The prevalence and morbidity of asthma, a chronic inflammatory airway disease, is increasing. Animal models provide a meaningful but limited view of the mechanisms of asthma in humans. To provide a systems level view of asthma we compiled a gene expression compendium from five publicly available mouse microarray datasets and a gene knowledge base of 4305 gene annotation sets. Using this collection we generated a high level map of the functional themes that characterize animal models of asthma, dominated by innate and adaptive immune response. We used Module Networks analysis to identify co-regulated gene modules. The resulting modules reflect four distinct responses to treatment, including early response, general induction, repression and IL13 dependent response. One module with a persistent induction in response to treatment is mainly composed of genes with suggested roles in asthma, suggesting a similar role for the other module members. Analysis of IL13 dependent response using protein interaction networks highlights a role for TGF1 as a key regulator of asthma. Our analysis demonstrates the discovery potential of systems level approaches and provides a framework for applying such approaches to asthma.