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The plant genome integrative explorer resource : PlantGenIE.org

David Sundell, Chanaka Mannapperuma, Sergiu Netotea, Nicolas Delhomme, Yao-Cheng Lin (UGent) , Andreas Sjödin, Yves Van de Peer (UGent) , Stefan Jansson, Torgeir R Hvidsten and Nathaniel R Street
(2015) NEW PHYTOLOGIST. 208(4). p.1149-1156
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Abstract
Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, BLAST homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the COMPLEX resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.
Keywords
SEQUENCE, BIOLOGY, NETWORKS, DATABASE, SYSTEM, ANNOTATION, POPULUS, BROWSER, ARABIDOPSIS-THALIANA, GENE-EXPRESSION, web resource, transcriptomics, Populus, genome browser, database, annotation, conifer, coexpression

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Citation

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MLA
Sundell, David, et al. “The Plant Genome Integrative Explorer Resource : PlantGenIE.Org.” NEW PHYTOLOGIST, vol. 208, no. 4, 2015, pp. 1149–56, doi:10.1111/nph.13557.
APA
Sundell, D., Mannapperuma, C., Netotea, S., Delhomme, N., Lin, Y.-C., Sjödin, A., … Street, N. R. (2015). The plant genome integrative explorer resource : PlantGenIE.org. NEW PHYTOLOGIST, 208(4), 1149–1156. https://doi.org/10.1111/nph.13557
Chicago author-date
Sundell, David, Chanaka Mannapperuma, Sergiu Netotea, Nicolas Delhomme, Yao-Cheng Lin, Andreas Sjödin, Yves Van de Peer, Stefan Jansson, Torgeir R Hvidsten, and Nathaniel R Street. 2015. “The Plant Genome Integrative Explorer Resource : PlantGenIE.Org.” NEW PHYTOLOGIST 208 (4): 1149–56. https://doi.org/10.1111/nph.13557.
Chicago author-date (all authors)
Sundell, David, Chanaka Mannapperuma, Sergiu Netotea, Nicolas Delhomme, Yao-Cheng Lin, Andreas Sjödin, Yves Van de Peer, Stefan Jansson, Torgeir R Hvidsten, and Nathaniel R Street. 2015. “The Plant Genome Integrative Explorer Resource : PlantGenIE.Org.” NEW PHYTOLOGIST 208 (4): 1149–1156. doi:10.1111/nph.13557.
Vancouver
1.
Sundell D, Mannapperuma C, Netotea S, Delhomme N, Lin Y-C, Sjödin A, et al. The plant genome integrative explorer resource : PlantGenIE.org. NEW PHYTOLOGIST. 2015;208(4):1149–56.
IEEE
[1]
D. Sundell et al., “The plant genome integrative explorer resource : PlantGenIE.org,” NEW PHYTOLOGIST, vol. 208, no. 4, pp. 1149–1156, 2015.
@article{7035450,
  abstract     = {{Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. 
We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, BLAST homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. 
We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the COMPLEX resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. 
The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.}},
  author       = {{Sundell, David and Mannapperuma, Chanaka and Netotea, Sergiu and Delhomme, Nicolas and Lin, Yao-Cheng and Sjödin, Andreas and Van de Peer, Yves and Jansson, Stefan and Hvidsten, Torgeir R and Street, Nathaniel R}},
  issn         = {{0028-646X}},
  journal      = {{NEW PHYTOLOGIST}},
  keywords     = {{SEQUENCE,BIOLOGY,NETWORKS,DATABASE,SYSTEM,ANNOTATION,POPULUS,BROWSER,ARABIDOPSIS-THALIANA,GENE-EXPRESSION,web resource,transcriptomics,Populus,genome browser,database,annotation,conifer,coexpression}},
  language     = {{eng}},
  number       = {{4}},
  pages        = {{1149--1156}},
  title        = {{The plant genome integrative explorer resource : PlantGenIE.org}},
  url          = {{http://doi.org/10.1111/nph.13557}},
  volume       = {{208}},
  year         = {{2015}},
}
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