PharmGEO: A Curated Atlas of Drug-Response Transcriptomes Enabling Cross-Study Comparisons

Drug-induced transcriptomic profiles capture how compounds reprogram genes and pathways across dose and time, supporting drug–gene associations and interaction analysis. The field faces a practical bottleneck: GEO drug studies are scattered, metadata for dose, exposure time, and cell type are inconsistent, and processing pipelines differ, which limits reuse and fair comparison. We built PharmGEO, an interactive Shiny resource that curates and standardizes 7,931 pharmaco-transcriptomic experiments across 1,334 drugs. Key variables are harmonized, and all data sets are reprocessed through a single pipeline, yielding transcriptome-wide results with a mean of 17,776 genes per experiment. PharmGEO supports interactive differential expression and pathway enrichment, prioritizes high-confidence drug–gene associations using cross-data set consistency, and provides a directionally annotated drug–drug interaction network with 115,264 interactions derived from transcriptomic overlap. Case studies in target validation and combination assessment show how PharmGEO enables drug repurposing and interaction evaluation by turning heterogeneous studies into a coherent, searchable atlas of drug responses. PharmGEO is available at http://www.pharmgeo.net.