ARCHS4: Massive Mining of Publicly Available RNA Sequencing Data

ARCHS4：大规模挖掘公开的 RNA 测序数据

基本信息

批准号：
10814654
负责人：
Avi Ma'ayan
金额：
$ 15万
依托单位：
ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-09-01 至 2027-08-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10814654
关键词：
Advanced Development Antibody-drug conjugates Atlases CAR T cell therapy Cancerous Cell Line Cell secretion Cell surface Cells Child Communities Data Data Set Databases Development Disease Excision Feedback Funding Future Gene Expression Genes Genotype-Tissue Expression Project Goals Grant Human BioMolecular Atlas Program Human Gene Mapping Human body Immunotherapy Individual Mining Molecular Target Normal tissue morphology Ontology Organ Patients Physiology Process Protein Secretion Proteins Research Research Personnel Resources Surface The Cancer Genome Atlas Time Tissues Visualization Work bioinformatics tool cell type computerized data processing document outlines experience improved individual patient information organization knowledge integration neoplastic cell novel online resource protein expression repository single-cell RNA sequencing statistics transcriptome sequencing tumor web server

项目摘要

Summary This supplement project will contribute to the enhancement of the TragetRanger and GeneRanger web-based resources. The work will include: 1) Adding HuBMAP as an additional background atlas for GeneRanger and TargetRanger; 2) Providing the HuBMAP team with feedback about our experience with processing and utilizing the HuBMAP data for incorporation it in GeneRanger and TargetRanger; and 3) Upgrading GeneRanger and TargetRanger box plot visualizations to organize the information in ontological hierarchies that group together cells into tissues, and tissues into organs. The project will be a supplement to the NCI ITCR U24CA264250 grant that was funded to support the advanced development of the widely accessed resource ARCHS4. Data processed from ARCHS4 is already incorporated into GeneRanger and TargetRanger but it is currently not organized into hierarchies. In addition, TargetRanger is mainly useful for discovering novel targets for identifying and removing cancerous cells in tumors. Hence, the incorporation of HuBMAP data as normal tissue background will further strengthen our ability to distill useful targets for the removal of specific cells from tumors while causing minimal damages to normal healthy cells and tissues throughout the human body. Our goal is to make HuBMAP and ARCHS4 data more accessible to researchers while enabling comparisons with other atlasing projects. By processing and incorporating HuBMAP datasets into GeneRanger and TargetRanger resources, we can identify ways to improve the accessibility of HuBMAP data for others seeking to utilize it for analysis, and for adding value to bioinformatics tools and databases. We believe that this knowledge integration effort will enhance the utility of HuBMAP, ARCHS4, as well as GeneRanger and TargetRanger for the research community.

概括该补充项目将有助于增强基于网络的 TragetRanger 和 GeneRanger 资源。这项工作将包括：1) 添加 HuBMAP 作为 GeneRanger 的附加背景图集和目标游侠； 2) 向 HuBMAP 团队提供有关我们处理和利用经验的反馈用于将其合并到 GeneRanger 和 TargetRanger 中的 HuBMAP 数据； 3) 升级 GeneRanger 和 TargetRanger 箱线图可视化可将信息组织到组合在一起的本体层次结构中细胞分化为组织，组织分化为器官。该项目将作为 NCI ITCR U24CA264250 赠款的补充该资金用于支持广泛访问的资源 ARCHS4 的高级开发。数据从 ARCHS4 处理的数据已合并到 GeneRanger 和 TargetRanger 中，但目前尚未合并组织成层次结构。此外，TargetRanger主要用于发现新目标以识别并去除肿瘤中的癌细胞。因此，将 HuBMAP 数据纳入正常组织背景将进一步增强我们提取有用靶标的能力，以从肿瘤中去除特定细胞，同时引起对人体正常健康细胞和组织的损害最小。我们的目标是让HuBMAP 研究人员可以更轻松地访问 ARCHS4 数据，同时可以与其他图集项目进行比较。经过处理 HuBMAP 数据集并将其合并到 GeneRanger 和 TargetRanger 资源中，我们可以识别提高 HuBMAP 数据的可访问性的方法，供其他寻求利用该数据进行分析和添加的人使用对生物信息学工具和数据库的价值。我们相信，这种知识整合工作将增强 HuBMAP、ARCHS4 以及 GeneRanger 和 TargetRanger 对于研究界的实用性。