Drug repositioning is an innovative approach to identify new therapeutic indications for existing drugs. Drug repositioning offers the promise of reducing drug development timeframes and costs, and because it involves drugs that are already in the clinic, it might remedy some of the drug safety challenges traditionally associated with drug candidates that are not yet available in the clinic. The gene-by-drug interactions are an important dimension of optimal drug repositioning and development strategies. While gene-by-drug interactions have been curated and presented in various databases, novel bioinformatics tools and approaches are timely, and required with a specific focus to support drug positioning. We report, in this study, the design of a public web-accessible transcriptomic-/gene expression-guided pharmaceuticals search tool, geneXpharma (www.genexpharma.org). GeneXpharma is a public platform with user-centric interface that provides statistically evaluated gene expressions and their drug interactions for 48 diseases under seven different disease categories. GeneXpharma is designed and organized to generate hypotheses on druggable genome within the disease-gene-drug triad and thus, help repositioning of drugs against diseases. The search system accommodates various entry points using drugs, genes, or diseases, which then enable researchers to extract drug repurposing candidates and readily export for further evaluation. Future developments aim to improve the geneXpharma algorithm, enrich its content, and enhance the website interface through addition of network visualizations and graphical display items. Bioinformatics search tools can help enable the convergence of drug repositioning and gene-by-drug interactions so as to further optimize drug development efforts in the future.