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.

抽象的 该申请是根据特殊利益通知（NOSI）提交的 被确定为非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 与组织结构有关。各种ST技术，例如10倍基因组学景观和 纳米弦GEOMX DSP已提高了我们的知识，但是结果数据很大，复杂， 并且产生昂贵。研究人员之间的合作和数据共享 这些数据可以极大地使科学界受益。但是，挑战之类的困难 分析来自不同平台的数据以及计算和管理负担 下载大型数据集当前阻碍了有效的协作。为了解决这些问题， 我们提出了原型空间转录组学探索器（Ste）的开发，一个模块化， 用户友好的应用程序可视化癌症生物学（DCB）内的ST数据 财团。 Ste将提供平台不合时宜的开源可视化资源，兼容 带有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患病和地区的基因或地区 正常组织。在DCB财团中广泛地部署该资源将提供有价值的 具有不同计算专业知识的研究人员和临床医生的工具，促进包容性 空间转录组学中的数据共享和加速发现。