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The populus genome integrative explorer (PopGenIE): a new resource for exploring the populus genome
Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. (CBRN Defence and Security, FOI—Swedish Defence Research Agency, Cementvägen 20, 901 82 Umeå, Sweden)
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).ORCID iD: 0000-0001-6031-005X
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).ORCID iD: 0000-0002-2147-7428
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2009 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 182, no 4, 1013-1025 p.Article in journal (Refereed) Published
Abstract [en]

* Populus has become an important model plant system. However, utilization of the increasingly extensive collection of genetics and genomics data created by the community is currently hindered by the lack of a central resource, such as a model organism database (MOD). Such MODs offer a single entry point to the collection of resources available within a model system, typically including tools for exploring and querying those resources. * As a starting point to overcoming the lack of such an MOD for Populus, we present the Populus Genome Integrative Explorer (PopGenIE), an integrated set of tools for exploring the Populus genome and transcriptome. The resource includes genome, synteny and quantitative trait locus (QTL) browsers for exploring genetic data. * Expression tools include an electronic fluorescent pictograph (eFP) browser, expression profile plots, co-regulation within collated transcriptomics data sets, and identification of over-represented functional categories and genomic hotspot locations. A number of collated transcriptomics data sets are made available in the eFP browser to facilitate functional exploration of gene function. Additional homology and data extraction tools are provided. * PopGenIE significantly increases accessibility to Populus genomics resources and allows exploration of transcriptomics data without the need to learn or understand complex statistical analysis methods. PopGenIE is available at http://www.popgenie.org or via http://www.populusgenome.info.

Place, publisher, year, edition, pages
2009. Vol. 182, no 4, 1013-1025 p.
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:umu:diva-25706DOI: 10.1111/j.1469-8137.2009.02807.xPubMedID: 19383103OAI: oai:DiVA.org:umu-25706DiVA: diva2:233315
Available from: 2009-08-31 Created: 2009-08-31 Last updated: 2017-12-13Bibliographically approved

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Sjödin, AndreasStreet, Nathaniel RSandberg, GöranGustafsson, PetterJansson, Stefan
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