PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

By Huaiyu Mi, Anushya Muruganujan, Paul D. Thomas. Nucleic Acids Res., 2012

1,769 citations recorded by the source corpus.

The data and tools in PANTHER—a comprehensive, curated database of protein families, trees, subfamilies and functions available at http://pantherdb.org—have undergone continual, extensive improvement for over a decade. Here, we describe the current PANTHER process as a whole, as well as the website tools for analysis of user-uploaded data. The main goals of PANTHER remain essentially unchanged: the accurate inference (and practical application) of gene and protein function over large sequence databases, using phylogenetic trees to extrapolate from the relatively sparse experimental information from a few model organisms. Yet the focus of PANTHER has continually shifted toward more accurate and detailed representations of evolutionary events in gene family histories. The trees are now designed to represent gene family evolution, including inference of evolutionary events, such as speciation and gene duplication. Subfamilies are still curated and used to define HMMs, but gene ontology functional annotations can now be made at any node in the tree, and are designed to represent gain and loss of function by ancestral genes during evolution. Finally, PANTHER now includes stable database identifiers for inferred ancestral genes, which are used to associate inferred gene attributes with particular genes in the common ancestral genomes of extant species.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f0e420b57065da2d189288925ec044323bafa26a

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Citations in the corpus

Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes (2016, methodology): “The GO Phylogenetic Annotation Project applies PAINT to annotate PANTHER families (8), each containing between 5 and 5000 proteins.”
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update (2016, background): “…from the LINCS L1000 data set; NCI-Nature pathways (17); protein complexes from the NURSA project (18); pathways from the PANTHER resource (19); targets of phosphatases from DEPOD (20); human phenotypes from the Human Pheno-type Ontology (HPO) (21); genes associated with grants us-ing NIH…”
Harnessing Connectivity in a Large-Scale Small-Molecule Sensitivity Dataset (2015, positive): “Sunburst visualization of validated protein targets of the small molecules in the Informer Set using protein family hierarchy from the Panther database (12).”
Phylogenetic tree building in the genomic age (2020, neutral): “Homologous sequences that have diverged due to speciation events.”
Large-scale gene function analysis with PANTHER Classification System (2013, methodology): “The PANTHER classification system is designed to be a comprehensive platform for the analysis of gene function on a genome-wide scale 1 .”
InterProScan 5: genome-scale protein function classification (2014, methodology): “As InterProScan 5 makes use of the Hibernate object-relational mapping tool (http://www.hibernate.org/), it should be possible to port the back-end to run on most relational database management systems.”
Genenames.org: the HGNC resources in 2015 (2014, methodology): “HCOP currently collates orthology assertions from eggNOG (34), Ensembl Compara (2), HGNC, HomoloGene (31), InParanoid (35), OMA (36), OrthoDB (37), OrthoMCL (38), PANTHER (39), PhylomeDB (40), Treefam (41) and ZFIN (18) into a single tool, enabling comparison of these data to identify a consensus or”
Ensembl 2016 (2015, methodology): “It will be replaced with a more straightforward HMM classification based upon PANTHER (34).”
Ensembl comparative genomics resources (2016, background): “Panther also infers phylogenetic trees on a large set of species with the specific aim of facilitating high-throughput annotation of genes (19).”