The PANTHER Classification System is a comprehensive platform for analyzing gene function on a genome-wide scale. It combines gene function, ontology, pathways, and statistical analysis tools to facilitate the analysis of large-scale genome-wide experimental data. The system is built with 82 complete genomes organized into gene families and subfamilies, with evolutionary relationships captured in phylogenetic trees, multiple sequence alignments, and statistical models (Hidden-Markov Models, or HMMs). Genes are classified by their functions using ontology terms (Gene Ontology and PANTHER Protein Class) and assigned to PANTHER pathways. The PANTHER website offers a suite of tools for browsing and querying gene functions and analyzing experimental data with statistical tests. It is widely used by researchers in various fields, including cancer, neurological disorders, and autoimmune diseases. The 2013 release of PANTHER (v.8.0) included updates to the data content and a redesigned user interface to improve the user experience and analytical capabilities. This protocol provides a detailed guide on how to analyze genome-wide experimental data using the PANTHER Classification System.The PANTHER Classification System is a comprehensive platform for analyzing gene function on a genome-wide scale. It combines gene function, ontology, pathways, and statistical analysis tools to facilitate the analysis of large-scale genome-wide experimental data. The system is built with 82 complete genomes organized into gene families and subfamilies, with evolutionary relationships captured in phylogenetic trees, multiple sequence alignments, and statistical models (Hidden-Markov Models, or HMMs). Genes are classified by their functions using ontology terms (Gene Ontology and PANTHER Protein Class) and assigned to PANTHER pathways. The PANTHER website offers a suite of tools for browsing and querying gene functions and analyzing experimental data with statistical tests. It is widely used by researchers in various fields, including cancer, neurological disorders, and autoimmune diseases. The 2013 release of PANTHER (v.8.0) included updates to the data content and a redesigned user interface to improve the user experience and analytical capabilities. This protocol provides a detailed guide on how to analyze genome-wide experimental data using the PANTHER Classification System.