The PANTHER Classification System is a comprehensive tool for analyzing gene function on a genome-wide scale. It integrates gene function, ontology, pathways, and statistical analysis to help biologists interpret large-scale experimental data. The system is built using 82 complete genomes organized into gene families and subfamilies, with evolutionary relationships captured in phylogenetic trees, multiple sequence alignments, and Hidden-Markov Models (HMMs). Genes are classified based on function, with families and subfamilies annotated with ontology terms and sequences assigned to PANTHER pathways. The PANTHER website provides tools for browsing gene functions and analyzing data with statistical tests. It is widely used by bench scientists, bioinformaticians, and systems biologists. The 2013 release (v.8.0) included updated data and a redesigned interface to improve user experience and analytical capabilities. The system includes a protein library with over 640,000 proteins from 82 organisms, curated by expert biologists. The PANTHER pathway module contains 176 expert-curated pathways, linked to proteins through manual curation and phylogenetic information. The system also includes a suite of tools for gene list analysis, such as the PANTHER HMM Scoring Tool, cSNP Analysis Tool, and Gene List Analysis Tool. These tools allow users to analyze genome-wide data, including gene expression, proteomics, and genome-wide association studies (GWAS). The system supports various statistical tests, including overrepresentation and enrichment tests, and integrates with the Gene Ontology (GO) Consortium. PANTHER is part of the InterPro and GO consortia, and its pathways are being integrated into Pathway Commons. The system provides a user-friendly interface for storing and analyzing gene lists, with support for multiple organisms and data formats. The PANTHER tools enable users to perform functional classification, statistical overrepresentation tests, and statistical enrichment tests, with results visualized in gene lists, pie charts, and pathway diagrams. The system is widely used in research areas such as cancer, neurological disorders, autoimmune diseases, and cardiac disease. PANTHER is supported by the NIH/NIGMS and has been cited in over 3600 publications since 2003. The system is accessible online and includes downloadable tools for large-scale data analysis.The PANTHER Classification System is a comprehensive tool for analyzing gene function on a genome-wide scale. It integrates gene function, ontology, pathways, and statistical analysis to help biologists interpret large-scale experimental data. The system is built using 82 complete genomes organized into gene families and subfamilies, with evolutionary relationships captured in phylogenetic trees, multiple sequence alignments, and Hidden-Markov Models (HMMs). Genes are classified based on function, with families and subfamilies annotated with ontology terms and sequences assigned to PANTHER pathways. The PANTHER website provides tools for browsing gene functions and analyzing data with statistical tests. It is widely used by bench scientists, bioinformaticians, and systems biologists. The 2013 release (v.8.0) included updated data and a redesigned interface to improve user experience and analytical capabilities. The system includes a protein library with over 640,000 proteins from 82 organisms, curated by expert biologists. The PANTHER pathway module contains 176 expert-curated pathways, linked to proteins through manual curation and phylogenetic information. The system also includes a suite of tools for gene list analysis, such as the PANTHER HMM Scoring Tool, cSNP Analysis Tool, and Gene List Analysis Tool. These tools allow users to analyze genome-wide data, including gene expression, proteomics, and genome-wide association studies (GWAS). The system supports various statistical tests, including overrepresentation and enrichment tests, and integrates with the Gene Ontology (GO) Consortium. PANTHER is part of the InterPro and GO consortia, and its pathways are being integrated into Pathway Commons. The system provides a user-friendly interface for storing and analyzing gene lists, with support for multiple organisms and data formats. The PANTHER tools enable users to perform functional classification, statistical overrepresentation tests, and statistical enrichment tests, with results visualized in gene lists, pie charts, and pathway diagrams. The system is widely used in research areas such as cancer, neurological disorders, autoimmune diseases, and cardiac disease. PANTHER is supported by the NIH/NIGMS and has been cited in over 3600 publications since 2003. The system is accessible online and includes downloadable tools for large-scale data analysis.