Gramene 2016: comparative plant genomics and pathway resources.
Gramene 2016: comparative plant genomics and pathway resources.
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DOI：
10.1093/nar/gkv1179
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发表时间：
2016-01-04
影响因子：
14.9
通讯作者：
Ware D
中科院分区：
文献类型：
--
作者：
Tello-Ruiz MK;Stein J;Wei S;Preece J;Olson A;Naithani S;Amarasinghe V;Dharmawardhana P;Jiao Y;Mulvaney J;Kumari S;Chougule K;Elser J;Wang B;Thomason J;Bolser DM;Kerhornou A;Walts B;Fonseca NA;Huerta L;Keays M;Tang YA;Parkinson H;Fabregat A;McKay S;Weiser J;D'Eustachio P;Stein L;Petryszak R;Kersey PJ;Jaiswal P;Ware D
Gramene （http://www.gramene.org）是一个用于比较作物和模式植物物种功能基因组学的在线资源。它的两个主要框架是基因组（与Ensembl Plants合作）和途径（植物反应组和档案BioCyc数据库）。自从上一次NAR更新以来，数据库网站采用了新的Drupal管理平台。基因组部分以39个完全组装的参考基因组为特色，这些基因组使用基于本体的注释和比较分析进行集成，并通过视觉和编程界面进行访问。其他的群体数据，如遗传变异、表达和甲基化，也绘制了基因组子集的图谱。Plant Reactome pathway portal （http://plantreactome.gramene.org）为分析植物代谢和调控途径提供了参考资源。除了200个经过筛选的水稻参考途径外，该门户网站还对33个植物物种进行了基于基因同源性的途径预测。基因组和通路浏览器都可以与EMBL-EBI的表达图谱接口，从而能够从植物的精心策划的表达研究中投影基线和差异表达数据。Gramene的档案网站（http://archive.gramene.org）继续提供以前报道的关于比较地图、标记和QTL的资源。为了进一步帮助我们的用户，我们还推出了一个每月直播的教育网络研讨会系列和一个带有视频教程的Gramene YouTube频道。
Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces. Additional community data, such as genetic variation, expression and methylation, are also mapped for a subset of genomes. The Plant Reactome pathway portal (http://plantreactome.gramene.org) provides a reference resource for analyzing plant metabolic and regulatory pathways. In addition to ∼200 curated rice reference pathways, the portal hosts gene homology-based pathway projections for 33 plant species. Both the genome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants. Gramene's archive website (http://archive.gramene.org) continues to provide previously reported resources on comparative maps, markers and QTL. To further aid our users, we have also introduced a live monthly educational webinar series and a Gramene YouTube channel carrying video tutorials.