We demonstrate our framework in three case studies: identifying the downstream targets of an oncogenic lncRNA based on transcriptomic profiles from functional experiments in cancer cells; integrating transcriptomic and proteomic data with patient clinical information for cancer biomarker discovery; and characterising IDH-mutant subtype of glioma by integrating epigenetic, transcriptomic, and proteomic data. This evidence concerns the gene IDH1 and central nervous system cancer.