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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, 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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Sixty-three out of the 163 genes did not have a recorded annotation regarding a function in heart development or disease in PANTHER.
“Sixty-three out of the 163 genes did not have a recorded annotation regarding a function in heart development or disease in PANTHER [37] (Fig. 4, gray squares).”
From A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease (2021) · cites this paper as [37]
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Research works printed but not linked: 23
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- Mi, 2019, Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0), Nat. Protoc., 14, 703, 10.1038/s41596-019-0128-8 · DOI
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Metadata
- Authors
- Mi, H., Ebert, D., Muruganujan, A., Mills, C., Albou, L.-P., Mushayamaha, T., & Thomas, P. D.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-12-08
- Volume
- 49
- Issue
- D1
- Pages
- D394-D403
- ISSN
- 0305-1048
- 1362-4962
- Cited by
- 1,332
- References
- 1
- Language
- en
- Funders
- National Science Foundation (1458808, 1661543, 1917302)
- National Institutes of Health (U41HG002273)
- National Cancer Institute (P01CA196569)
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