The innate immune system is a highly conserved, first line of host defence against infections and other disease stimuli. It initiates inflammatory responses and is important in surveillance of developing cancers. As a result of recent discoveries and an increased understanding of the components of this response, we are now able to better determine its role in diseases, assess human susceptibilities to disease and target therapeutics to this system. A key component of the innate response is the production of hormone-like proteins called interferons (IFNs). These proteins induce several thousand genes, which are responsible for constituting each of the many biological effects of interferons—they inhibit viral replication, prevent cell growth and activate cells of the immune response. The Interferome collection is a database of IFN regulated genes published in 2009 (Interferome.org; Samarajiwa et al., Nucleic Acids Res. 37, 852). This represents the initial stages in capture and integration of IFN treated microarray datasets, incorporating over 40 published and internally generated microarray datasets. This approach enables identification of interferon regulated gene sets in many biologically diverse high throughput microarray experiments.