ARCHS4: Massive Mining of Publicly Available RNA Sequencing Data

Icahn School Of Medicine At Mount Sinai, New York NY

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Abstract

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.