Current data suggest that by quantifying pathway reporter gene expression, molecular phenotyping is able to cluster compounds based on pathway profiles and dissect associations between pathway activities and disease phenotypes simultaneously. Furthermore, molecular phenotyping can be applicable to compounds with a range of binding specificities and is able to triage false positives derived from high-content screening assays. Furthermore, molecular phenotyping allows integration of data derived from in vitro and in vivo models as well as patient data into the drug discovery process.