Fig. 4: Spatial 3′ end transcript diversity in adult mouse brain extends beyond alternative polyadenylation and shows functional convergence on signaling pathways.
From: Mapping isoforms and regulatory mechanisms from spatial transcriptomics data with SPLISOSM
a, Workflow overview. b, Comparison of SV in gene expression (x axis) versus TREND usage (y axis) in the SR coronal brain section sample. Points colored by expression perplexity (effective number of isoforms per gene). Inset: significant events (adjusted P < 0.01). c, TREND event annotation with overlapping with genomic features. Alternative exons (Alt-exon) are defined as exons located within introns of other transcript variants. Bold numbers are the absolute number of events. CDS, coding sequence. De novo motif enrichment results shown at bottom. P value computed using a one-sided chi-square test. d, Pathway enrichment analysis comparing SVP and SVENP genes, arranged by precision. e, Spatial log-normalized expression of the neuronal (chr. 9:110005229) and glial (chr. 9:110083783) Map4 variants. f, Unsupervised clustering based on gene-level expression of top 200 SVE genes (left), relative TREND ratios of top 200 SVP genes (middle) and gene expression of all SVE RBPs (right). g, Gnao1 transcript structure (left) and spatial log-normalized expression patterns (middle). Right: the likely protein sequence variation, color-coded by solvent-accessible surface area. FDR, false discovery rate. h, Arpp21 transcript structure and spatial log-normalized expression patterns. aa, amino acid. i, Top RBPs associated with TREND usage in Arpp21, Celf2 and Pcbp2. Dashed line indicates P = 0.01. Panel a created using BioRender.com.
