The Innate Immune Database (IIDB) is a repository of genomic annotations and experimental data for over 2000 genes associated with immune response behavior in the mouse genome. A specific focus of IIDB is on Toll-like Receptor (TLR) genes, which are key components of innate immunity. As part of our research a customised Affymetrix gene chip was developed to generate and explore ChIP-chip binding data specific to TLR mouse genes. The selection of genes on the customised gene chip was based on the mouse assembly NCBI Build 33 and as such, the annotations in IIDB are by necessity mapped to this assembly.

The annotations contained within IIDB are derived using data from over 100 microarray experiments, the NCBI and ENSEMBL annotation databases, computationally predicted transcription factor binding sites, co-expression clusters, predicted cis-regulatory modules, evolutionary conserved regulatory sequences, and sample ChIP-chip data. For each gene, we have analyzed the sequence from at least 20 kb upstream of the transcription start site to at least 10kb downstream of the transcription end site, including all exons and introns. Annotations for DNase hypersensitive sites, as well as exon/intron boundaries, CpG islands, repeats, Affymetrix GeneChip expression array probes are included in the database to facilitate analysis for users with ChIP-chip data.

IIDB offers users multiple, flexible ways to interrogate the database. Search results can be generated by analysing single genes for all available sources of annotations. Groups of co-expressed genes can also be analysed to determine, for example, whether these genes share common transcription factor binding sites. Search results are automatically annotated on the genomic DNA sequence and can be viewed using the Argo genome browser or saved to the user's own computer.