The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome Export

@article{citeulike:4185555, abstract = {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. New Phytologist (2009) 182 101320131025doi: 10.1111/j.1469-8137.2009.02807.x}, address = {Ume Plant Science Centre, Department of Plant Physiology, University of Ume, SE-901-87 Ume, Sweden; ; CBRN Security and Defence, Swedish Defence Research Agency, SE-90182 Ume, Sweden}, author = {Sj\"{o}din, Andreas and Street, Nathaniel R. and Sandberg, G\"{o}ran and Gustafsson, Petter and Jansson, Stefan}, citeulike-article-id = {4185555}, citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1469-8137.2009.02807.x}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19383103}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19383103}, citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/122264549/ABSTRACT}, doi = {10.1111/j.1469-8137.2009.02807.x}, issn = {1469-8137}, journal = {New Phytologist}, number = {4}, pages = {1013--1025}, posted-at = {2009-03-17 12:50:02}, priority = {2}, title = {The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome}, url = {http://dx.doi.org/10.1111/j.1469-8137.2009.02807.x}, volume = {182}, year = {2009} }

TY - JOUR ID - citeulike:4185555 L3 - citeulike-article-id:4185555 N2 - 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. New Phytologist (2009) 182 101320131025doi: 10.1111/j.1469-8137.2009.02807.x IS - 4 JF - New Phytologist SN - 1469-8137 AD - Ume Plant Science Centre, Department of Plant Physiology, University of Ume, SE-901-87 Ume, Sweden; ; CBRN Security and Defence, Swedish Defence Research Agency, SE-90182 Ume, Sweden EP - 1025 TI - The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome VL - 182 SP - 1013 AU - Sjödin, Andreas AU - Street, Nathaniel AU - Sandberg, Göran AU - Gustafsson, Petter AU - Jansson, Stefan PY - 2009/// UR - http://dx.doi.org/10.1111/j.1469-8137.2009.02807.x ER -