Genevestigator V3 is a web-based tool for analyzing gene expression across various biological contexts. It provides powerful tools for biologists to explore gene expression data, including new features for analyzing gene expression in different contexts, identifying biomarker genes, clustering genes into expression modules, and modeling expression responses in metabolic and regulatory networks. The system is based on a client/server architecture, with large-scale manual curation and quality control of microarray data for several organisms, and curation of pathway data for mouse and Arabidopsis. It includes improved querying features and new tools for biomarker identification, clustering, and pathway analysis. The system was developed to address the limitations of earlier versions, which had limited analysis tools and scalability. Genevestigator V3 includes more than 20,000 Affymetrix expression microarrays from human, mouse, rat, Arabidopsis, and barley, and provides a reference expression database for meta-analysis. It allows users to analyze gene expression across a wide variety of biological contexts, including anatomy, development, stimulus, and mutation. The system also includes tools for clustering gene expression data, pathway analysis, and visualization of expression data on a pathway or network level. The system is accessible through a user-friendly interface and includes several toolsets for analyzing transcriptomes: Meta-Profile analysis, Biomarker Search, Clustering Analysis, and Pathway Projector. These tools allow users to analyze gene expression data in various ways, including identifying biomarker genes, clustering genes into expression modules, and projecting expression data onto pathways or networks. Genevestigator V3 is available in three forms: OPEN-ACCESS, CLASSIC, and ADVANCED. The first two are freely available for academic users, while the ADVANCED version requires a subscription fee. The system is designed to facilitate discovery research and hypothesis validation, and it is accessible at http://www.genevestigator.ethz.ch.Genevestigator V3 is a web-based tool for analyzing gene expression across various biological contexts. It provides powerful tools for biologists to explore gene expression data, including new features for analyzing gene expression in different contexts, identifying biomarker genes, clustering genes into expression modules, and modeling expression responses in metabolic and regulatory networks. The system is based on a client/server architecture, with large-scale manual curation and quality control of microarray data for several organisms, and curation of pathway data for mouse and Arabidopsis. It includes improved querying features and new tools for biomarker identification, clustering, and pathway analysis. The system was developed to address the limitations of earlier versions, which had limited analysis tools and scalability. Genevestigator V3 includes more than 20,000 Affymetrix expression microarrays from human, mouse, rat, Arabidopsis, and barley, and provides a reference expression database for meta-analysis. It allows users to analyze gene expression across a wide variety of biological contexts, including anatomy, development, stimulus, and mutation. The system also includes tools for clustering gene expression data, pathway analysis, and visualization of expression data on a pathway or network level. The system is accessible through a user-friendly interface and includes several toolsets for analyzing transcriptomes: Meta-Profile analysis, Biomarker Search, Clustering Analysis, and Pathway Projector. These tools allow users to analyze gene expression data in various ways, including identifying biomarker genes, clustering genes into expression modules, and projecting expression data onto pathways or networks. Genevestigator V3 is available in three forms: OPEN-ACCESS, CLASSIC, and ADVANCED. The first two are freely available for academic users, while the ADVANCED version requires a subscription fee. The system is designed to facilitate discovery research and hypothesis validation, and it is accessible at http://www.genevestigator.ethz.ch.