PLEXdb: Plant Expression Database

爱荷华州立大学被授予启动PLEXdb（植物表达数据库）的拨款，这是一个统一的、符合miame标准的大规模植物基因表达数据公共资源。目前，在植物群落中还没有将数量迅速增加的基因表达谱数据集与传统的结构基因组学和表型数据相结合的资源。PLEXdb的目标是为这样的社区工作提供电子框架。用户将从多个相互关联的来源执行假设构建查询，例如特定基因，蛋白质类，EST条目，物理或遗传图谱位置-所有这些都与来自各种作物和模式植物物种的并行表达数据相耦合。数据将链接到分析和生物学功能（例如，BLAST，拼接比对，多重比对，调控基序鉴定和表达分析）。用户反馈将通过网络和通过pi与用户社区的联系征求，并纳入数据库界面。由于这种综合的国家和国际努力，高通量平行表达实验的分析将有助于为新一代功能实验建立智能假设。PLEXdb将提供一个重要的公共资源，作为通过转录（最终是蛋白质和代谢物）分析从序列到特征本体的桥梁。潜在的前提是，这些分子水平的表型表现为植物育种者选择的性状，并将导致食物和营养的改善。通过积极参与爱荷华州立大学生物信息学和计算生物学的NSF-NIH生物工程和生物信息学暑期研究所（BBSI），那些可能没有机会参与本国机构研究的科学本科生将参与其中，特别是来自代表性不足的群体。对中学生的拓展将包括通过NSF-RET计划在我们的实验室接待7-12年级的生物教师进行暑期实习。PLEXdb是一个多学科项目，将为研究生和博士后研究人员提供指导本科生和教师实习生的机会。

Iowa State University is awarded a grant to launch PLEXdb (Plant Expression Database), a unified, MIAME-compliant public resource for large-scale plant gene expression data. Currently, there is no resource in the plant community that integrates the rapidly expanding number of gene expression profile data sets with traditional structural genomics and phenotypic data. The goal for PLEXdb is to provide the electronic framework for such community effort. Users will perform hypothesis-building queries from multiple interlinked sources, e.g. a particular gene, a protein class, EST entries, physical or genetic map position - all coupled to parallel expression data from a variety of crop and model plant species. Data will be linked to analytical and biological functions (e.g., BLAST, spliced alignment, multiple alignment, regulatory motif identification, and expression analysis). User feedback will be solicited via the web and through connections of the PIs with the user community and incorporated into the database interface. As a result of this integrated national and international effort, analysis of high-throughput parallel expression experiments will help build intelligent hypotheses for a new generation of functional experiments. PLEXdb will provide an essential public resource that serves as a bridge from sequence to trait ontology through transcript (and eventually protein and metabolite) profiling. The underlying premise is that these molecular level phenotypes manifest as traits plant breeders select for and will lead to improvements in food and nutrition. Through active participation in the NSF-NIH Bioengineering and Bioinformatics Summer Institute (BBSI) in Bioinformatics and Computational Biology at Iowa State University, science-bound undergraduates will be involved who may not have the opportunity to participate in research at their home institutions, particularly from underrepresented groups. Outreach to secondary school students will include hosting grade 7-12 biology teachers in our laboratories for summer internships through the NSF-RET program. PLEXdb is a multi-disciplinary project that will provide graduate students and postdoctoral researchers opportunities to mentor undergraduate and teacher interns.