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(The FASEB Journal. 2008;22:lb541)
© 2008 FASEB
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lb541

InnateDB & Cerebral: user-friendly tools for the systems-level analysis of innate immunity

Jennifer Gardy1, D Lynn3, G Winsor3, A Barsky2, F Roche3, T Chan1, M Laird3, C Chan1, N Shah3, N Richard3, R Lo3, M Naseer1, J Que1, M Yau1, M Acab3, D Tulpan3, M Whiteside3, T Munzner2, R Hancock1 and F Brinkman3

1 CMDR,
2 CS, University of British Columbia, Vancouver, Canada,
3 MBB, Simon Fraser University, Burnaby, Canada

ABSTRACT

InnateDB is a publicly available knowledgebase of genes, proteins, interactions, and pathways involved in innate immunity. It integrates known interactions and pathways from public databases and manually curated data into a centralized resource, which includes data on >100,000 human and mouse interactions, cross-references to innate immunity relevant pathways, and detailed annotation from a variety of sources.

Building on this data we provide several bioinformatics tools to facilitate systems-level investigations of the innate immune response. These include the ability to upload expression datasets, which can be integrated with network/pathway data to investigate changes in gene expression in a network of interest. This data can be investigated using our network visualization tool, Cerebral, a Cytoscape plugin which allows the generation of intuitive pathway and cell localization-oriented views of interaction data. Cerebral allows the overlay of expression data from multiple experiments on top of interaction network data from InnateDB. We also provide orthology predictions for human, mouse & bovine genes to facilitate the construction of orthologous networks in different species.

InnateDB is funded by Genome Canada, the Foundation for the National Institutes of Health, & the Canadian Institutes of Health Research under the Grand Challenges in Global Health Initiative.





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