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PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways
Open accessAbstract
PANTHER is a freely available, comprehensive software system for relating protein sequence evolution to the evolution of specific protein functions and biological roles. Since 2005, there have been three main improvements to PANTHER. First, the sequences used to create evolutionary trees are carefully selected to provide coverage of phylogenetic as well as functional information. Second, PANTHER is now a member of the InterPro Consortium, and the PANTHER hidden markov Models (HMMs) are distributed as part of InterProScan. Third, we have dramatically expanded the number of pathways associated with subfamilies in PANTHER. Pathways provide a detailed, structured representation of protein function in the context of biological reaction networks. PANTHER pathways were generated using the emerging Systems Biology Markup Language (SBML) standard using pathway network editing software called CellDesigner. The pathway collection currently contains approximately 1500 reactions in 130 pathways, curated by expert biologists with authorship attribution. The curation environment is designed to be easy to use, and the number of pathways is growing steadily. Because the reaction participants are linked to subfamilies and corresponding HMMs, reactions can be inferred across numerous different organisms. The HMMs can be downloaded by FTP, and tools for analyzing data in the context of pathways and function ontologies are available at http://www.pantherdb.org.
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Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
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Using process diagrams for the graphical representation of biological networks
Kitano, H., Funahashi, A., Matsuoka, Y., & Oda, K. (2005) · Nature Biotechnology · doi:10.1038/nbt1111 · Cited by 483
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Genetic Evidence for High-Altitude Adaptation in Tibet
Simonson, T. S., Yang, Y., Huff, C. D., Yun, H., Qin, G., Witherspoon, D. J., Bai, Z., Lorenzo, F. R., Xing, J., Jorde, L. B., et al. (2010) · Science · doi:10.1126/science.1189406 · Cited by 1,227
The BioPAX community standard for pathway data sharing
Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1666 · Cited by 745
Self-citationA human functional protein interaction network and its application to cancer data analysis
Wu, G., Feng, X., & Stein, L. (2010) · Genome Biology · doi:10.1186/gb-2010-11-5-r53 · Cited by 692
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis
Ostlund, G., Schmitt, T., Forslund, K., Kostler, T., Messina, D. N., Roopra, S., Frings, O., & Sonnhammer, E. L. L. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp931 · Cited by 623
Ruan, J., Li, H., Chen, Z., Coghlan, A., Coin, L. J. M., Guo, Y., Heriche, J.-K., Hu, Y., Kristiansen, K., Li, R., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm1005 · Cited by 332
Cosseau, C., Devine, D. A., Dullaghan, E., Gardy, J. L., Chikatamarla, A., Gellatly, S., Yu, L. L., Pistolic, J., Falsafi, R., Tagg, J., et al. (2008) · Infection and Immunity · doi:10.1128/iai.00188-08 · Cited by 293
Liver-specific deletion of histone deacetylase 3 disrupts metabolic transcriptional networks
Knutson, S. K., Chyla, B. J., Amann, J. M., Bhaskara, S., Huppert, S. S., & Hiebert, S. W. (2008) · The EMBO Journal · doi:10.1038/emboj.2008.51 · Cited by 271
Llorian, M., Schwartz, S., Clark, T. A., Hollander, D., Tan, L.-Y., Spellman, R., Gordon, A., Schweitzer, A. C., de la Grange, P., Ast, G., et al. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1881 · Cited by 263
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Hansson, J., Rafiee, M. R., Reiland, S., Polo, J. M., Gehring, J., Okawa, S., Huber, W., Hochedlinger, K., & Krijgsveld, J. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.10.014 · Cited by 229
Hurov, K. E., Cotta-Ramusino, C., & Elledge, S. J. (2010) · Genes & Development · doi:10.1101/gad.1934210 · Cited by 210
Michaelis, M., Rothweiler, F., Barth, S., Cinatl, J., van Rikxoort, M., Löschmann, N., Voges, Y., Breitling, R., von Deimling, A., Rödel, F., et al. (2011) · Cell Death & Disease · doi:10.1038/cddis.2011.129 · Cited by 190
Morris, A. R., Mukherjee, N., & Keene, J. D. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.00155-08 · Cited by 155
Dittmar, K. A., Jiang, P., Park, J. W., Amirikian, K., Wan, J., Shen, S., Xing, Y., & Carstens, R. P. (2012) · Molecular and Cellular Biology · doi:10.1128/mcb.06536-11 · Cited by 139
A comprehensive modular map of molecular interactions in RB/E2F pathway
Calzone, L., Gelay, A., Zinovyev, A., Radvanyi, F., & Barillot, E. (2008) · Molecular Systems Biology · doi:10.1038/msb.2008.7 · Cited by 132
Khymenets, O., Fitó, M., Covas, M.-I., Farré, M., Pujadas, M.-A., Muñoz, D., Konstantinidou, V., & Torre, R. D. L. (2009) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2008.0079 · Cited by 68
Gene expression reveals overlap between normal aging and Alzheimer's disease genes
Avramopoulos, D., Szymanski, M., Wang, R., & Bassett, S. (2011) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2010.04.019 · Cited by 67
Zhang, L., Zhang, Z.-P., Zhang, X.-E., Lin, F.-S., & Ge, F. (2010) · Journal of Virology · doi:10.1128/jvi.00213-10 · Cited by 60
Metadata
- Authors
- Mi, H., Guo, N., Kejariwal, A., & Thomas, P. D.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-01-03
- Volume
- 35
- Issue
- Database
- Pages
- D247-D252
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2135252110
- Cited by
- 372
- References
- 2
- FWCI
- 13.38
- Type
- journal article
- Language
- en
- Open access
- gold
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