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.

YhcB coordinates peptidoglycan and LPS biogenesis with phospholipid synthesis duringEscherichia colicell growth

“…To determine whether other cellular processes or pathways are enriched among the genes identified as synthetically lethal with yhcB , we used the PANTHER overrepresentation test (Mi et al 2021). This analysis compares the identified proportion of genes in a given functional category to the expected number of genes in a pathway derived from whole genome data (Table S6).…”

Cartilage Protective and Immunomodulatory Features of Osteoarthritis Synovial Fluid-Treated Adipose-Derived Mesenchymal Stem Cells Secreted Factors and Extracellular Vesicles-Embedded miRNAs

“…All experimentally validated strong miRNA–mRNA interactions were submitted to GOrilla web interface ( , accessed on April 2021) [ 30 ] to search for enriched Gene Ontology (GO) terms that appear densely at the top of a ranked list of genes (unbiased, against whole genome) or, after filtering againsts first quartile OA-cartilage or OA-sinovia infiltrative macrophages for shared candidates, for enriched GO terms in a target list of genes compared to a background list of genes (against the same OA cartilage or macrophage first quartile gene expression datasets), under default settings except for p -value threshold run as specified in the Results. Eventually, filtered interactions were also submitted to the PANTHER web interface ( , accessed on April 2021) [ 31 ] to identify genes belonging to the same functional classifications, following default settings.…”

G-quadruplex RNA motifs influence gene expression in the malaria parasitePlasmodium falciparum

“…GO term annotations for P. falciparum genes were downloaded from PlasmoDB 29 . GO enrichment analysis were conducted on the PANTHER platform 47 , using a de-duplicated list of rG4-harbouring gene IDs as input.…”