{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T18:03:08Z","timestamp":1778090588497,"version":"3.51.4"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,12,8]],"date-time":"2020-12-08T00:00:00Z","timestamp":1607385600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1458808"],"award-info":[{"award-number":["1458808"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1661543"],"award-info":[{"award-number":["1661543"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1917302"],"award-info":[{"award-number":["1917302"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U41HG002273"],"award-info":[{"award-number":["U41HG002273"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["P01CA196569"],"award-info":[{"award-number":["P01CA196569"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>","DOI":"10.1093\/nar\/gkaa1106","type":"journal-article","created":{"date-parts":[[2020,10,29]],"date-time":"2020-10-29T12:11:10Z","timestamp":1603973470000},"page":"D394-D403","source":"Crossref","is-referenced-by-count":1269,"title":["PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API"],"prefix":"10.1093","volume":"49","author":[{"given":"Huaiyu","family":"Mi","sequence":"first","affiliation":[{"name":"Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA"}]},{"given":"Dustin","family":"Ebert","sequence":"additional","affiliation":[{"name":"Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA"}]},{"given":"Anushya","family":"Muruganujan","sequence":"additional","affiliation":[{"name":"Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA"}]},{"given":"Caitlin","family":"Mills","sequence":"additional","affiliation":[{"name":"Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5801-1974","authenticated-orcid":false,"given":"Laurent-Philippe","family":"Albou","sequence":"additional","affiliation":[{"name":"Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA"}]},{"given":"Tremayne","family":"Mushayamaha","sequence":"additional","affiliation":[{"name":"Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9074-3507","authenticated-orcid":false,"given":"Paul D","family":"Thomas","sequence":"additional","affiliation":[{"name":"Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,12,8]]},"reference":[{"key":"2021010313131903600_B1","doi-asserted-by":"crossref","first-page":"2129","DOI":"10.1101\/gr.772403","article-title":"PANTHER: a library of protein families and subfamilies indexed by function","volume":"13","author":"Thomas","year":"2003","journal-title":"Genome Res."},{"key":"2021010313131903600_B2","doi-asserted-by":"crossref","first-page":"W645","DOI":"10.1093\/nar\/gkl229","article-title":"Applications for protein sequence-function evolution data: mRNA\/protein expression analysis and coding SNP scoring tools","volume":"34","author":"Thomas","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2021010313131903600_B3","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1038\/s41596-019-0128-8","article-title":"Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0)","volume":"14","author":"Mi","year":"2019","journal-title":"Nat. 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Biol."},{"key":"2021010313131903600_B7","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/S1478-5382(03)02370-9","article-title":"CellDesigner: a process diagram editor for gene-regulatory and biochemical networks","volume":"1","author":"Funahashi","year":"2003","journal-title":"BIOSILICO"},{"key":"2021010313131903600_B8","first-page":"D498","article-title":"The reactome pathway knowledgebase","volume":"48","author":"Jassal","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2021010313131903600_B9","doi-asserted-by":"crossref","first-page":"1551","DOI":"10.1038\/nprot.2013.092","article-title":"Large-scale gene function analysis with the PANTHER classification system","volume":"8","author":"Mi","year":"2013","journal-title":"Nat. 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