Abstract Mechanistic studies of biological specimens obtained during the conduct of clinical trials are frequently used to identify markers of therapeutic responses and to understand the underlying physiological processes associated with therapeutic efficacy. The Immunology Database and Analysis Portal (ImmPort; www.immport.org) is a public database resource funded by NIAID to support the management and analysis of clinical and mechanistic data generated by their funded investigators. We demonstrate the use of the ImmPort clinical data management platform and novel data analysis methods in the analysis of the allergen immunotherapy experiments conducted by the Casale group of Immune Tolerance Network. In the Casale study, immune response assays were conducted on samples taken before, during and after a 12-week course of allergen-specific immunotherapy to investigate whether anti-IgE antibody (omalizumab) can enhance the safety and efficacy of rush immunotherapy. Flow cytometry data was re-analyzed with FLOCK, a novel automated flow cytometry analysis pipeline in ImmPort, to determine if the level of any blood cell population correlated with treatment conditions. The analysis has identified a unique cell population expressing CD14, CXCR3 and high levels of the Fc-epsilon receptor (CD23), which is significantly increased in patients undergoing rush immunotherapy. Such data-driven analysis using ImmPort can generate hypotheses for further experimental design and verification.