The plant genome integrative explorer resource : PlantGenIE.org

dc.contributor.authorSundell, David
dc.contributor.authorMannapperuma, Chanaka
dc.contributor.authorNetotea, Sergiu
dc.contributor.authorDelhomme, Nicolas
dc.contributor.authorLin, Yao-Cheng
dc.contributor.authorSjodin, Andreas
dc.contributor.authorVan de Peer, Yves
dc.contributor.authorJansson, Stefan
dc.contributor.authorHvidsten, Torgeir R.
dc.contributor.authorStreet, Nathaniel R.
dc.date.accessioned2015-08-28T09:15:31Z
dc.date.available2015-08-28T09:15:31Z
dc.date.issued2015-12
dc.description.abstractAccessing 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.en_ZA
dc.description.librarianam2015en_ZA
dc.description.sponsorshipThis work was supported by funds from the Alice Wallenberg Foundation, the Swedish Research Council (VR), the Swedish Governmental Agency for Innovation Systems (Vinnova), the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (Formas), and the Swedish Foundation for Strategic Research (SSF), in part through the UPSC Berzelii Centre for Forest Biotechnology. NRS is supported by the Trees and Crops for the Future (TC4F) project.en_ZA
dc.description.urihttp://www.newphytologist.comen_ZA
dc.identifier.citationSundell, D, Mannapperuma, C, Netotea, S, Delhomme, N, Lin, Y-C, Sjodin, A, Van de Peer, Y, Jansson, S, Hvidsten, TR & Street, NR 2015, 'The plant genome integrative explorer resource : PlantGenIE.org', New Phytologist, vol. 208, no. 4, pp. 1149-1156..en_ZA
dc.identifier.issn0028-646X (print)
dc.identifier.issn1469-813X (online)
dc.identifier.other10.1111/nph.13557
dc.identifier.urihttp://hdl.handle.net/2263/49643
dc.language.isoenen_ZA
dc.publisherWileyen_ZA
dc.rights© 2015 The Authors. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.en_ZA
dc.subjectAnnotationen_ZA
dc.subjectCoexpressionen_ZA
dc.subjectConiferen_ZA
dc.subjectDatabaseen_ZA
dc.subjectGenome browseren_ZA
dc.subjectPopulusen_ZA
dc.subjectTranscriptomicsen_ZA
dc.subjectWeb resourceen_ZA
dc.titleThe plant genome integrative explorer resource : PlantGenIE.orgen_ZA
dc.typeArticleen_ZA

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