PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API

Abstract PANTHER (Protein Analysis Through Evolutionary Relationships, http://www.pantherdb.org) is a resource for the evolutionary and functional classification of protein-coding genes from all domains of life. The evolutionary classification is based on a library of over 15,000 phylogenetic trees,...

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Veröffentlicht in:Nucleic acids research Jg. 49; H. D1; S. D394 - D403
Hauptverfasser: Mi, Huaiyu, Ebert, Dustin, Muruganujan, Anushya, Mills, Caitlin, Albou, Laurent-Philippe, Mushayamaha, Tremayne, Thomas, Paul D
Format: Journal Article
Sprache:Englisch
Veröffentlicht: England Oxford University Press 08.01.2021
Schlagworte:
Computational Biology - methods
Database Issue
Enhancer Elements, Genetic - genetics
Evolution, Molecular
Gene Ontology
Genome
Molecular Sequence Annotation
Open Reading Frames - genetics
Phylogeny
Software
User-Computer Interface
ISSN:0305-1048, 1362-4962, 1362-4962
Online-Zugang:Volltext
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Zusammenfassung:Abstract PANTHER (Protein Analysis Through Evolutionary Relationships, http://www.pantherdb.org) is a resource for the evolutionary and functional classification of protein-coding genes from all domains of life. The evolutionary classification is based on a library of over 15,000 phylogenetic trees, and the functional classifications include Gene Ontology terms and pathways. Here, we analyze the current coverage of genes from genomes in different taxonomic groups, so that users can better understand what to expect when analyzing a gene list using PANTHER tools. We also describe extensive improvements to PANTHER made in the past two years. The PANTHER Protein Class ontology has been completely refactored, and 6101 PANTHER families have been manually assigned to a Protein Class, providing a high level classification of protein families and their genes. Users can access the TreeGrafter tool to add their own protein sequences to the reference phylogenetic trees in PANTHER, to infer evolutionary context as well as fine-grained annotations. We have added human enhancer-gene links that associate non-coding regions with the annotated human genes in PANTHER. We have also expanded the available services for programmatic access to PANTHER tools and data via application programming interfaces (APIs). Other improvements include additional plant genomes and an updated PANTHER GO-slim.
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ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkaa1106