The DOI matches its Crossref record; 64 of the 64 references it cites were found in a registry or an index.
PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants
Open accessAbstract
The number of sequenced genomes of representatives within the green lineage is rapidly increasing. Consequently, comparative sequence analysis has significantly altered our view on the complexity of genome organization, gene function, and regulatory pathways. To explore all this genome information, a centralized infrastructure is required where all data generated by different sequencing initiatives is integrated and combined with advanced methods for data mining. Here, we describe PLAZA, an online platform for plant comparative genomics (http://bioinformatics.psb.ugent.be/plaza/). This resource integrates structural and functional annotation of published plant genomes together with a large set of interactive tools to study gene function and gene and genome evolution. Precomputed data sets cover homologous gene families, multiple sequence alignments, phylogenetic trees, intraspecies whole-genome dot plots, and genomic colinearity between species. Through the integration of high confidence Gene Ontology annotations and tree-based orthology between related species, thousands of genes lacking any functional description are functionally annotated. Advanced query systems, as well as multiple interactive visualization tools, are available through a user-friendly and intuitive Web interface. In addition, detailed documentation and tutorials introduce the different tools, while the workbench provides an efficient means to analyze user-defined gene sets through PLAZA's interface. In conclusion, PLAZA provides a comprehensible and up-to-date research environment to aid researchers in the exploration of genome information within the green plant lineage.
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Cites
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Self-citationThe map-based sequence of the rice genome
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Cited by
Mittler, R., Vanderauwera, S., Suzuki, N., Miller, G., Tognetti, V. B., Vandepoele, K., Gollery, M., Shulaev, V., & Van Breusegem, F. (2011) · Trends in Plant Science · doi:10.1016/j.tplants.2011.03.007 · Cited by 2,305
Self-citationThe genome sequence of the orchid Phalaenopsis equestris
Cai, J., Liu, X., Vanneste, K., Proost, S., Tsai, W.-C., Liu, K.-W., Chen, L.-J., He, Y., Xu, Q., Bian, C., et al. (2015) · Nature Genetics · doi:10.1038/ng.3149 · Cited by 480
Self-citationPLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics
Van Bel, M., Diels, T., Vancaester, E., Kreft, L., Botzki, A., Van de Peer, Y., Coppens, F., & Vandepoele, K. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1002 · Cited by 450
Self-citationThe Legume Phylogeny Working Group, Bruneau, A., Doyle, J. J., Herendeen, P., Hughes, C., Kenicer, G., Lewis, G., Mackinder, B., Pennington, R. T., Sanderson, M. J., et al. (2013) · TAXON · doi:10.12705/622.8 · Cited by 437
PLAZA 3.0: an access point for plant comparative genomics
Proost, S., Van Bel, M., Vaneechoutte, D., Van de Peer, Y., Inzé, D., Mueller-Roeber, B., & Vandepoele, K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku986 · Cited by 317
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Metadata
- Authors
- Proost, S., Van Bel, M., Sterck, L., Billiau, K., Van Parys, T., Van de Peer, Y., & Vandepoele, K.
- Venue
- The Plant Cell
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-12-01
- Volume
- 21
- Issue
- 12
- Pages
- 3718-3731
- ISSN
- 1040-4651 (ISSN-L)
- 1532-298X
- OpenAlex
- W2151404319
- Cited by
- 287
- References
- 64
- FWCI
- 9.48
- Type
- journal article
- Language
- en
- Open access
- bronze
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