PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

By Huaiyu Mi, Q. Dong, Anushya Muruganujan, Pascale Gaudet, Suzanna Lewis, Paul D. Thomas. Nucleic Acids Res., 2009

606 citations recorded by the source corpus.

Protein Analysis THrough Evolutionary Relationships (PANTHER) is a comprehensive software system for inferring the functions of genes based on their evolutionary relationships. Phylogenetic trees of gene families form the basis for PANTHER and these trees are annotated with ontology terms describing the evolution of gene function from ancestral to modern day genes. One of the main applications of PANTHER is in accurate prediction of the functions of uncharacterized genes, based on their evolutionary relationships to genes with functions known from experiment. The PANTHER website, freely available at http://www.pantherdb.org, also includes software tools for analyzing genomic data relative to known and inferred gene functions. Since 2007, there have been several new developments to PANTHER: (i) improved phylogenetic trees, explicitly representing speciation and gene duplication events, (ii) identification of gene orthologs, including least diverged orthologs (best one-to-one pairs), (iii) coverage of more genomes (48 genomes, up to 87% of genes in each genome; see http://www.pantherdb.org/panther/summaryStats.jsp), (iv) improved support for alternative database identifiers for genes, proteins and microarray probes and (v) adoption of the SBGN standard for display of biological pathways. In addition, PANTHER trees are being annotated with gene function as part of the Gene Ontology Reference Genome project, resulting in an increasing number of curated functional annotations.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/27d942d4ae218d0f0f8d784f745e5324e067eea5

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Citations in the corpus

Mutual exclusivity analysis identifies oncogenic network modules. (2012, background): “The second network, HRN2, is derived from Wu et al. (2010) and consists of manually curated interactions (Reactome, Matthews et al. 2009; Panther, Mi et al. 2010; KEGG, Kanehisa et al. 2008; and INOH, Fukuda 2008), plus additional inferred interactions derived from non-curated sources of information”
DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes (2015, background): “In addition, genes are classified according to the PANTHER Protein Class Ontology (22, 23) and Reactome top-level pathways (24) (Figure 3a and b, respectively).”
Advances and Applications in the Quest for Orthologs (2019, methodology): “The benchmarks are phylogeny-based or function-based, and a user can compare their performance to other methods such as PhylomeDB, InParanoid, OMA, Ensembl Compara, Hieranoid, PANTHER, MetaPhOrs, OrthoInspector, eggNOG, SonicParanoid.”
Developmental heterogeneity of microglia and brain myeloid cells revealed by deep single-cell RNA sequencing (2018, neutral): “PANTHER Classification System was used to perform Gene Ontology term analysis (Mi et al., 2010).”
PANTHER: Making genome‐scale phylogenetics accessible to all (2021, background): “22 Since 2010, PANTHER has been continually expanded to cover more families (Table 1) and more species (Supplementary Table).”
InterPro in 2011: new developments in the family and domain prediction database (2011, methodology): “The InterPro database integrates predictive models, or signatures, from multiple, diverse source repositories: Pfam (1), PRINTS (2), PROSITE (3), SMART (4), ProDom (5), PIRSF (6), SUPERFAMILY (7), PANTHER (8), CATHGene3D (9), TIGRFAMs (10) and HAMAP (11).”
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium (2011, methodology): “PAINT allows querying and retrieval of protein family trees, multiple sequence alignments and sequence annotation data from the PANTHER database [9].”
TSGene: a web resource for tumor suppressor genes (2012, methodology): “For functional annotations, we retrieved the pathways that the genes are involved in from BioCyc (29), KEGG Pathway (30), PID Curated (31), PANTHER (32) and Reactome (33); we also extracted possible association with diseases from KEGG Disease (30), Fundo (34,35), GAD (36), NHGIR (37) and OMIM (24) u”