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Development of Compendium for Esophageal Squamous Cell Carcinoma

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PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool

Huaiyu Mi¹, Xiaosong Huang², Anushya Muruganujan²

¹Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA 90033, USA huaiyumi@usc.edu.

Nucleic Acids Research

|December 1, 2016

Summary

The PANTHER database now offers expanded protein evolution and function data for 104 genomes. Enhanced analysis tools improve gene list classification and genetic variant data interpretation for researchers.

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Area of Science:

Genomics
Bioinformatics
Evolutionary Biology

Background:

The PANTHER database provides evolutionary and functional information for protein-coding genes.
It supports the analysis of gene lists from large-scale genomics experiments.

Purpose of the Study:

To detail recent major improvements and enhancements to the PANTHER database and its associated software tools.
To highlight expanded classification information and advanced analysis capabilities for researchers.

Main Methods:

Expansion of protein subfamily functional classifications through the Gene Ontology Phylogenetic Annotation Project.
Integration of Reactome pathway classifications for enrichment analysis of human genes.
Enhancements to gene list enrichment tools, including a hierarchical view and direct genetic variant data upload.
Updates to the coding single-nucleotide polymorphism (SNP) scoring tool and hidden Markov model (HMM) search tools using HMMER3.
Implementation of a JavaScript-based PANTHER Tree-Attribute Viewer for exploring protein sequence evolution.

Main Results:

Protein subfamily functional classifications have more than doubled.
PANTHER now supports Reactome pathway enrichment analysis for human genes.
Gene list enrichment tools offer a new hierarchical view and direct genetic variant data upload.
HMM search tools show dramatically reduced search times and improved accuracy.
The PANTHER Tree-Attribute Viewer provides new visualization capabilities for protein sequence evolution.

Conclusions:

The PANTHER database has undergone significant updates, enhancing its utility for protein analysis and gene function studies.
These improvements provide researchers with more powerful and efficient tools for exploring evolutionary relationships and analyzing genomic data.
The expanded resources and enhanced tools facilitate deeper insights into protein evolution and functional genomics.