Current Bioinformatics Seminar
Time: 11AM Tuesdays.
Venue: Davis Auditorium and Online
18 March 2025
This is a WEHI only event.Gene set testing for spatial transcriptomics data
Melody JinWEHI Bioinformatics
Spatial transcriptomics enables the understanding of the spatial organization of tissues, providing deeper insight into tissue structures and cellular neighborhoods. Recent advancements in image-based spatial transcriptomics technology allow for the profiling of an expanded gene panel at subcellular resolution. A crucial step to make biological interpretations about the spatial data is gene set testing, which involves using pre-defined gene sets from comprehensive databases to statistically test for over-representation in one condition relative to other conditions. Tools originally developed for bulk or single-cell RNA sequencing data are used for analyzing spatial transcriptomics data, ignoring the rich spatial information from this technology. There is limited literature on gene set testing methods for spatial transcriptomics data. We develop two statistical testing methods for performing gene set testing for enrichment using the spatial coordinates. We have tested our framework on two public Xenium datasets with the 5k gene panel. Our framework prioritizes biologically significant gene sets that show strong spatial relevance over the tissue space and effectively controls the false discovery rate.