Bioinformatics Seminar
Time: 11AM
Venue: Davis Auditorium and Online
12 March 2024
This is a WEHI only event.SpaceMarker: a hybrid approach to find spatially relevant marker genes in image-based spatial transcriptomics data
Melody JinWEHI Bioinformatics
Spatial transcriptomics allows deeper understanding of the spatial architecture of tissues, and provides more insight into tissue structures and cellular neighborhoods. In single cell RNA-seq, marker analysis identifies genes highly expressed in each cluster compared to the remaining clusters, and these marker genes are used to annotate clusters with cell types. For spatial data, there is limited literature on developing marker gene detection methods that account for the spatial distribution of gene expression. We develop a hybrid approach to prioritize marker genes that uses the spatial coordinates of gene detections and cells. We encode the spatial coordinates as spatial vectors and propose two approaches to detect and prioritize marker genes. We have tested our methods on several public datasets across different technologies, including Xenium, Merscope, and Cosmx. The marker genes detected by our method show strong spatial correlation with their corresponding clusters and have increased specificity compared to other popular methods.