Enhanced Echinobase: A Community Genomics Research Resource For The Future

增强型 Echinobase：未来的社区基因组学研究资源

• 批准号: 10715578
• 负责人: CHARLES A. ETTENSOHN
• 金额: $ 78.69万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-22 至 2028-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10715578
• 关键词: ATAC-seq; Access to Information; Address; Atlases; Biological Models; Cells; Code; Communication; Communities; Computer software; Consultations; Consumption; Controlled Vocabulary; DNA methylation profiling; Data; Databases; Development; Developmental Gene; Disease; EchinoBase; Echinodermata; Embryonic Development; Experimental Models; FAIR principles; Fostering; Funding; Future; Gene Expression; Genes; Genetic Transcription; Genome; Genomics; Goals; Health; Human; Infrastructure; Investments; Knowledge; Letters; Link; Logic; Mission; Names; Nomenclature; Ontology; Organism; Pattern; Performance; Play; Process; Research; Research Personnel; Resources; Role; Sea Urchins; Systems Analysis; Taxonomy; Time; Tissues; United States National Institutes of Health; Untranslated RNA; Update; Visualization software; Work; XCL1 gene; XenBase; base; bioinformatics tool; cost; data integration; data management; data mining; data sharing; design; empowerment; gene regulatory network; genome resource; genomic data; improved; interoperability; knowledge base; knowledgebase; model organism; ontology development; predictive modeling; relational database; repository; tool; transcriptome sequencing; usability; user-friendly; web app; web site; web-accessible

SUMMARY OF OVERALL COMPONENT Enhanced Echinobase: A Community Genomics Research Resource for the Future Echinobase (Echinobase.org) is the central repository and web-accessible resource for all of the diverse genomic data types produced by biologists working with echinoderms. Echinobase was cloned from Xenbase to enhance database functionality, web application capabilities, and performance, all at a fraction of the cost of doing this independently. A key added feature developed through this work are database modules that support curation and searches of gene expression data. The look and feel of Echinobase is unique, and is tailored to its user base including the creation of a multi-species viewer. The website provides rapid integrated capabilities for search, view and download of a range of datatypes to empower their own research. Echinoderms are one of only three major phyla within the deuterostomes, and therefore the species within this clade encompass a large taxonomic diversity of body plans. Species of echinoderms are powerful model systems for understanding the processes by which the genome controls development. The strengths of this experimental model will continue to make it a preeminent system for the analysis of the genomic control of embryogenesis and for analyses of developmental gene regulatory networks (GRNs) to reveal the mechanistic links between the genome and development and consequently the genomic basis of congenital diseases.

总体组成部分总结 增强的Echinobase：未来的社区基因组学研究资源 Echinobase（Echinobase.org）是所有不同的 由研究棘皮动物的生物学家制作的基因组数据类型。Echinobase从Xenbase克隆 增强数据库功能、Web应用程序功能和性能，而所有这些的成本都是 独立做这件事。通过这项工作开发的一个关键的附加功能是数据库模块， 基因表达数据的管理和搜索。Echinobase的外观和感觉是独一无二的，并且是根据其 用户群，包括创建一个多物种的观众。网站提供快速集成功能 搜索，查看和下载一系列数据库，以增强自己的研究能力。棘皮动物是一种 只有三个主要门内的后口，因此，在这个分支的物种包括一个 身体计划的巨大分类多样性。棘皮动物的物种是强大的模型系统， 了解基因组控制发育的过程。这个实验的优势 该模型将继续使其成为分析胚胎发生基因组控制的卓越系统 并用于分析发育基因调控网络（GRNs），以揭示 基因组和发育以及先天性疾病的基因组基础。

项目成果

Genome-wide identification and spatiotemporal expression analysis of cadherin superfamily members in echinoderms.

• DOI: 10.1186/s13227-023-00219-7
• 发表时间: 2023-12-20
• 期刊: EvoDevo
• 影响因子: 4.1

Evolutionary analyses of genes in Echinodermata offer insights towards the origin of metazoan phyla.

• DOI: 10.1016/j.ygeno.2022.110431
• 发表时间: 2022-07
• 期刊: GENOMICS
• 影响因子: 4.4
• 作者: Foley, Saoirse;Vlasova, Anna;Marcet-Houben, Marina;Gabaldon, Toni;Hinman, Veronica F.
• 通讯作者: Hinman, Veronica F.

A nomenclature for echinoderm genes.

• DOI: 10.1093/database/baab052
• 发表时间: 2021-08-07
• 期刊: Database : the journal of biological databases and curation
• 作者: Beatman TR;Buckley KM;Cary GA;Hinman VF;Ettensohn CA
• 通讯作者: Ettensohn CA

Integration of 1:1 orthology maps and updated datasets into Echinobase.

• DOI: 10.1093/database/baab030
• 发表时间: 2021-05-19
• 期刊: Database : the journal of biological databases and curation
• 作者: Foley S;Ku C;Arshinoff B;Lotay V;Karimi K;Vize PD;Hinman V
• 通讯作者: Hinman V

Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms.

• DOI: 10.1093/nar/gkab1005
• 发表时间: 2022-01-07
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Arshinoff BI;Cary GA;Karimi K;Foley S;Agalakov S;Delgado F;Lotay VS;Ku CJ;Pells TJ;Beatman TR;Kim E;Cameron RA;Vize PD;Telmer CA;Croce JC;Ettensohn CA;Hinman VF
• 通讯作者: Hinman VF