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

Nucleic Acids Research

Volumn 44, Issue D1, 2016, Pages D336-D342

  Mi, Huaiyu ^a   Poudel, Sagar ^a   Muruganujan, Anushya ^a   Casagrande, John T ^a   Thomas, Paul D ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; CLASSIFICATION; DATA ANALYSIS SOFTWARE; EVOLUTION; GENE DUPLICATION; GENE ONTOLOGY; HORIZONTAL GENE TRANSFER; INFORMATION RETRIEVAL; INFORMATION SERVICE; INTERNET; PANTHER DATABASE; PHYLOGENETIC TREE; PLANT GENOME; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN FAMILY; SPECIES DIFFERENTIATION; WEB BROWSER; GENETICS; GENOMICS; HUMAN; MOLECULAR GENETICS; PHYLOGENY; PHYSIOLOGY; SOFTWARE;

PROTEIN;

DATABASES, PROTEIN; GENOMICS; HUMANS; MOLECULAR SEQUENCE ANNOTATION; PHYLOGENY; PROTEINS; SOFTWARE;

EID: 84976875034     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1194     Document Type: Article

References (18)

1. UniProt Consortium. (2015) UniProt: a hub for protein information. Nucleic Acids Res., 43, D204-D212.
2. Koonin, E. V. and Galperin, M. Y. (2003) Evolutionary Concept in Genetics and Genomics. In: Sequence - Evolution - Function: Computational Approaches in Comparative Genomics. Kluwer Academic, Boston.
3. Thomas, P. D. (2006) PANTHER: Protein families and subfamilies modeled on the divergence of function. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Wiley, Chichester, pp. 1-5.
4. Gaudet, P., Livstone, M. S., Lewis, S. E. and Thomas, P. D. (2011) Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Brief Bioinform, 12, 449-462.
5. Eisen, J. A. (1998) A phylogenomic study of the MutS family of proteins. Nucleic Acids Res., 26, 4291-4300.
6. Clark, A. G., Glanowski, S., Nielsen, R., Thomas, P. D., Kejariwal, A., Todd, M. A., Tanenbaum, D. M., Civello, D., Lu, F. et al. (2003) Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science, 302, 1960-1963.
7. Mi, H., Lazareva-Ulitsky, B., Loo, R., Kejariwal, A., Vandergriff, J., Rabkin, S., Guo, N., Muruganujan, A., Doremieux, O. et al. (2005) The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res., 33, D284-D288.
8. Thomas, P. D., Kejariwal, A., Guo, N., Mi, H., Campbell, M. J., Muruganujan, A. and Lazareva-Ulitsky, B. (2006) Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. Nucleic Acids Res., 34, W645-W650.
9. Mi, H., Muruganujan, A., Casagrande, J. T. and Thomas, P. D. (2013) Large-scale gene function analysis with the PANTHER classification system. Nat. Protoc., 8, 1551-1566.
10. Mi, H., Muruganujan, A. and Thomas, P. D. (2013) PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res., 41, D377-D386.
11. Goodstein, D. M., Shu, S., Howson, R., Neupane, R., Hayes, R. D., Fazo, J., Mitros, T., Dirks, W., Hellsten, U. et al. (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res., 40, D1178-D1186.
12. Enright, A. J., Van Dongen, S. and Ouzounis, C. A. (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res., 30, 1575-1584.
13. Thomas, P. D. (2010) GIGA: a simple, efficient algorithm for gene tree inference in the genomic age. BMC Bioinformatics, 11, 312.
14. Mirkin, B. G., Fenner, T. I., Galperin, M. Y. and Koonin, E. V. (2003) Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol. Biol., 3, 2.
15. Thomas, P. D., Campbell, M. J., Kejariwal, A., Mi, H., Karlak, B., Daverman, R., Diemer, K., Muruganujan, A. and Narechania, A. (2003) PANTHER: a library of protein families and subfamilies indexed by function. Genome Res., 13, 2129-2141.
16. Mi, H. and Thomas, P. (2009) PANTHER pathway: an ontology-based pathway database coupled with data analysis tools. Methods Mol. Biol., 563, 123-140.
17. NCBI Resource Coordinators (2014) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 42, D7-D17.
18. Fang, H., Oates, M. E., Pethica, R. B., Greenwood, J. M., Sardar, A. J., Rackham, O. J., Donoghue, P. C., Stamatakis, A., de Lima Morais, D. A. and Gough, J. (2013) A daily-updated tree of (sequenced) life as a reference for genome research. Sci. Rep., doi:10.1038/srep02015.