GoMiner is a program package designed to facilitate the biological interpretation of genomic and proteomic data, particularly microarray data. It organizes lists of 'interesting' genes (e.g., under- and overexpressed genes) within the context of the Gene Ontology (GO) hierarchy, providing quantitative and statistical output files and two visualizations: a tree-like structure and a directed acyclic graph (DAG). GoMiner links genes to major public bioinformatics resources, enhancing the interpretability of results. The program is freely available and can be run on multiple operating systems. It addresses the challenges of experimental design, statistical analysis, and biological interpretation, making it a valuable tool for researchers in the field of genomics and proteomics. GoMiner is compared with other related programs, highlighting its flexibility, platform independence, and comprehensive integration with external resources.GoMiner is a program package designed to facilitate the biological interpretation of genomic and proteomic data, particularly microarray data. It organizes lists of 'interesting' genes (e.g., under- and overexpressed genes) within the context of the Gene Ontology (GO) hierarchy, providing quantitative and statistical output files and two visualizations: a tree-like structure and a directed acyclic graph (DAG). GoMiner links genes to major public bioinformatics resources, enhancing the interpretability of results. The program is freely available and can be run on multiple operating systems. It addresses the challenges of experimental design, statistical analysis, and biological interpretation, making it a valuable tool for researchers in the field of genomics and proteomics. GoMiner is compared with other related programs, highlighting its flexibility, platform independence, and comprehensive integration with external resources.