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Nucleic Acids Res. 2016 Jan 4;44(D1):D336-42. doi: 10.1093/nar/gkv1194. Epub 2015 Nov 17.

PANTHER version 10: expanded protein families and functions, and analysis tools.

Author information

1
Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA 90089, USA huaiyumi@usc.edu.
2
Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA 90089, USA.
3
Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA 90089, USA pdthomas@usc.edu.

Abstract

PANTHER (Protein Analysis THrough Evolutionary Relationships, http://pantherdb.org) is a widely used online resource for comprehensive protein evolutionary and functional classification, and includes tools for large-scale biological data analysis. Recent development has been focused in three main areas: genome coverage, functional information ('annotation') coverage and accuracy, and improved genomic data analysis tools. The latest version of PANTHER, 10.0, includes almost 5000 new protein families (for a total of over 12 000 families), each with a reference phylogenetic tree including protein-coding genes from 104 fully sequenced genomes spanning all kingdoms of life. Phylogenetic trees now include inference of horizontal transfer events in addition to speciation and gene duplication events. Functional annotations are regularly updated using the models generated by the Gene Ontology Phylogenetic Annotation Project. For the data analysis tools, PANTHER has expanded the number of different 'functional annotation sets' available for functional enrichment testing, allowing analyses to access all Gene Ontology annotations--updated monthly from the Gene Ontology database--in addition to the annotations that have been inferred through evolutionary relationships. The Prowler (data browser) has been updated to enable users to more efficiently browse the entire database, and to create custom gene lists using the multiple axes of classification in PANTHER.

PMID:
26578592
PMCID:
PMC4702852
DOI:
10.1093/nar/gkv1194
[Indexed for MEDLINE]
Free PMC Article

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