Bayesian Flexible Modelling of Spatially Resolved Transcriptomic Data

Abstract

Single-cell RNA-sequencing technologies may provide valuable insights to the understanding of the composition of different cell types and their functions within a tissue. Recent technologies such as spatial transcriptomics, enable the measurement of gene expressions at the single cell level along with the spatial locations of these cells in the tissue. Dimension-reduction and spatial clustering are two of the most common exploratory analysis strategies for spatial transcriptomic data. However, existing dimension reduction methods may lead to a loss of inherent dependency structure among genes at any spatial location in the tissue and hence do not provide insights of gene co-expression pattern. In spatial transcriptomics, the matrix-variate gene expression data, along with spatial co-ordinates of the single cells, provides information on both gene expression dependencies and cell spatial dependencies through its row and column covariances. In this work, we propose a flexible Bayesian approach to simultaneously estimate the row and column covariances for the matrix-variate spatial transcriptomic data. The posterior estimates of the row and column covariances provide data summaries for downstream exploratory analysis. We illustrate our method with simulations and two analyses of real data generated from a recent spatial transcriptomic platform. Our work elucidates gene co-expression networks as well as clear spatial clustering patterns of the cells.