A publicly-accessible Cryptococcus genome database: annotation of the Cryptococcu

公开可访问的隐球菌基因组数据库：隐球菌的注释

• 批准号: 8601428
• 负责人: Gavin J Sherlock
• 金额: $ 7.79万
• 依托单位: UNIVERSITY OF CALIFORNIA RIVERSIDE
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-01-01 至 2014-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8601428
• 关键词: Acquired Immunodeficiency Syndrome; Animal Model; Aspergillus; Basidiomycota; Biogenesis; Biology; Breathing; Candida; Cell physiology; Cells; Collection; Columbidae; Communities; Complication; Cryptococcus; Cryptococcus neoformans; Cryptococcus neoformans infection; Crystallization; Data; Databases; Deposition; Disease; Environment; Epidemiologic Studies; Equipment and supply inventories; Eucalyptus; Funding; Future; Gene Deletion; Gene Expression Profiling; Gene Proteins; Genes; Genetic; Genetic Models; Genetic Screening; Genome; Genomics; Goals; Growth and Development function; HIV; Human; Human Genome; Immunocompetent; Immunocompromised Host; Individual; Infection; Knock-out; Knowledge; Lead; Link; Literature; Manuals; Manuscripts; Modeling; Molecular; Molecular Genetics; Names; Online Systems; Ontology; Organism; Pacific Northwest; Pathogenesis; Pathway interactions; Patients; Pattern; Phenotype; Prevention strategy; Process; Proteins; Publishing; RNA Interference; Reading; Reporting; Reproduction spores; Research; Research Personnel; Resources; Role; Saccharomyces; Saccharomyces cerevisiae; Serotyping; Sexual Development; Speed; Stress; System; Temperature; Therapeutic; Trees; Virulence; Work; Yeasts; capsule; comparative; comparative genomics; data integration; data mining; functional genomics; fungal genetics; fungus; gene function; genome annotation; genome database; genome sequencing; genome-wide; improved; insight; killings; knockout gene; mutant; pathogen; public health relevance; research study; response; therapeutic target; tool; transcriptome sequencing; web site; web-accessible

DESCRIPTION (provided by applicant): In this project we will provide a manual curation of the literature and gene function for the genomes of the human pathogenic fungus Cryptococcus neoformans and C. gattii. The summary of gene function from published literature, linked it to the genome annotation is a significant result, as it will enable more comprehensive understanding of the biology of the organism as a whole. While genome sequencing of multiple species and years of genetic experiments with Cryptococcus have provided a rich understanding of gene pathways for growth, development, and pathogenesis, the crystallization of this information into curated functions for most genes is lacking. C. neoformans is an effective model genetic system for fungal biology of Basidiomycetes and for investigating mechanisms of pathogenesis so this resource will have importance to a broad collection of researchers. Here we will generate a resource for the community of gene function annotations and linking genes to published literature made freely available through FungiDB, a web-based database with powerful tools for data querying. The two goals of this project are to create a high quality, manual-curated annotation of the function of Cryptococcus genes from the published literature and to make this information easy to search through a website that is connected to sequence information and comparative genomics tools. 1. Literature curation will be performed by an expert curator to associate functions and mutant phenotypes to genes in the 5 sequenced Cryptococcus genomes. Capturing information from published manuscripts will provide clear summary of findings from experiments and associate these functions and cellular roles with specific genes. Similar resources for Saccharomyces and Aspergillus have become essential tools for those research communities. 2. Provide a publically available and searchable website to the curated annotation. The captured knowledge from the manual curation will be deposited into FungiDB to provide researchers with access to data mining and search tools to identify patterns in their data from Cryptococcus genomes. FungiDB provides access to functional or comparative genomics data which will be combined with this new gene annotation information.

描述(由申请人提供)：在这个项目中，我们将为人类致病真菌新生隐球菌属和加蒂隐球菌属的基因组提供文献和基因功能的人工整理。从已发表的文献中总结基因功能，将其与基因组注释联系起来是一个重要的结果，因为它将使人们能够更全面地了解整个生物体的生物学。虽然多个物种的基因组测序和多年来对隐球菌的遗传实验已经为生长、发育和致病的基因途径提供了丰富的理解，但这些信息的结晶成大多数基因的精选功能是缺乏的。新生革兰氏杆菌是一种有效的 担子菌真菌生物学和致病机理研究的模式遗传系统，因此这一资源将对广大研究人员具有重要意义。在这里，我们将为基因功能注释社区生成一个资源，并将基因链接到通过FungiDB免费提供的出版文献，FungiDB是一个基于Web的数据库，具有强大的数据查询工具。该项目的两个目标是从已发表的文献中创建高质量的、人工精选的隐球菌基因功能注释，并使这些信息易于通过连接到序列信息和比较基因组学工具的网站进行搜索。1.将由专家馆长进行文献整理，将5个已测序的隐球菌基因组中的功能和突变表型与基因联系起来。从已发表的手稿中获取信息将提供实验结果的清晰总结，并将这些功能和细胞角色与特定基因联系起来。酵母菌和曲霉菌的类似资源已经成为这些研究社区的必要工具。2.为经过整理的注释提供一个可供公众使用和可搜索的网站。从人工筛选中捕获的知识将存储到FungiDB中，为研究人员提供访问数据挖掘和搜索工具的途径，以识别他们从隐球菌基因组中获得的数据模式。FungiDB提供对功能或比较基因组学数据的访问，这些数据将与这一新的基因注释信息结合在一起。