The ConsensusPathDB is a molecular functional interaction database

Database

A database is an organized collection of data for one or more purposes, usually in digital form. The data are typically organized to model relevant aspects of reality , in a way that supports processes requiring this information...

, integrating information on protein interactions, signaling, 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 gene regulation in humans. ConsensusPathDB includes functional interactions from 12 databases. ConsensusPathDB is freely available for academic use under http://cpdb.molgen.mpg.de/.

Integrated Databases

• Reactome
  Reactome
  Reactome is a database of biological pathways. 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...
  
   (metabolic
  Metabolic pathway
  In biochemistry, metabolic pathways are series of chemical reactions occurring within a cell. In each pathway, a principal chemical is modified by a series of chemical reactions. Enzymes catalyze these reactions, and often require dietary minerals, vitamins, and other cofactors in order to function...
  
   and signaling pathways)
• KEGG (metabolic pathways only have been integrated in ConsensusPathDB)
• HumanCyc (metabolic pathways)
• PID - Pathway Interaction Database (signaling pathways)
• BioCarta (signaling pathways)
• Netpath
  Netpath
  NetPath is a manually curated resource of human signal transduction pathways. It is a joint effort between Pandey Lab at the Johns Hopkins University and the Institute of Bioinformatics , Bangalore, India, and is also worked on by other parties....
  
   (signaling pathways)
• IntAct (protein interactions)
• DIP
  Database of Interacting Proteins
  The catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein–protein interactions...
  
   (protein interactions)
• MINT (protein interactions)
• HPRD (protein interactions)
• BioGRID
  BioGRID
  The Biological General Repository for Interaction Datasets is a curated biological database of protein-protein and genetic interactions created in 2003 The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein and genetic interactions...
  
   (protein interactions)
• SPIKE (protein interactions, signaling reactions)
• PIG - Pathogen Interaction Gateway (host-pathogenic and host-host protein interactions)

Functionalities

The ConsensusPathDB is accessible via a web interface providing a variety of functions.

Search and visualization

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

Protein

Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

s, metabolite

Metabolite

Metabolites are the intermediates and products of metabolism. The term metabolite is usually restricted to small molecules. A primary metabolite is directly involved in normal growth, development, and reproduction. Alcohol is an example of a primary metabolite produced in large-scale by industrial...

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

 identifiers). Selected interactions can be visualized in an interactive environment as expandable networks. ConsensusPathDB currently allows users to export their models in 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....

 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 network

Interaction network

Interaction network is a network of nodes that are connected by features. If the feature is a physical and molecular, the interaction network is molecular interactions usually found in cells...

s in 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....

, PSI-MI or 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...

 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 pathways 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

P-value

In statistical significance testing, the p-value is the probability of obtaining a test statistic at least as extreme as the one that was actually observed, assuming that the null hypothesis is true. One often "rejects the null hypothesis" when the p-value is less than the significance level α ,...

 is computed based on the hypergeometric distribution. It reflects the significance of the observed overlap between the user-specific input gene list and the members of the predefined set.