The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome
The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome
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DOI：
10.1111/j.1469-8137.2009.02807.x
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发表时间：
2009-01-01
期刊：
影响因子：
9.4
通讯作者：
Jansson, Stefan
中科院分区：
文献类型：
--
作者：
Sjodin, Andreas;Street, Nathaniel Robert;Jansson, Stefan
胡杨已成为重要的模式植物系统。然而，由于缺乏模型生物数据库（MOD）等中央资源，目前对社区创建的日益广泛的遗传学和基因组学数据的利用受到阻碍。此类 MOD 提供了模型系统内可用资源集合的单一入口点，通常包括用于探索和查询这些资源的工具。作为克服杨树缺乏此类 MOD 的起点，我们推出了杨树基因组综合浏览器 (PopGenIE)，这是一套用于探索杨树基因组和转录组的集成工具。该资源包括用于探索遗传数据的基因组、同线性和数量性状基因座 (QTL) 浏览器。表达工具包括电子荧光象形文字 (eFP) 浏览器、表达谱图、整理的转录组数据集中的共同调节以及过度代表性的功能类别和基因组热点位置的识别。 eFP 浏览器中提供了许多整理的转录组数据集，以促进基因功能的功能探索。提供了额外的同源性和数据提取工具。PopGenIE 显着提高了杨树基因组学资源的可访问性，并允许探索转录组学数据，而无需学习或理解复杂的统计分析方法。 PopGenIE 可在 www.popgenie.org 或通过 www.popgenie.org 获取。杨树基因组。信息。
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 www.popgenie.org or via www. populusgenome. info.