Nucleic Acids Research, 2005, Vol. 33, Database issue D284-D288
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
The PANTHER database of protein families, subfamilies, functions and pathways
Computational Biology, Applied Biosystems, 850 Lincoln Center Drive, Foster City, CA 94404, USA and 1 The Systems Biology Institute and ERATO-SORST Kitano Symbiotic Systems Project/Japan Science and Technology Agency, Suite 6A, M31, 6-31-15 Jingumae, Shibuya, Tokyo 150-0001, Japan
* To whom correspondence should be addressed. Tel: +1 650 554 2723; Fax: +1 650 554 2344; Email: paul.thomas{at}appliedbiosystems.com
Received September 15, 2004; Revised and Accepted October 8, 2004
PANTHER is a large collection of protein families that have been subdivided into functionally related subfamilies, using human expertise. These subfamilies model the divergence of specific functions within protein families, allowing more accurate association with function (ontology terms and pathways), as well as inference of amino acids important for functional specificity. Hidden Markov models (HMMs) are built for each family and subfamily for classifying additional protein sequences. The latest version, 5.0, contains 6683 protein families, divided into 31 705 subfamilies, covering
90% of mammalian protein-coding genes. PANTHER 5.0 includes a number of significant improvements over previous versions, most notably (i) representation of pathways (primarily signaling pathways) and association with subfamilies and individual protein sequences; (ii) an improved methodology for defining the PANTHER families and subfamilies, and for building the HMMs; (iii) resources for scoring sequences against PANTHER HMMs both over the web and locally; and (iv) a number of new web resources to facilitate analysis of large gene lists, including data generated from high-throughput expression experiments. Efforts are underway to add PANTHER to the InterPro suite of databases, and to make PANTHER consistent with the PIRSF database. PANTHER is now publicly available without restriction at http://panther.appliedbiosystems.com.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.
![]()
CiteULike
Connotea
Del.icio.us What's this?
This article has been cited by other articles:
![]() |
N. F. W. Saunders and B. Kobe The Predikin webserver: improved prediction of protein kinase peptide specificity using structural information Nucleic Acids Res., July 1, 2008; 36(suppl_2): W286 - W290. [Abstract] [Full Text] [PDF] |
||||
![]() |
X. Wang miRDB: A microRNA target prediction and functional annotation database with a wiki interface RNA, June 1, 2008; 14(6): 1012 - 1017. [Abstract] [Full Text] [PDF] |
||||
![]() |
K. Akagi, J. Li, R. M. Stephens, N. Volfovsky, and D. E. Symer Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition Genome Res., June 1, 2008; 18(6): 869 - 880. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. Singh, A. Olowoyeye, P. H. Baenziger, J. Dantzer, M. G. Kann, P. Radivojac, R. Heiland, and S. D. Mooney MutDB: update on development of tools for the biochemical analysis of genetic variation Nucleic Acids Res., January 11, 2008; 36(suppl_1): D815 - D819. [Abstract] [Full Text] [PDF] |
||||
![]() |
G. Alexe, G. S. Dalgin, D. Scanfeld, P. Tamayo, J. P. Mesirov, C. DeLisi, L. Harris, N. Barnard, M. Martel, A. J. Levine, et al. High Expression of Lymphocyte-Associated Genes in Node-Negative HER2+ Breast Cancers Correlates with Lower Recurrence Rates Cancer Res., November 15, 2007; 67(22): 10669 - 10676. [Abstract] [Full Text] [PDF] |
||||
![]() |
T C T M van der Pouw Kraan, C A Wijbrandts, L G M van Baarsen, A E Voskuyl, F Rustenburg, J M Baggen, S M Ibrahim, M Fero, B A C Dijkmans, P P Tak, et al. Rheumatoid arthritis subtypes identified by genomic profiling of peripheral blood cells: assignment of a type I interferon signature in a subpopulation of patients Ann Rheum Dis, August 1, 2007; 66(8): 1008 - 1014. [Abstract] [Full Text] [PDF] |
||||
![]() |
D. Kultz, D. Fiol, N. Valkova, S. Gomez-Jimenez, S. Y. Chan, and J. Lee Functional genomics and proteomics of the cellular osmotic stress response in `non-model' organisms J. Exp. Biol., May 1, 2007; 210(9): 1593 - 1601. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. A. Bakewell, P. Shi, and J. Zhang More genes underwent positive selection in chimpanzee evolution than in human evolution PNAS, May 1, 2007; 104(18): 7489 - 7494. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. S. Chang and M. A. F. Noor The Genetics of Hybrid Male Sterility Between the Allopatric Species Pair Drosophila persimilis and D. pseudoobscura bogotana: Dominant Sterility Alleles in Collinear Autosomal Regions Genetics, May 1, 2007; 176(1): 343 - 349. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Agrawal, W.-K. Hofmann, N. Tidow, M. Ehrich, D. v. d. Boom, S. Koschmieder, W. E. Berdel, H. Serve, and C. Muller-Tidow The C/EBP{delta} tumor suppressor is silenced by hypermethylation in acute myeloid leukemia Blood, May 1, 2007; 109(9): 3895 - 3905. [Abstract] [Full Text] [PDF] |
