title: The Plant Genome Integrative Explorer Resource: PlantGenIE.org.
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.
authors.affiliation: Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-907 81, Umeå, Sweden.|Computational Life Science Cluster (CLiC), Umeå University, SE-907 81, Umeå, Sweden.
authors.forename: David
authors.initials: D
authors.lastname: Sundell
authors.affiliation: Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-907 81, Umeå, Sweden.
authors.forename: Chanaka
authors.initials: C
authors.lastname: Mannapperuma
authors.affiliation: Computational Life Science Cluster (CLiC), Umeå University, SE-907 81, Umeå, Sweden.
authors.forename: Sergiu
authors.initials: S
authors.lastname: Netotea
authors.affiliation: Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-907 81, Umeå, Sweden.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Delhomme
authors.affiliation: Department of Plant Systems Biology, VIB, Ghent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
authors.forename: Yao-Cheng
authors.initials: YC
authors.lastname: Lin
authors.affiliation: Computational Life Science Cluster (CLiC), Umeå University, SE-907 81, Umeå, Sweden.|Department of Chemistry, Umeå University, SE-907 81, Umeå, Sweden.
authors.forename: Andreas
authors.initials: A
authors.lastname: Sjödin
authors.affiliation: Department of Plant Systems Biology, VIB, Ghent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.|Genomics Research Institute, University of Pretoria, Hatfield Campus, 0028, Pretoria, South Africa.
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
authors.affiliation: Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-907 81, Umeå, Sweden.
authors.forename: Stefan
authors.initials: S
authors.lastname: Jansson
authors.affiliation: Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-907 81, Umeå, Sweden.|Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway.
authors.forename: Torgeir R
authors.initials: TR
authors.lastname: Hvidsten
authors.affiliation: Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-907 81, Umeå, Sweden.|Computational Life Science Cluster (CLiC), Umeå University, SE-907 81, Umeå, Sweden.
authors.forename: Nathaniel R
authors.initials: NR
authors.lastname: Street
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D019295:Computational Biology; D016208:Databases, Factual; D065928:Forests; D015870:Gene Expression; D017343:Genes, Plant; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D020407:Internet; D008954:Models, Biological; D032107:Populus / Q000235:genetics*; D018749:RNA, Plant; D017422:Sequence Analysis, DNA; D064028:Tracheophyta / Q000235:genetics*; D014197:Trees / Q000235:genetics*
chemical_list: D018749:RNA, Plant
keywords: Populus; annotation; coexpression; conifer; database; genome browser; transcriptomics; web resource