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

By Huaiyu Mi, Anushya Muruganujan, Dustin Ebert, Xiaosong Huang, Paul D. Thomas. Nucleic Acids Res., 2018

2,640 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e08791ddbca9e5716e9b53d417e24962964f4edb

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Citations in the corpus

Genenames.org: the HGNC and VGNC resources in 2021 (2020, background): “This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. nloaded from https://aca”
Advances and Applications in the Quest for Orthologs (2019, background): “2019), PANTHER all, PANTHER LDO only (Mi et al. 2019), best bidirectional hit (BBH), and reciprocal smallest distance (RSD).”
SynGO: an evidence-based, expert-curated knowledgebase for the synapse (2019, background): “Ages (time in million years ago) are obtained from dating of gene duplication events (relative to speciation events) in PANTHER gene trees (Mi et al., 2018).”
The InterPro protein families and domains database: 20 years on (2020, background): “In addition, PANTHER updates involve a large number of deleted or changed signatures, potentially resulting in a large number of lost integrated signatures.”
miRDB: an online database for prediction of functional microRNA targets (2019, methodology): “The GO enrichment analysis is performed by employing the PANTHER web server engine (16) using up-to-date GO terms (17).”
PANTHER: Making genome‐scale phylogenetics accessible to all (2021, methodology): “All PANTHER GO-slim annotations to proteins are inferred from these curated tree annotations; the terms commonly used in tree annotations represent only a subset of all GO terms, and this subset is used to create a slim, or simplified, ontology structure that we call PANTHER GO-slim.(31) In addition”
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API (2020, methodology): “The number of classes has increased by 289 terms compared to the one reported in our last update in 2019 (13), due to the number of additional GO terms that have been used by the GO Phylogenetic Annotation project.”
The reactome pathway knowledgebase (2019, methodology): “org link next to an event of interest (3) opens an e-mail message (4) pre-populated with the event’s details with slots to accommodate personal details.”
The Gene Ontology resource: enriching a GOld mine (2020, neutral): “]; MGI is supported by the National Human Genome Research Institute [HG 000330, HG 002273]; RGD is supported by the National Heart, Lung, and Blood Institute [HL 64541]; Reactome is supported by the National Human Genome Research Institute [HG 003751]; the TAIR project is funded by academic institut”