||||
![]() |
Rhesus Macaque Genome Sequencing and Analysis Cons, R. A. Gibbs, J. Rogers, M. G. Katze, R. Bumgarner, G. M. Weinstock, E. R. Mardis, K. A. Remington, R. L. Strausberg, J. C. Venter, et al. Evolutionary and Biomedical Insights from the Rhesus Macaque Genome Science, April 13, 2007; 316(5822): 222 - 234. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Richardt, D. Lang, R. Reski, W. Frank, and S. A. Rensing PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins Plant Physiology, April 1, 2007; 143(4): 1452 - 1466. [Abstract] [Full Text] [PDF] |
||||
![]() |
N. J. Mulder, R. Apweiler, T. K. Attwood, A. Bairoch, A. Bateman, D. Binns, P. Bork, V. Buillard, L. Cerutti, R. Copley, et al. New developments in the InterPro database Nucleic Acids Res., January 12, 2007; 35(suppl_1): D224 - D228. [Abstract] [Full Text] [PDF] |
||||
![]() |
H. Mi, N. Guo, A. Kejariwal, and P. D. Thomas PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways Nucleic Acids Res., January 12, 2007; 35(suppl_1): D247 - D252. [Abstract] [Full Text] [PDF] |
||||
![]() |
C. Voolstra, D. Tautz, P. Farbrother, L. Eichinger, and B. Harr Contrasting evolution of expression differences in the testis between species and subspecies of the house mouse Genome Res., January 1, 2007; 17(1): 42 - 49. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. J. Moehring, K. C. Teeter, and M. A. F. Noor Genome-Wide Patterns of Expression in Drosophila Pure Species and Hybrid Males. II. Examination of Multiple-Species Hybridizations, Platforms, and Life Cycle Stages Mol. Biol. Evol., January 1, 2007; 24(1): 137 - 145. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. Ng, B. Bursteinas, Q. Gao, E. Mollison, and M. Zvelebil Resources for integrative systems biology: from data through databases to networks and dynamic system models Brief Bioinform, December 1, 2006; 7(4): 318 - 330. [Abstract] [Full Text] [PDF] |
||||
![]() |
K. I. Zeller, X. Zhao, C. W. H. Lee, K. P. Chiu, F. Yao, J. T. Yustein, H. S. Ooi, Y. L. Orlov, A. Shahab, H. C. Yong, et al. Global mapping of c-Myc binding sites and target gene networks in human B cells PNAS, November 21, 2006; 103(47): 17834 - 17839. [Abstract] [Full Text] [PDF] |
||||
![]() |
G. M LENK, G. TROMP, M. SKUNCA, Z. GATALICA, R. BERGUER, and H. KUIVANIEMI Global Expression Profiles in Human Normal and Aneurysmal Abdominal Aorta Based on Two Distinct Whole Genome Microarray Platforms Ann. N.Y. Acad. Sci., November 1, 2006; 1085(1): 360 - 362. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. V. Ivshina, J. George, O. Senko, B. Mow, T. C. Putti, J. Smeds, T. Lindahl, Y. Pawitan, P. Hall, H. Nordgren, et al. Genetic Reclassification of Histologic Grade Delineates New Clinical Subtypes of Breast Cancer Cancer Res., November 1, 2006; 66(21): 10292 - 10301. [Abstract] [Full Text] [PDF] |
||||
![]() |
I. Friedberg Automated protein function prediction--the genomic challenge Brief Bioinform, September 1, 2006; 7(3): 225 - 242. [Abstract] [Full Text] [PDF] |
||||
![]() |
K. Bryson, V. Loux, R. Bossy, P. Nicolas, S. Chaillou, M. van de Guchte, S. Penaud, E. Maguin, M. Hoebeke, P. Bessieres, et al. AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system Nucleic Acids Res., July 19, 2006; 34(12): 3533 - 3545. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. P. Duffy, A. M. Young, B. Morin, C. J. Lucarotti, B. F. Koop, and D. B. Levin Sequence Analysis and Organization of the Neodiprion abietis Nucleopolyhedrovirus Genome J. Virol., July 15, 2006; 80(14): 6952 - 6963. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. D. Thomas, A. Kejariwal, N. Guo, H. Mi, M. J. Campbell, A. Muruganujan, and B. Lazareva-Ulitsky Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W645 - W650. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. S. Dasika, A. Burgard, and C. D. Maranas A Computational Framework for the Topological Analysis and Targeted Disruption of Signal Transduction Networks Biophys. J., July 1, 2006; 91(1): 382 - 398. [Abstract] [Full Text] [PDF] |
||||
![]() |
B. Harr Genomic islands of differentiation between house mouse subspecies Genome Res., June 1, 2006; 16(6): 730 - 737. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. Sivakumar, C. Wilton, and L. Holm From sequences to a functional unit Physiol Genomics, March 13, 2006; 25(1): 1 - 8. [Abstract] [Full Text] [PDF] |
||||
![]() |
H. Li, A. Coghlan, J. Ruan, L. J. Coin, J.-K. Heriche, L. Osmotherly, R. Li, T. Liu, Z. Zhang, L. Bolund, et al. TreeFam: a curated database of phylogenetic trees of animal gene families Nucleic Acids Res., January 1, 2006; 34(suppl_1): D572 - D580. [Abstract] [Full Text] [PDF] |
||||
![]() |
E. Quevillon, V. Silventoinen, S. Pillai, N. Harte, N. Mulder, R. Apweiler, and R. Lopez InterProScan: protein domains identifier Nucleic Acids Res., July 1, 2005; 33(suppl_2): W116 - W120. [Abstract] [Full Text] [PDF] |
||||
















