The plant genome integrative explorer resource :

Show simple item record Sundell, David Mannapperuma, Chanaka Netotea, Sergiu Delhomme, Nicolas Lin, Yao-Cheng Sjodin, Andreas Van de Peer, Yves Jansson, Stefan Hvidsten, Torgeir R. Street, Nathaniel R. 2015-08-28T09:15:31Z 2015-08-28T09:15:31Z 2015-12
dc.description.abstract Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated 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 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.librarian am2015 en_ZA
dc.description.sponsorship This 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.uri en_ZA
dc.identifier.citation Sundell, 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 :', New Phytologist, vol. 208, no. 4, pp. 1149-1156.. en_ZA
dc.identifier.issn 0028-646X (print)
dc.identifier.issn 1469-813X (online)
dc.identifier.other 10.1111/nph.13557
dc.language.iso en en_ZA
dc.publisher Wiley en_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.subject Annotation en_ZA
dc.subject Coexpression en_ZA
dc.subject Conifer en_ZA
dc.subject Database en_ZA
dc.subject Genome browser en_ZA
dc.subject Populus en_ZA
dc.subject Transcriptomics en_ZA
dc.subject Web resource en_ZA
dc.title The plant genome integrative explorer resource : en_ZA
dc.type Article en_ZA

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