Spatial Transcriptomics Explorer (STE): An open-source resource for visualizing spatial gene expression data

Spatial Transcriptomics Explorer (STE)：用于可视化空间基因表达数据的开源资源

• 批准号: 10830668
• 负责人: Julie Ann Bletz
• 金额: $ 15.25万
• 依托单位: SAGE BIONETWORKS
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-14 至 2027-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10830668
• 关键词: Acceleration; Address; Architecture; Area; Clinical; Collaborations; Communities; Complex; Data; Data Set; Development; Disease; Division of Cancer Biology; Ensure; Fostering; Foundations; Future; Gene Expression; Gene Expression Profile; Generations; Genes; Genomics; Image; Investigation; Knowledge; Malignant Neoplasms; Metadata; Methodology; Multimodal Imaging; Normal tissue morphology; Play; Research; Research Personnel; Resources; Sampling; Services; Side; Standardization; Techniques; Technology; Testing; Tissues; Visualization; Visualization software; access restrictions; cancer genomics; cohort; complex data; computerized data processing; computing resources; cost; data access; data modeling; data sharing; data visualization; design; experience; genomics cloud; image visualization; insight; interest; large datasets; multidimensional data; nano-string; open source; prototype; repository; response; spatial integration; tool; transcriptomics; user-friendly; web app

Abstract This application is being submitted in response to the Notice of Special Interest (NOSI) identified as NOT-CA-23-045. Spatial transcriptomics (ST) is transforming our understanding of gene expression patterns in relation to tissue architecture. Various ST techniques such as 10x Genomics Visium and Nanostring GeoMx DSP have advanced our knowledge, but the resulting data is large, complex, and costly to generate. Collaborations and data sharing among researchers with respect to these data can greatly benefit the scientific community. However, challenges like difficulties in analyzing data from different platforms and the computational and administrative burden of downloading large datasets currently hinder effective collaborations. To address these issues, we propose the development of a prototype Spatial Transcriptomics Explorer (STE), a modular, user-friendly application for visualizing ST data within various Division of Cancer Biology (DCB) consortia. STE will offer a platform-agnostic, open-source visualization resource, compatible with data from multiple platforms. Through the cohort builder, gene-based query, and spatial query modules, the STE will help researchers quickly examine genes or regions in diseased and normal tissues. Deployment of this resource widely in the DCB consortia will provide a valuable tool for researchers and clinicians with varying computational expertise, promoting inclusive data sharing and accelerating discoveries in spatial transcriptomics.

摘要 本申请是根据特别利益通知（NOSI）提交的。 标识为NOT-CA-23-045。 空间转录组学（ST）正在改变我们对基因表达模式的理解， 与组织结构的关系。各种ST技术，如10 x Genomics Visium和 Nanostring GeoMx DSP推进了我们的知识，但产生的数据是大的，复杂的， 而且成本高昂。研究人员之间的合作和数据共享， 这些数据可使科学界受益匪浅。然而，挑战，如困难， 分析来自不同平台的数据， 下载大型数据集目前阻碍了有效的协作。为了解决这些问题， 我们建议开发一个原型空间转录组学探索者（STE），一个模块化的， 用户友好的应用程序，用于可视化癌症生物学（DCB）各部门的ST数据 财团。STE将提供与平台无关的开源可视化资源， 来自多个平台的数据。通过队列构建器、基于基因的查询和空间 查询模块，STE将帮助研究人员快速检查基因或区域， 正常组织在DCB联盟中广泛部署此资源将提供 为具有不同计算专业知识的研究人员和临床医生提供的工具， 数据共享和加速空间转录组学的发现。