PANTHER Version 7: Improved Phylogenetic Trees, Orthologs and Collaboration with the Gene Ontology Consortium

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2009 Dec 18

PMID 20015972

Citations 337

Authors

Huaiyu Mi

Qing Dong

Anushya Muruganujan

Pascale Gaudet

Suzanna Lewis

Paul D Thomas

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

Identification of novel microRNAs: Biomarkers for pathogenesis of hepatocellular carcinoma in mice model.

Priya S, Kma L Biochem Biophys Rep. 2025; 41:101896.

PMID: 39881957 PMC: 11774814. DOI: 10.1016/j.bbrep.2024.101896.

Systematic ocular phenotyping of 8,707 knockout mouse lines identifies genes associated with abnormal corneal phenotypes.

Vo P, Imai-Leonard D, Yang B, Briere A, Shao A, Casanova M BMC Genomics. 2025; 26(1):48.

PMID: 39833678 PMC: 11744888. DOI: 10.1186/s12864-025-11222-8.

Transcriptome profiling of eight Zea mays lines identifies genes responsible for the resistance to Fusarium verticillioides.

Tran T, Lanubile A, Marocco A, Pe M, DellAcqua M, Miculan M BMC Plant Biol. 2024; 24(1):1107.

PMID: 39574004 PMC: 11580207. DOI: 10.1186/s12870-024-05697-y.

Confronting the data deluge: How artificial intelligence can be used in the study of plant stress.

Koh E, Sunil R, Lam H, Mutwil M Comput Struct Biotechnol J. 2024; 23:3454-3466.

PMID: 39415960 PMC: 11480249. DOI: 10.1016/j.csbj.2024.09.010.

Examining the liver-pancreas crosstalk reveals a role for the molybdenum cofactor in β-cell regeneration.

Karampelias C, Baloiu B, Rathkolb B, da Silva-Buttkus P, Bachar-Wikstrom E, Marschall S Life Sci Alliance. 2024; 7(11).

PMID: 39159974 PMC: 11333758. DOI: 10.26508/lsa.202402771.

References

Blake J, Bult C, Eppig J, Kadin J, Richardson J . The Mouse Genome Database genotypes::phenotypes. Nucleic Acids Res. 2008; 37(Database issue):D712-9. PMC: 2686566. DOI: 10.1093/nar/gkn886. View

Hunter S, Apweiler R, Attwood T, Bairoch A, Bateman A, Binns D . InterPro: the integrative protein signature database. Nucleic Acids Res. 2008; 37(Database issue):D211-5. PMC: 2686546. DOI: 10.1093/nar/gkn785. View

Pruitt K, Tatusova T, Klimke W, Maglott D . NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res. 2008; 37(Database issue):D32-6. PMC: 2686572. DOI: 10.1093/nar/gkn721. View

Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J . Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1):25-9. PMC: 3037419. DOI: 10.1038/75556. View

Dwinell M, Worthey E, Shimoyama M, Bakir-Gungor B, DePons J, Laulederkind S . The Rat Genome Database 2009: variation, ontologies and pathways. Nucleic Acids Res. 2008; 37(Database issue):D744-9. PMC: 2686558. DOI: 10.1093/nar/gkn842. View

Hong E, Balakrishnan R, Dong Q, Christie K, Park J, Binkley G . Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2007; 36(Database issue):D577-81. PMC: 2238894. DOI: 10.1093/nar/gkm909. View

Hubbard T, Aken B, Ayling S, Ballester B, Beal K, Bragin E . Ensembl 2009. Nucleic Acids Res. 2008; 37(Database issue):D690-7. PMC: 2686571. DOI: 10.1093/nar/gkn828. View

. The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res. 2008; 37(Database issue):D169-74. PMC: 2686606. DOI: 10.1093/nar/gkn664. View

Sprague J, Bayraktaroglu L, Bradford Y, Conlin T, Dunn N, Fashena D . The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res. 2007; 36(Database issue):D768-72. PMC: 2238839. DOI: 10.1093/nar/gkm956. View

10.

Hertz-Fowler C, Peacock C, Wood V, Aslett M, Kerhornou A, Mooney P . GeneDB: a resource for prokaryotic and eukaryotic organisms. Nucleic Acids Res. 2003; 32(Database issue):D339-43. PMC: 308742. DOI: 10.1093/nar/gkh007. View

11.

Keseler I, Bonavides-Martinez C, Collado-Vides J, Gama-Castro S, Gunsalus R, Johnson D . EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res. 2008; 37(Database issue):D464-70. PMC: 2686493. DOI: 10.1093/nar/gkn751. View

12.

Thomas P, Kejariwal A, Guo N, Mi H, Campbell M, Muruganujan A . Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. Nucleic Acids Res. 2006; 34(Web Server issue):W645-50. PMC: 1538848. DOI: 10.1093/nar/gkl229. View

13.

Lynch M, Katju V . The altered evolutionary trajectories of gene duplicates. Trends Genet. 2004; 20(11):544-9. DOI: 10.1016/j.tig.2004.09.001. View

14.

Swarbreck D, Wilks C, Lamesch P, Berardini T, Garcia-Hernandez M, Foerster H . The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res. 2007; 36(Database issue):D1009-14. PMC: 2238962. DOI: 10.1093/nar/gkm965. View

15.

Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S . FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res. 2008; 37(Database issue):D555-9. PMC: 2686450. DOI: 10.1093/nar/gkn788. View

16.

Fey P, Gaudet P, Curk T, Zupan B, Just E, Basu S . dictyBase--a Dictyostelium bioinformatics resource update. Nucleic Acids Res. 2008; 37(Database issue):D515-9. PMC: 2686522. DOI: 10.1093/nar/gkn844. View

17.

. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 2009; 38(Database issue):D331-5. PMC: 2808930. DOI: 10.1093/nar/gkp1018. View

18.

Rogers A, Antoshechkin I, Bieri T, Blasiar D, Bastiani C, Canaran P . WormBase 2007. Nucleic Acids Res. 2007; 36(Database issue):D612-7. PMC: 2238927. DOI: 10.1093/nar/gkm975. View

19.

Maglott D, Ostell J, Pruitt K, Tatusova T . Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. 2006; 35(Database issue):D26-31. PMC: 1761442. DOI: 10.1093/nar/gkl993. View

20.

Mi H, Guo N, Kejariwal A, Thomas P . PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. Nucleic Acids Res. 2006; 35(Database issue):D247-52. PMC: 1716723. DOI: 10.1093/nar/gkl869. View