To investigate molecular-genetic causes and effects of diseases and their therapies it becomes increasingly important to combine data from clinical trials with high volumes of experimental data generated using various chip technologies and their annotations. We present our approach to integrate such data for two large collaborative cancer research studies in Germany – the Molecular Mechanism of Malignant Lymphoma (MMML) and the German Glioma Network. Our platform interconnects a commercial study management system (eRN) with a data warehouse-based gene expression analysis system (GeWare) . We utilize a generic approach to import different anonymized pathological and patient-related annotations into the warehouse. The platform also integrates different forms of experimental data and public molecular-genetic annotation data and thus supports a wide range of collaborative analyses for both clinical and non-clinical parameters.