Spatial Transcriptomics Explorer (STE): An open-source resource for visualizing spatial gene expression data

Sage Bionetworks, Seattle WA

Investigators

Abstract

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.