ABI Development: Gene function visualization and inference across all plants

ABI 开发：所有植物的基因功能可视化和推理

• 批准号: 1661543
• 负责人: Eva Huala
• 金额: $ 126.12万
• 依托单位: Phoenix Bioinformatics Corporation
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-01-01 至 2020-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1661543&HistoricalAwards=false
• 关键词: ABI; Development; Gene; function; visualization

Addressing the food needs of an increasing global population in the 21st century will require significant improvements in agriculture akin to the Green Revolution of the previous century. To address this goal it is of critical importance to understand as much as possible about the functions of the tens of thousands of genes present in each plant species, in order to select those functions of most relevance to engineering favorable traits such as drought tolerance or increased grain quality. Much of what is currently known about plant gene function comes from experiments in model plant systems such as Arabidopsis thaliana, but because of evolutionary relatedness this information can be used to predict the functions of genes in crop species such as maize and rice, and to provide targeted hypotheses that can be followed up by further experiments. This project will increase both the efficiency and accuracy of gene function prediction in plants by organizing and integrating high quality data from a number of sources and presenting it in a user-friendly format that makes clear the evolutionary relationships between genes. The team will develop software for visualizing the evolutionary relationships as a gene family tree, providing an organizing framework for disparate experimental observations from a number of experimental systems. The project will provide software for use, and for data sharing, by a broad community of both researchers and students. The project?s inclusion of local community college students will provide training and increase participation in computer science, genomics and plant biology by groups that are underrepresented in these fields.The project output will be a powerful and intuitive software tool for inferring plant gene function from phylogenetic relationships and experimental evidence. To achieve this goal the project aims are to: 1) assemble sets of phylogenetic trees using selected model organism and plant genomes, along with a suite of web services to ensure easy access to the data; 2) follow user-driven design principles to design and build the user interface, in order to visualize the phylogenetic trees and associate the genes within each tree with high quality functional information including Gene Ontology annotations, gene expression patterns, protein domains, sequence variations and mutant phenotypes; 3) provide an analysis platform that streamlines workflows and includes personal workspaces for users to add their own data and make it public when their work is completed, thus enriching the knowledgebase; and 4) produce workshops, course materials and online content to train scientists at all academic levels on how to use the software. The results of the project will be available at http://www.phoenixbioinformatics.org/treevision/.

要满足21世纪日益增长的全球人口的粮食需求，就需要像上个世纪的绿色革命那样，对农业进行重大改进。为了实现这一目标，尽可能多地了解每个植物物种中存在的数万个基因的功能至关重要，以便选择与工程有利性状（如耐旱性或提高谷物品质）最相关的功能。 目前对植物基因功能的大部分了解来自模式植物系统（如拟南芥）的实验，但由于进化相关性，这些信息可用于预测作物物种（如玉米和水稻）中基因的功能，并提供有针对性的假设，可以通过进一步的实验进行后续研究。 该项目将通过组织和整合来自多个来源的高质量数据，并以用户友好的格式呈现，从而明确基因之间的进化关系，从而提高植物基因功能预测的效率和准确性。 该团队将开发软件，将进化关系可视化为基因家族树，为来自许多实验系统的不同实验观察提供组织框架。 该项目将提供软件供广大研究人员和学生使用和共享数据。 项目？该项目的结果将是一个强大而直观的软件工具，用于从系统发育关系和实验证据推断植物基因功能。 为了实现这一目标，该项目的目标是：1）使用选定的模式生物和植物基因组组装系统发育树，沿着一套网络服务，以确保轻松访问数据; 2）遵循用户驱动的设计原则来设计和构建用户界面，为了可视化系统发育树，并将每个树中的基因与包括基因本体在内的高质量功能信息相关联，该软件包括：（1）提供一个分析平台，用于分析基因注释、基因表达模式、蛋白质结构域、序列变异和突变表型;（2）提供一个分析平台，简化工作流程，并包括个人指南，供用户添加自己的数据，并在工作完成后公布，从而丰富知识库;（3）举办讲习班、编写课程材料和在线内容，培训各级学术科学家如何使用该软件。该项目的结果将在http://www.phoenixbioinformatics.org/treevision/上公布。