Fig. 1: A computational toolbox for spatial isoform pattern discovery.
From: Mapping isoforms and regulatory mechanisms from spatial transcriptomics data with SPLISOSM
a, Alternative pre-mRNA processing generates multiple isoforms from the same gene, creating varying molecular transcript diversity detectable by major ST platforms. b, Isoform quantification from ST data is multivariate, sparse and confounded by gene expression and spatial autocorrelation. c, SPLISOSM addresses challenges in spatial isoform analysis by recasting SV and DU detections as multivariate independence tests. For SV testing, isoform usage and spatial coordinates are projected into feature spaces to assess nonlinear dependencies using the HSIC with optimized spatial and isoform kernels. For DU testing, nonparametric conditional HSIC test and parametric GLMM control for confounding spatial autocorrelation and reduce spurious associations. d, SPLISOSM enables cell-type-agnostic detection of SVP genes and their potential regulators. Figure created using BioRender.com.
