- PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements. [PMID: 27899595]
Huaiyu Mi, Xiaosong Huang, Anushya Muruganujan, Haiming Tang, Caitlin Mills, Diane Kang, Paul D Thomas
Nucleic acids research 2017:45(D1)
2 Citations (Google Scholar as of 2017-02-13)
- PANTHER version 10: expanded protein families and functions, and analysis tools. [PMID: 26578592]
Huaiyu Mi, Sagar Poudel, Anushya Muruganujan, John T Casagrande, Paul D Thomas
Nucleic acids research 2016:44(D1)
159 Citations (Google Scholar as of 2017-02-13)
Abstract: PANTHER (Protein Analysis THrough Evolutionary Relationships, http://pantherdb.org) is a widely used online resource for comprehensive protein evolutionary and functional classification, and includes tools for large-scale biological data analysis. Recent development has been focused in three main areas: genome coverage, functional information ('annotation') coverage and accuracy, and improved genomic data analysis tools. The latest version of PANTHER, 10.0, includes almost 5000 new protein families (for a total of over 12 000 families), each with a reference phylogenetic tree including protein-coding genes from 104 fully sequenced genomes spanning all kingdoms of life. Phylogenetic trees now include inference of horizontal transfer events in addition to speciation and gene duplication events. Functional annotations are regularly updated using the models generated by the Gene Ontology Phylogenetic Annotation Project. For the data analysis tools, PANTHER has expanded the number of different 'functional annotation sets' available for functional enrichment testing, allowing analyses to access all Gene Ontology annotations-updated monthly from the Gene Ontology database-in addition to the annotations that have been inferred through evolutionary relationships. The Prowler (data browser) has been updated to enable users to more efficiently browse the entire database, and to create custom gene lists using the multiple axes of classification in PANTHER. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
- PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. [PMID: 23193289]
Huaiyu Mi, Anushya Muruganujan, Paul D Thomas
Nucleic acids research 2013:41(Database issue)
693 Citations (Google Scholar as of 2017-02-13)
Abstract: The data and tools in PANTHER-a comprehensive, curated database of protein families, trees, subfamilies and functions available at http://pantherdb.org-have undergone continual, extensive improvement for over a decade. Here, we describe the current PANTHER process as a whole, as well as the website tools for analysis of user-uploaded data. The main goals of PANTHER remain essentially unchanged: the accurate inference (and practical application) of gene and protein function over large sequence databases, using phylogenetic trees to extrapolate from the relatively sparse experimental information from a few model organisms. Yet the focus of PANTHER has continually shifted toward more accurate and detailed representations of evolutionary events in gene family histories. The trees are now designed to represent gene family evolution, including inference of evolutionary events, such as speciation and gene duplication. Subfamilies are still curated and used to define HMMs, but gene ontology functional annotations can now be made at any node in the tree, and are designed to represent gain and loss of function by ancestral genes during evolution. Finally, PANTHER now includes stable database identifiers for inferred ancestral genes, which are used to associate inferred gene attributes with particular genes in the common ancestral genomes of extant species.