PANTHER

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


References in zbMATH (referenced in 15 articles , 1 standard article )

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  1. Huang, Hailin; Shangguan, Jizi; Ruan, Peifeng; Liang, Hua: Bi-level feature selection in high dimensional AFT models with applications to a genomic study (2019)
  2. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  3. Keith, Jonathan M. (ed.): Bioinformatics. Volume II: structure, function, and applications (2017)
  4. Shafaghati, Leila; Razaghi-Moghadam, Zahra; Mohammadnejad, Javad: A systems biology approach to understanding alcoholic liver disease molecular mechanism: the development of static and dynamic models (2017)
  5. Stojkovic, Ivan; Obradovic, Zoran: Sparse learning of the disease severity score for high-dimensional data (2017)
  6. Bag, Susmita; Ramaiah, Sudha; Anbarasu, Anand: fabp4 is central to eight obesity associated genes: a functional gene network-based polymorphic study (2015)
  7. Dondi, Riccardo; El-Mabrouk, Nadia; Swenson, Krister M.: Gene tree correction for reconciliation and species tree inference: complexity and algorithms (2014)
  8. Qin, Wenli; Li, Yizhou; Li, Juan; Yu, Lezheng; Wu, Di; Jing, Runyu; Pu, Xuemei; Guo, Yanzhi; Li, Menglong: Predicting deleterious non-synonymous single nucleotide polymorphisms in signal peptides based on hybrid sequence attributes (2012)
  9. Li, Yizhou; Wen, Zhining; Xiao, Jiamin; Yin, Hui; Yu, Lezheng; Yang, Li; Li, Menglong: Predicting disease-associated substitution of a single amino acid by analyzing residue interactions (2011) ioport
  10. H├╝ffner, Falk; Betzler, Nadja; Niedermeier, Rolf: Separator-based data reduction for signed graph balancing (2010)
  11. Mi, Huaiyu; Dong, Qing; Muruganujan, Anushya; Gaudet, Pascale; Lewis, Suzanna; Thomas, Paul D.: PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the gene ontology consortium (2010) ioport
  12. Paszkowski-Rogacz, Maciej; Slabicki, Mikolaj; Pisabarro, M. Teresa; Buchholz, Frank: Phenofam-gene set enrichment analysis through protein structural information (2010) ioport
  13. Thomas, Paul D.: GIGA: a simple, efficient algorithm for gene tree inference in the genomic age (2010) ioport
  14. Mi, Huaiyu; Lazareva-Ulitsky, Betty; Loo, Rozina; Kejariwal, Anish; Vandergriff, Jody A.; Rabkin, Steven; Guo, Nan; Muruganujan, Anushya; Doremieux, Olivier; Campbell, Michael J.; Kitano, Hiroaki; Thomas, Paul D.: The PANTHER database of protein families, subfamilies, functions and pathways. (2005) ioport
  15. Thomas, Paul D.; Kejariwal, Anish; Campbell, Michael J.; Mi, Huaiyu; Diemer, Karen; Guo, Nan; Ladunga, Istvan; Lazareva-Ulitsky, Betty; Muruganujan, Anushya; Rabkin, Steven; Vandergriff, Jody A.; Doremieux, Olivier: PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. (2003) ioport