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

Huaiyu Mi1, Dustin Ebert1, Anushya Muruganujan1

  • 1Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.

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Summary

The Protein Analysis Through Evolutionary Relationships (PANTHER) database enhances protein classification with updated ontologies, phylogenetic trees, and improved gene coverage. New features include human enhancer-gene links and expanded API access for researchers.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Evolutionary Biology

Background:

  • The Protein Analysis Through Evolutionary Relationships (PANTHER) database provides evolutionary and functional classifications for protein-coding genes.
  • It utilizes a large library of phylogenetic trees and Gene Ontology (GO) terms for classification.

Purpose of the Study:

  • To analyze the current gene coverage across different taxonomic groups within the PANTHER database.
  • To detail recent improvements and new features implemented in PANTHER over the past two years.

Main Methods:

  • Analysis of gene coverage across various taxonomic groups.
  • Refactoring of the PANTHER Protein Class ontology and manual assignment of protein families.
  • Integration of human enhancer-gene links.
  • Expansion of programmatic access through APIs.
  • Inclusion of additional plant genomes and an updated PANTHER GO-slim.

Main Results:

  • Comprehensive analysis of PANTHER's gene coverage across diverse genomes.
  • Complete refactoring of the Protein Class ontology with 6101 PANTHER families assigned.
  • Introduction of TreeGrafter tool for phylogenetic tree analysis.
  • Addition of human enhancer-gene links for non-coding region association.
  • Expanded API services and updated genomic and GO data.

Conclusions:

  • PANTHER offers enhanced evolutionary and functional classification of proteins with improved usability and data scope.
  • The recent updates provide researchers with more comprehensive tools and data for gene analysis and annotation.