As an important part of functional genomics, gene expression profiling plays an important role in many fields, such as biology, medicine and drug discovery. With the advent of precision medicine, integration of multi-omics data for personalized health care is becoming the trend of future medicine. In this review, Relevant databases of gene expression profile were introduced first. And then three general methods for gene expression profile analysis, i.e., connectivity map method, gene regulatory network method and multi-omics data integration methods were focused. The latest usage of these methods in drug discovery, especially in cancer drug development was reviewed. This review would serve as a guide for transcriptome-based drug discovery.