Video Tip of the Week: InnateDB, Systems Biology of the Innate Immune Response

The immune system is challenging to study. Different people may mount different responses to assaults on their system–and sometimes the systems go into overdrive on stuff they shouldn’t. Cracking the details of the functions of the immune system could help us to combat actual pathogens better, and might also help us to tune down inappropriate responses. The developers of the InnateDB resource hope to help researchers learn more about the relevant genes, pathways, and systems to wrangle the responses.

The InnateDB team has been building their resource for years, and the growth of the information is impressive. Their statistics page shows you how many genes and interactions their curation team has assembled–it is approaching 20,000 manually curated items at this point. But they also include data from other interaction resources (such as IntAct and MINT and more) to help provide context for their data.

Another interesting aspect of this data for me was the species selection. Human and mouse are pretty common choices, of course–but I didn’t expect to see the bovine data. I’m glad though–I think there are many ways in which the agricultural genomics folks are way ahead of other species, but that’s often not recognized. And there are human health-related issues that arise from animal microbial pathogen situations that are also important to understand. They note about the bovine data:

As bovine experimentally validated interactions and pathways are virtually non-existent, InnateDB uses an orthology-based approach to predict bovine pathways and interactions primarily from human data….Through collaboration with colleagues at the United States Department of Agriculture, InnateDB now integrates bovine tissue expression data for >13 000 genes.

For further details about how they collect and curate their data, be sure to check out their paper (linked below). They also explore the strategies they have created for users to browse and visualize the data that they are interested in. A neat feature is their “Cerebral” tool for visualizing the data with Cytoscape plug-in or app. This tool offers a subcellular localization view that’s really interesting. Check out their slides that show this (PDF, see ~slide 5-6 to see a sample).

In their NAR database issue paper, they also note their expansion into allergy and asthma data.

They have a video tour of their site to help people get started. You can access this tour in several formats from their main page. I couldn’t find an embedded version, so I’ll just lure you over there with this image from part of the way though one video. On their page see the section that says: A video tour of the database highlighting InnateDB capabilities is available in the following formats…

Click to visit their homepage and locate their tour videos.

Click to visit their homepage and locate their tour videos.

Quick link:



Breuer, K., Foroushani, A., Laird, M., Chen, C., Sribnaia, A., Lo, R., Winsor, G., Hancock, R., Brinkman, F., & Lynn, D. (2012). InnateDB: systems biology of innate immunity and beyond–recent updates and continuing curation Nucleic Acids Research, 41 (D1) DOI: 10.1093/nar/gks1147