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PLAZA: a comparative genomics resource to study gene and genome evolution in plants

Sebastian Proost UGent, Michiel Van Bel UGent, Lieven Sterck UGent, Kenny Billiau UGent, Thomas Van Parys UGent, Yves Van de Peer UGent and Klaas Vandepoele UGent (2009) PLANT CELL. 21(12). p.3718-3731
abstract
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
PLATFORM, DATABASE, SEQUENCE, WHOLE-GENOME, HIGH-THROUGHPUT, REGULATORY ELEMENTS, ARABIDOPSIS-THALIANA, BIOLOGY, HISTONE GENES, TRANSCRIPTION
journal title
PLANT CELL
Plant Cell
volume
21
issue
12
pages
3718 - 3731
Web of Science type
Article
Web of Science id
000274196000003
JCR category
PLANT SCIENCES
JCR impact factor
9.293 (2009)
JCR rank
5/172 (2009)
JCR quartile
1 (2009)
ISSN
1040-4651
DOI
10.1105/tpc.109.071506
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
873589
handle
http://hdl.handle.net/1854/LU-873589
date created
2010-02-22 14:57:43
date last changed
2012-12-18 13:42:17
@article{873589,
  abstract     = {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.},
  author       = {Proost, Sebastian and Van Bel, Michiel and Sterck, Lieven and Billiau, Kenny and Van Parys, Thomas and Van de Peer, Yves and Vandepoele, Klaas},
  issn         = {1040-4651},
  journal      = {PLANT CELL},
  keyword      = {PLATFORM,DATABASE,SEQUENCE,WHOLE-GENOME,HIGH-THROUGHPUT,REGULATORY ELEMENTS,ARABIDOPSIS-THALIANA,BIOLOGY,HISTONE GENES,TRANSCRIPTION},
  language     = {eng},
  number       = {12},
  pages        = {3718--3731},
  title        = {PLAZA: a comparative genomics resource to study gene and genome evolution in plants},
  url          = {http://dx.doi.org/10.1105/tpc.109.071506},
  volume       = {21},
  year         = {2009},
}

Chicago
Proost, Sebastian, Michiel Van Bel, Lieven Sterck, Kenny Billiau, Thomas Van Parys, Yves Van de Peer, and Klaas Vandepoele. 2009. “PLAZA: a Comparative Genomics Resource to Study Gene and Genome Evolution in Plants.” Plant Cell 21 (12): 3718–3731.
APA
Proost, S., Van Bel, M., Sterck, L., Billiau, K., Van Parys, T., Van de Peer, Y., & Vandepoele, K. (2009). PLAZA: a comparative genomics resource to study gene and genome evolution in plants. PLANT CELL, 21(12), 3718–3731.
Vancouver
1.
Proost S, Van Bel M, Sterck L, Billiau K, Van Parys T, Van de Peer Y, et al. PLAZA: a comparative genomics resource to study gene and genome evolution in plants. PLANT CELL. 2009;21(12):3718–31.
MLA
Proost, Sebastian, Michiel Van Bel, Lieven Sterck, et al. “PLAZA: a Comparative Genomics Resource to Study Gene and Genome Evolution in Plants.” PLANT CELL 21.12 (2009): 3718–3731. Print.