ARCHS4: Massive Mining of Publicly Available RNA Sequencing Data

ARCHS4：大规模挖掘公开的 RNA 测序数据

• 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
• 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

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.

总结 该补充项目将有助于增强基于网络的TracetRanger和GeneRanger 资源工作将包括：1）添加HuBMAP作为GeneRanger的额外背景图谱， TargetRanger; 2）向HuBMAP团队提供有关我们处理和利用经验的反馈 用于将其并入GeneRanger和TargetRanger的HuBMAP数据;以及3）升级GeneRanger， TargetRanger箱形图可视化，用于在分组在一起的本体层次结构中组织信息 细胞转化为组织，组织转化为器官。该项目将是NCI ITCR U24 CA 264250赠款的补充 这是资助支持广泛访问的资源ARCHS 4的高级开发。数据 从ARCHS 4处理的数据已经整合到GeneRanger和TargetRanger中，但目前还没有 组织成等级。此外，TargetRanger主要用于发现用于识别的新颖目标 以及移除肿瘤中的癌细胞。因此，将HuBMAP数据作为正常组织背景 这将进一步加强我们提取有用靶点的能力，用于从肿瘤中去除特定细胞， 对整个人体的正常健康细胞和组织的损害最小。我们的目标是让HuBMAP 和ARCHS 4数据更容易访问的研究人员，同时使比较与其他地图集项目。通过 处理HuBMAP数据集并将其整合到GeneRanger和TargetRanger资源中，我们可以识别 如何提高HuBMAP数据的可访问性，以供其他寻求利用其进行分析和添加的人使用 生物信息学工具和数据库的价值。我们相信，这一知识整合工作将提高 HuBMAP、ARCHS 4以及GeneRanger和TargetRanger在研究界的实用性。