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A video tour of the database highlighting InnateDB capabilities is available in the following formats:

InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans and mice 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. 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 and mouse interactomes by integrating data (115,000+ interactions & 3,000+ pathways) from the several of the major public interaction and pathway databases.

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 ...]

Please cite: Lynn et al, InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Molecular Systems Biology 2008; 4:218. 

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 Capabilities

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 3,000 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 over-representation analysis, construct orthologous interaction networks in other species and much more. See the tutorial on how to do these analyses.

News

XML file containing all curated InnateDB interaction data, as well as all XML files containing interaction data from external sources, have been reformatted for complete PSI-MI 2.5 XML compliance. (more)

InnateDB included in "Best of the web" article by the Genetic Engineering and Biotechnology News website. (more)

Fixed bug that caused old records to sometimes be returned with search results. (more)

InnateDB has joined the International Molecular Exchange Consortium (IMEx), a group of major public interaction data providers sharing curation efforts.

Updated InnateDB curation guide now available made available on March 24, 2010. (more)

Updated version of InnateDB and new pathway data released on March 12, 2010. (more)

A new XML file for InnateDB-curated interactions was made available on November 9, 2009. (more)

New website features, analyses and external data released on Oct 20th, 2009. (more)

As of Oct 20th, 2009, the InnateDB curation team has contextually annotated more than 10,000 innate immunity relevant interactions. Thanks to everyone who has helped us achieve this goal. (more)

Our review of systems-level approaches to investigating innate immunity is published in Trends in Immunology, June, 2009. (more)

Upgraded to Cytoscape 2.6.2 on April 1, 2009. This fixes a bug that was causing an incompatibility with cerebral for Mac OS X users.

Updated version of InnateDB released on Jan 29th, 2009. (more)

InnateDB paper reviewed in Cell Host & Microbe on Oct 16, 2008. (more)

Updated version of InnateDB released on Oct 14th, 2008. (more)

Updated version of InnateDB released on Oct 3rd, 2008. (more)

InnateDB paper published in Molecular Systems Biology on Sept 02, 2008.

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