Research article2015Peer reviewedOpen access
The Plant Genome Integrative Explorer Resource: PlantGenIE.org
Sundell, David; Mannapperuma, Chanaka; Netotea, Sergiu; Delhomme, Nicolas; Lin, Yao-Cheng; Sjödin, Andreas; Van de Peer, Yves; Jansson, Stefan; Hvidsten, Torgeir R.; Street, Nathaniel R.
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
annotation; coexpression; conifer; database; genome browser; Populus; transcriptomics; web resource
Published in
New Phytologist
2015, Volume: 208, number: 4, pages: 1149-1156
Publisher: WILEY-BLACKWELL
UKÄ Subject classification
Forest Science
Publication identifier
DOI: https://doi.org/10.1111/nph.13557
Permanent link to this page (URI)
https://res.slu.se/id/publ/80808