Genevestigator V3 is an advanced web-based software tool designed for the meta-analysis of transcriptomes, offering powerful tools to explore gene expression across various biological contexts. The system has been significantly enhanced compared to its predecessors, addressing limitations in scaling, multi-organism data storage, and computational efficiency. Key improvements include: 1. **Data Curation and Quality Control**: Over 20,000 Affymetrix expression microarrays from human, mouse, rat, Arabidopsis, and barley have been curated and quality-controlled. 2. **Pathway Data**: Pathway reaction networks for mouse and Arabidopsis have been manually curated. 3. **Client/Server Architecture**: A new architecture distributes computationally intensive tasks to the client side, improving scalability and user experience. 4. **Database Model**: A highly scalable and organism-independent database model has been developed. 5. **Enhanced Analysis Tools**: Significant improvements and new tools for biomarker identification, clustering, biclustering, and pathway analysis have been implemented. 6. **User-Friendly Interface**: The system includes workspace storage, figure export, and a community platform for sharing results. Genevestigator V3 facilitates discovery research and hypothesis validation by providing a comprehensive reference expression database and user-friendly tools. It supports a wide range of research interests, including plant and animal genomics, toxicogenomics, biomarker discovery, and clinical research. The tool is accessible at http://www.genevestigator.ethz.ch.Genevestigator V3 is an advanced web-based software tool designed for the meta-analysis of transcriptomes, offering powerful tools to explore gene expression across various biological contexts. The system has been significantly enhanced compared to its predecessors, addressing limitations in scaling, multi-organism data storage, and computational efficiency. Key improvements include: 1. **Data Curation and Quality Control**: Over 20,000 Affymetrix expression microarrays from human, mouse, rat, Arabidopsis, and barley have been curated and quality-controlled. 2. **Pathway Data**: Pathway reaction networks for mouse and Arabidopsis have been manually curated. 3. **Client/Server Architecture**: A new architecture distributes computationally intensive tasks to the client side, improving scalability and user experience. 4. **Database Model**: A highly scalable and organism-independent database model has been developed. 5. **Enhanced Analysis Tools**: Significant improvements and new tools for biomarker identification, clustering, biclustering, and pathway analysis have been implemented. 6. **User-Friendly Interface**: The system includes workspace storage, figure export, and a community platform for sharing results. Genevestigator V3 facilitates discovery research and hypothesis validation by providing a comprehensive reference expression database and user-friendly tools. It supports a wide range of research interests, including plant and animal genomics, toxicogenomics, biomarker discovery, and clinical research. The tool is accessible at http://www.genevestigator.ethz.ch.