.
Practical applications of Reactome -- The Reactome website can be browsed like an online textbook.
The website's front page features a large 'reaction map' that summarizes all of the currently curated or inferred pathways, and a table of contents that describes each of the top-level pathways in the database.
The reactions are organized in distinctive patterns to allow researchers to become familiar with the different parts of the reaction network.
By default, human data are displayed for each top level pathway listed in the table of contents.
However, choosing an alternative species from the drop-down menu above the reaction map will take the researcher to the list of pathways that have been inferred in that organism.
The researcher can drill down into the database by clicking on a reaction in the reaction map or by clicking on any of the top-level pathways in the table of contents.
Pathways are organized in a hierarchy, so that as researchers drill down pathways are described with increasing detail.
At each level of description, researchers can view the direct or indirect evidence for the pathway or reaction. At the pathway level the evidence is usually a review article that describes the pathway in general terms.
At the reaction level, the evidence is one or more citations from the primary literature that confirm the reaction's existence.
From a pathway or reaction page, researchers can download lists of accession numbers for all involved genes and proteins.
They can also download a summary of the pathway or reaction in a PDF (human readable), Systems Biology Markup Language (SBML), or Biological Pathways Exchange (BioPAX) level 2 format for computational analysis.
SBML is an exchange format commonly used for kinetic modeling of biologic systems, whereas BioPAX is an exchange format designed to describe complex biologic systems.
Pathway and reaction pages are linked to genome databases at UniProt, Entrez Gene, OMIM, and elsewhere.
A button allows researchers to view the current pathway in the Cytoscape (see G6G Abstract Number 20092) network browser tool.
Reactome provides users with the ability to search the database using the name of a reaction, a gene name, a protein name, or any of several other identifiers.
SkyPainter -- a utility that allows researchers to visualize their own datasets on top of the reaction map. To use the SkyPainter, researchers cut and paste a list of gene identifiers into a web form, or upload a file of identifiers using an upload button.
After submitting the form, the SkyPainter uses statistical analysis based on the hyper-geometric test to color pathways according to the statistical likelihood that they would contain the listed genes by chance.
This highlights those pathways in which the uploaded genes are over- represented.
The SkyPainter recognizes a large number of gene identifiers, including Entrez Gene names, accession numbers, and Affymetrix probe sets. It also accepts numeric values, such as expression levels from a microarray experiment.
The SkyPainter can also render more complex data, such as a time course series, as an animated movie.
Because Reactome is heavily curated, the manufacturers believe it to have a low rate of false reactions.
This makes it a good 'gold standard' for training 'machine learning systems' that attempt to infer the presence of genetic or physical interactions from high-throughput datasets.
Reactome is distinguished by its uniform treatment of all biologic pathways.
It uses the same data model to describe metabolism, signal transduction, DNA replication, the regulation of the cell cycle, and all other biologic processes.
System Requirements
Reactome is a free on-line resource, and Reactome software is open- source.
Installation instructions assume that you have root access to the computer onto which you are planning to install Reactome database and website. The instrtuctions are split into two sections, non- Reactome and Reactome. The first of these involves the installation of applications/modules that are not part of the Reactome project but are necessary for the web site to work, such as Apache and MySQL. The second involves installing the Reactome data, modules and web site code.
You do need to have wget, tar, gcc and (gnu) make. Please make sure that those occur in your path and that the "right" one comes 1st.
Manufacturer
The Reactome project is a collaboration among
- Cold Spring Harbor Laboratory,
- The European Bioinformatics Institute, and
- The Gene Ontology Consortium
to develop a curated resource of core pathways and reactions in human biology.
Manufacturer Web Site Reactome site
Price Free
G6G Abstract Number 20267
G6G Manufacturer Number 100635