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

By Huaiyu Mi, Sagar Poudel, Anushya Muruganujan, John T. Casagrande, Paul D. Thomas. 2015

815 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

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Citations in the corpus

InterPro in 2017—beyond protein family and domain annotations (2016, background): “The integration of similar residue-level annotations from databases like Pfam and PIRSF, coupled with highly specific subfamily-level annotations from resources like PANTHER and PRINTS, extends this functionality even further.”
Intrinsically disordered proteins and structured proteins with intrinsically disordered regions have different functional roles in the cell (2019, methodology): “157 Clustering of the variants of disorder through functional profiles 158 The functional profiles of ORDPs, IDPRs and IDPs were defined considering several annotations, 159 such as: biological processes, cellular components and molecular functions from the Gene Ontology 160 database [52] and protei”
Pi-Pi contacts are an overlooked protein feature relevant to phase separation (2018, methodology): “Phase separation critical concentration values for the N-terminus (1-236) of human Ddx4 and three mutants, 9FtoA and 14FtoA, as reported in (14), and RtoK, where all arginine residues have been mutated to lysine, as well as for the C-terminus (445-632) of human FMR1 and one mutant with all arginine ”
Insights into Ciliary Genes and Evolution from Multi-Level Phylogenetic Profiling (2017, methodology): “GO Term Enrichment All Gene Ontology term enrichments were realized using Panther (Mi et al. 2016) with the list of 20,193 human protein-coding genes as a background.”
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API (2020, methodology): “Most of the new family name assignments utilize the PANTHER automatic subfamily name assignments, which in turn rely on protein names from UniProt (15) as described previously (19).”
HIPPIE v2.0: enhancing meaningfulness and reliability of protein–protein interaction networks (2016, methodology): “Disease and functional enrichment analyses for the members of the subnetwork resulting from a protein or network query are carried out via the third-party tools Gene Set to Diseases (32) and PANTHER (33), respectively.”
Reactome pathway analysis: a high-performance in-memory approach (2017, methodology): “On the other hand, DAVID, PANTHER and ConsensusPathDB provide online access to their analysis tools via a web interface, similarly to REACTOME.”
Marine Animal Microbiomes: Toward Understanding Host–Microbiome Interactions in a Changing Ocean (2017, background): “Algorithms utilizing gene function predictions do provide some assistance with this problem (Mi et al., 2015), and these tools may improve as more environmental microbial genomes are available.”
DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants (2016, background): “with their full name, the UniProt accession, the Reactome (17) upper level pathway and the Panther (18) protein class.”
PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools (2018, methodology): “These diverse families were subsequently reclustered using the standard PANTHER pipeline as described in (4,5), into 3026 new families in PANTHER 14.”
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species (2016, methodology): “…has integrated data from a variety of human, model organism, and other biomedical sources such as OMIM (1), Orphanet (3), Clin-Var (2), HPO (30), KEGG (31), CTD (4), MyGene (32), BioGrid (33) and via orthology in PantherDB (34) we also incorporate Fgg gene data from ZFIN (35) and from MGI (36).”
Protein Ontology (PRO): enhancing and scaling up the representation of protein entities (2016, methodology): “For example, PRO imports information from UniProtKB to create terms for selected species (2), and integrates information from the OMA (9) and PANTHER (10) databases to find connections between such terms.”
WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit (2017, background): “Under the pathway class, two new pathway databases, Reactome (10) and PANTHER (11) have been included in the new version, adding a total of 13 140 pathways.”
PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements (2016, methodology): “Recently, the PANTHER overrepresentation / enrichment tools were extended to include functional annotations directly down-loaded from the GO Consortium , in addition to the phylogenetically inferred annotations (1,12).”