Developing new computational tools for spatial transcriptomics data

开发空间转录组数据的新计算工具

• 批准号: 10278763
• 负责人: Mengjie Chen
• 金额: $ 39.73万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-16 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10278763
• 关键词: Achievement; Address; Algebra; Architecture; Awareness; Bioinformatics; Biological; Breast Cancer Patient; Case-Control Studies; Cell Culture Techniques; Clinical Research; Cohort Studies; Collection; Communities; Computer software; Data; Data Analyses; Data Set; Data Sources; Detection; Development; Dimensions; Disease; Event; Foundations; Gene Expression; Genes; Genomics; Goals; Health; Heterogeneity; Human; Image; Immune response; Investigation; Joints; Link; Location; Malignant Neoplasms; Measurement; Methodology; Methods; Neurodegenerative Disorders; Pattern; Performance; Phenotype; Postdoctoral Fellow; Property; Psychological Transfer; Resolution; Sample Size; Sampling; Slide; Software Tools; Structure; Technology; Tissue Sample; Tissues; Training; Treatment outcome; Validation; Variant; Work; base; bioinformatics infrastructure; cohort; computerized data processing; computerized tools; deep learning; deep neural network; digital; frontier; genomic data; histological image; innovation; learning strategy; multiple data sources; new technology; novel; open source; phase II trial; rapid detection; simulation; single-cell RNA sequencing; tissue culture; tool; transcriptomics; translational study; user friendly software; user-friendly

Project Summary Spatial transcriptomics is a groundbreaking new technology that allows measurement of gene ac- tivity in a tissue sample while mapping where the activity is occurring. It holds the promise to facilitate our understanding of spatial heterogeneity underlying essential phenotypes and diseases, such as neurodegenerative diseases and cancer. However, the development of bioinformatics infrastructures and computational tools has fallen seriously behind the technological advances. The lack of proper computational approaches presents current data analysis barriers that significantly hinder biological investigations. The overarching goal of this proposal is to address some of the most pressing ana- lytic challenges facing profiling and interpreting spatial transcriptomics data, including 1) lack of robust identification of genes with spatial expression patterns across a variety of technical platforms, 2) lack of tools to identify structures, microenvironments as well as developmental trajectory on the tissue, and 3) lack of tools that can jointly analyze spatial transcriptomic data across multiple samples and multiple data sources. In the proposal, we will work on the following aims: Aim 1. Develop nonpara- metric tools for identifying genes with spatial expression patterns. Aim 2. Develop spatially aware dimension reduction tools for detecting structures and developmental trajectories on the tissue. Aim 3. Develop integrative association tools for spatial transcriptomic analysis across multiple samples and datasets. All the methods will be implemented in user-friendly software and disseminated to the sci- entific community. Successful achievement of all aims will dramatically increase the power of spatial transcriptomics analysis, and facilitate the application of these cutting-edge technologies to transla- tional and clinical studies.

项目摘要 空间转录组学是一项突破性的新技术，可以测量基因ac- 在绘制活动发生的位置时，可以在组织样本中测量活动。它承诺促进 我们对基本表型和疾病的空间异质性的理解，例如 神经退行性疾病和癌症。然而，生物信息学基础设施的发展 计算工具已经严重落后于技术进步。缺乏适当的 计算方法提出了当前的数据分析障碍，这些障碍严重阻碍了生物学 调查事务所该提案的总体目标是解决一些最紧迫的问题， 分析和解释空间转录组学数据面临的裂解挑战，包括1）缺乏强大的 在各种技术平台上识别具有空间表达模式的基因，2）缺乏 用于识别组织结构、微环境以及发育轨迹的工具， 和3）缺乏可以跨多个样品联合分析空间转录组数据的工具， 多个数据源。在该提案中，我们将努力实现以下目标：目标1。发展非对位- 用于识别具有空间表达模式的基因的度量工具。目标2.开发空间感知 用于检测组织上的结构和发育轨迹的降维工具。目标3。 开发跨多个样品的空间转录组学分析的综合关联工具， 数据集。所有的方法将在用户友好的软件中实现，并分发给科学和技术研究所， 实体社区。所有目标的成功实现将大大增加空间的力量， 转录组学分析，并促进这些尖端技术的应用，以transla， 临床和临床研究。