April 28, 2013: Updated gene and pathway data (more)
March 25, 2013: Upgraded to MITAB 2.7 and updated our PSICQUIC web services to the latest reference implementation (more)
January 11, 2013: Updated network visualization tools (more)
November 24, 2012: Please see our new paper describing recent updates to InnateDB, which has just been published in the 2013 Database Issue of Nucleic Acids Research, featuring one of our figures on the cover page.
September 14, 2012: Improved user interface, new FAQ, updated graphs of transcript frequencies for bovine genes and more
Please note that if you have visited InnateDB before, you might have to press the F5 button or Ctrl+F5 to load the updated page layout properly.
Major update on February 16, 2012 - we are pleased to announce a new release of InnateDB.
This release includes ~18,000 annotated molecular interactions of relevance to innate immunity; a wide range of new features and analysis tools, completely updated gene, interaction and pathway data from a wide range of sources; and for the first time bovine genes, interactions and pathways (more)
InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved
in the innate immune response of humans, mice and bovines to microbial infection.
The database captures an improved coverage of the innate immunity
interactome by integrating known interactions and pathways from major public
databases together with manually-curated data into a
centralised resource. To date, 18,634 interactions have been manually curated by the InnateDB curation team.
The database can be mined as a knowledgebase or used with our integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response.
Going Beyond Innate Immunity: Although InnateDB curation focuses on innate immunity-relevant interactions and pathways, InnateDB also incorporates detailed annotation on the entire human, mouse and bovine interactomes by integrating data (178,000+ interactions & 4,400+ pathways) from several of the major public interaction and pathway databases.
A video tour of the database highlighting InnateDB capabilities is available in the following formats:
InnateDB has been developed as part of two major projects, the Genome Canada-funded Pathogenomics of Innate Immunity Project (PI2) and a project funded under the Grand Challenges in Global Health Initiative - Novel Therapeutics that Boost Innate Immunity To Treat Infectious Diseases. [More ...]
Lynn et al., InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Molecular Systems Biology 2008; 4:218
or our recent update:
Breuer et al., InnateDB: systems biology of innate immunity and beyond - recent updates and continuing curation. Nucl. Acids Res. (2013) 41 (D1)
Please also see our paper describing InnateDB curation of the innate immunity interactome which is published in BMC Systems Biology.
InnateDB is a member of the International Molecular Exchange Consortium (IMEx). This organization is dedicated to developing rules for capturing protein-protein interaction data, actively curating these interactions from the scientific literature and making them available through a common website.
InnateDB is designed with Mozilla Firefox Web Browser.
View statistics for manually-curated innate immunity relevant molecular interactions. New manually curated interactions are submitted weekly.
Search for genes and proteins of interest.
Search for experimentally-verified molecular interactions by gene/protein name, interaction type, cell type, etc.
Search genes/interactions belonging to 4,400 pathways.
Visualize interactions using an intuitive subcellular localization-based layout in Cerebral.
Upload your own list of genes along with associated gene expression data (from up to 10 experimental conditions) to interactively analyze this data in a molecular interaction network context.
Once you have uploaded your data, you will be able to interactively visualize interaction networks with expression data overlaid; carry out Pathway, Gene Ontology and Transcription Factor Binding Site over-representation analyses; construct orthologous interaction networks in other species; and much more. See the tutorial on how to do these analyses.
Access curated interaction data via a dedicated PSICQUIC webservice.