The ConsensusPathDB is a molecular functional interaction

database In computing, a database is an organized collection of data or a type of data store based on the use of a database management system (DBMS), the software that interacts with end users, applications, and the database itself to capture and a ...

, integrating information on protein interactions, genetic interactions signaling,

metabolism Metabolism (, from ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cellular processes; the co ...

gene regulation Regulation of gene expression, or gene regulation, includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA). Sophisticated programs of gene expression are wide ...

, and drug-target interactions in humans. ConsensusPathDB currently (release 30) includes such interactions from 32 databases. ConsensusPathDB is freely available for academic use under http://ConsensusPathDB.org.

Integrated Databases

* Reactome (

metabolic Metabolism (, from ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cellular processes; the ...

and

signaling pathway In biology, cell signaling (cell signalling in British English) is the process by which a cell interacts with itself, other cells, and the environment. Cell signaling is a fundamental property of all cellular life in both prokaryotes and eukary ...

s) *

KEGG KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis ...

(metabolic pathways only have been integrated in ConsensusPathDB) * HumanCyc (metabolic pathways) * PID - Pathway Interaction Database (signaling pathways) * BioCarta (signaling pathways) * Netpath (signaling pathways) * IntAct (protein interactions) * DIP (protein interactions) * MINT (protein interactions) * HPRD (protein interactions) * BioGRID (protein interactions) * SPIKE (protein interactions, signaling reactions) * WikiPathways (

and

s) * and many more.

Functionalities

The ConsensusPathDB is accessible via a

web interface In the industrial design field of human–computer interaction, a user interface (UI) is the space where interactions between humans and machines occur. The goal of this interaction is to allow effective operation and control of the machine fro ...

providing a variety of functions.

Search and visualization

Using the web interface users can search for physical entities (e.g.

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

metabolite In biochemistry, a metabolite is an intermediate or end product of metabolism. The term is usually used for small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, c ...

s etc.) or pathways using common names or accession numbers (e.g.

UniProt UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived fro ...

identifiers). Selected interactions can be visualized in an interactive environment as expandable networks. ConsensusPathDB currently allows users to export their models in BioPAX format or as image in several formats.

Shortest path

Users can search for shortest paths of functional interactions between physical entities, based on all interactions in the database. The pathway search can be constrained by forbidding passing through certain physical entities.

Data upload

Users can upload their own interaction networks in BioPAX, PSI-MI or SBML files in order to validate and/or extend those networks in the context of the interactions in ConsensusPathDB.

Over-representation analysis

Using the web-interface of the database, one can perform overrepresentation analysis, based on

biochemical pathway In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical ...

s or on neighbourhood-based entity sets (NESTs) that constitute sub-networks of the overall interaction network containing all physical entities around a central one within a "radius" (number of interactions from the center). For each predefined set (pathway / NEST), a

P-value In null-hypothesis significance testing, the ''p''-value is the probability of obtaining test results at least as extreme as the result actually observed, under the assumption that the null hypothesis is correct. A very small ''p''-value means ...

is computed based on the

hypergeometric distribution In probability theory and statistics, the hypergeometric distribution is a Probability distribution#Discrete probability distribution, discrete probability distribution that describes the probability of k successes (random draws for which the ...

. It reflects the significance of the observed overlap between the user-specific input gene list and the members of the predefined set. Over-representation analyses can be performed with user-specified genes or metabolites.

References

External links

* {{Official website, http://consensuspathdb.org Biological databases Systems biology