PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API
By Huaiyu Mi, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Laurent-Philippe Albou, Tremayne Mushayahama, Paul D. Thomas. Nucleic Acids Res., 2020
1,123 citations recorded by the source corpus.
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.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/e73d0d9be6aefd9e509779b89ee455564f80cb3e
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In Molecular Biology
- Anushya Muruganujan
- Huaiyu Mi
- Paul D. Thomas
- Dustin Ebert
- Tremayne Mushayahama
- Laurent-Philippe Albou
- Lei Kong
- Yi Zhao
Citations in the corpus
- InterPro in 2022 (2022, neutral): “Historically, both PANTHER family and subfamily HMMs have been integrated in InterPro entries, but the up-date of the PANTHER subfamilies has always been a challenge for the InterPro curators as it always brings a lot of changes in the signatures.”
- KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis (2021, methodology): “In total, 5944 species were annotated with KEGG pathways, 41 species with PANTHER pathways, 14 species with Reactome pathways, 18 species with BioCyc pathways and 71 species with GO annotations (Table 1, Figure 3).”
- PANTHER: Making genome‐scale phylogenetics accessible to all (2021, methodology): “PAN-THER/X has now been converted into a simpler, strictly hierarchical “ Protein Class ” used to classify entire protein families, 25 not functionally distinct subfamilies.”