PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools.

Huaiyu Mi,Xiaosong Huang,Dustin Ebert,Paul D Thomas,Anushya Muruganujan

doi:10.1093/nar/gky1038

Huaiyu Mi, Xiaosong Huang + Show 3 more

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https://doi.org/10.1093/nar/gky1038

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Abstract

PANTHER (Protein Analysis Through Evolutionary Relationships, http://pantherdb.org) is a resource for the evolutionary and functional classification of genes from organisms across the tree of life. We report the improvements we have made to the resource during the past two years. For evolutionary classifications, we have added more prokaryotic and plant genomes to the phylogenetic gene trees, expanding the representation of gene evolution in these lineages. We have refined many protein family boundaries, and have aligned PANTHER with the MEROPS resource for protease and protease inhibitor families. For functional classifications, we have developed an entirely new PANTHER GO-slim, containing over four times as many Gene Ontology terms as our previous GO-slim, as well as curated associations of genes to these terms. Lastly, we have made substantial improvements to the enrichment analysis tools available on the PANTHER website: users can now analyze over 900 different genomes, using updated statistical tests with false discovery rate corrections for multiple testing. The overrepresentation test is also available as a web service, for easy addition to third-party sites.

Highlights

PANTHER is a comprehensive resource for classification of genes according to their evolutionary history, and their functions [1,2]
The PANTHER evolutionary classification has three levels, from least to most specific: protein class, family, and subfamily. Protein class includes both homologous groups (‘superfamilies’ such as protein kinase, comprising multiple divergent families), and groups that are mostly analogous but may include homologs that are too diverged in sequence to reliably establish homology
For each of the over 15 000 families in PANTHER, the detailed relationships between family members are represented in terms of a phylogenetic tree that shows how the family evolved by the processes of speciation, gene duplication, and horizontal transfer [3]

Summary

Introduction

PANTHER is a comprehensive resource for classification of genes according to their evolutionary history, and their functions [1,2]. The PANTHER evolutionary classification has three levels, from least to most specific: protein class, family, and subfamily. PANTHER includes inferred annotations to a reduced (‘slim’) classification that includes only a subset of the Gene Ontology (comprising 655 distinct function terms in PANTHER versions 9.0 through 13.1, but substantially expanded in PANTHER 14.0 as described below).

Results

Conclusion