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PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees
Open accessAbstract
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.
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Cited by
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Reimand, J., Isserlin, R., Voisin, V., Kucera, M., Tannus-Lopes, C., Rostamianfar, A., Wadi, L., Meyer, M., Wong, J., Xu, C., et al. (2019) · Nature Protocols · doi:10.1038/s41596-018-0103-9 · Cited by 1,970
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Self-citationThe BioPlex network: a systematic exploration of the human interactome
Huttlin, E. L., Ting, L., Bruckner, R. J., Gebreab, F., Gygi, M. P., Szpyt, J., Tam, S., Zarraga, G., Colby, G., Baltier, K., et al. (2015) · Cell · doi:10.1016/j.cell.2015.06.043 · Cited by 1,425
“Functional classification using PANTHER (Mi et al., 2013) in conjunction with all UniProt proteins (Magrane and Consortium, 2011) revealed a distribution of baits and preys that closely matched UniProt functional categories (Figure 2D).”
Metadata
- Authors
- Mi, H., Muruganujan, A., & Thomas, P. D.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-11-26
- Volume
- 41
- Issue
- D1
- Pages
- D377-D386
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2022472106
- Cited by
- 1,733
- References
- 6
- FWCI
- 48.68
- Type
- journal article
- Language
- en
- Open access
- gold
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