Reactome
Encyclopedia
Reactome is a database of biological pathway
s. 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 set
s 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.
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.
and cellular biology. Details of current and future annotation projects can be found in the calendar of annotation projects.
Topics of annotation include;
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
.
Biological pathway
A biological pathway is a number of biochemical steps, linked together, with a start and an end. The activity within a pathway should is a flow of molecules. Some typical types of biochemical pathways are metabolic pathways and signaling pathways. The Reactome is a curated information source, with...
s. There are several Reactomes that concentrate on a specific organism, the largest of these is focused on human biology
Human biology
Human Biology is an interdisciplinary area of study that examines humans through the influences and interplay of many diverse fields such as genetics, evolution, physiology, epidemiology, ecology, nutrition, population genetics and sociocultural influences. It is closely related to...
, 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
Biological pathway
A biological pathway is a number of biochemical steps, linked together, with a start and an end. The activity within a pathway should is a flow of molecules. Some typical types of biochemical pathways are metabolic pathways and signaling pathways. The Reactome is a curated information source, with...
including DNA replication
DNA replication
DNA replication is a biological process that occurs in all living organisms and copies their DNA; it is the basis for biological inheritance. The process starts with one double-stranded DNA molecule and produces two identical copies of the molecule...
, transcription
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
, translation
Translation
Translation is the communication of the meaning of a source-language text by means of an equivalent target-language text. Whereas interpreting undoubtedly antedates writing, translation began only after the appearance of written literature; there exist partial translations of the Sumerian Epic of...
, the cell cycle
Cell cycle
The cell cycle, or cell-division cycle, is the series of events that takes place in a cell leading to its division and duplication . In cells without a nucleus , the cell cycle occurs via a process termed binary fission...
, metabolism
Metabolism
Metabolism is the set of chemical reactions that happen in the cells of living organisms to sustain life. These processes allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolism is usually divided into two categories...
, 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 set
Data set
A data set is a collection of data, usually presented in tabular form. Each column represents a particular variable. Each row corresponds to a given member of the data set in question. Its values for each of the variables, such as height and weight of an object or values of random numbers. Each...
s like those generated by DNA microarray
DNA microarray
A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome...
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.
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
UniProt
UniProt is a comprehensive, high-quality and freely accessible database of protein sequence and functional information, many of which are derived from genome sequencing projects...
for proteins and ChEBI
ChEBI
Chemical Entities of Biological Interest, also known as ChEBI, is a database and ontology of molecular entities focused on 'small' chemical compounds, that is part of the Open Biomedical Ontologies effort...
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
Gene Ontology
The Gene Ontology, or GO, is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species...
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 database contains curated annotations that cover a diverse set of topics in molecularMolecular biology
Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...
and cellular biology. Details of current and future annotation projects can be found in the calendar of annotation projects.
Topics of annotation include;
- cell cycleCell cycleThe cell cycle, or cell-division cycle, is the series of events that takes place in a cell leading to its division and duplication . In cells without a nucleus , the cell cycle occurs via a process termed binary fission...
- metabolismMetabolismMetabolism is the set of chemical reactions that happen in the cells of living organisms to sustain life. These processes allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolism is usually divided into two categories...
- signaling
- transportTransportTransport or transportation is the movement of people, cattle, animals and goods from one location to another. Modes of transport include air, rail, road, water, cable, pipeline, and space. The field can be divided into infrastructure, vehicles, and operations...
- cell motility
- immune function
- host-virus interaction
- neural function
Tools
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
BioPAX
BioPAX is a RDF/OWL-basedstandard language to represent biological pathwaysat the molecular and cellular level. Its major use is to facilitate the exchange of pathway data....
, and SBML
SBML
The Systems Biology Markup Language is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers...
.
See also
- KEGG (The Kyoto Encyclopedia of Genes and Genomes)
- WikiPathwaysWikiPathwaysWikiPathways is a community resource for biological pathways.-What is WikiPathways:WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways represents a new model for pathway databases that enhances complementary...
- Comparative Toxicogenomics DatabaseComparative Toxicogenomics DatabaseThe Comparative Toxicogenomics Database is a public website and research tool that curates scientific data describing relationships between chemicals, genes, and human diseases....
External links
- Reactome homepage
- Reactome article in MetaBaseMetaBaseMetaBase is a user-contributed database of biological databases, listing all the biological databases currently available on the internet. The initial release of MetaBase was derived entirely from the content of the Nucleic Acids Research 2007 Database Issue...
Related resources
Other molecular pathway databases- HumanCyc
- GeneNetwork
- Panther Pathways
- WikiPathways
- Pathway CommonsPathway commonsPathway Commons is a database of biological pathways from multiple organisms....