Fig. 3

Compartment-specific RNA colocalization with RNAcoloc. A Transcripts are separated by compartment (nucleus and cytoplasm) before CLQ scores are calculated for every gene pair across all cells. This yields a cell × gene pair × compartment tensor. B Pairwise comparison of log CLQ distributions for gene pairs and self-pairs, further categorized by compartment. The Mann–Whitney U test was used for comparisons. Stars denote p-values below the legend threshold with Benjamini–Hochberg correction controlling for false-discovery rate. From top to bottom, group sizes are 12,254,430 (cytoplasm gene pairs), 115,187 (nucleus gene pairs), 6,778,402 (cytoplasm self-pairs), and 86,474 (nucleus self-pairs). C Tensor decomposition yields 4 factors. From left to right, the three heatmaps show the loadings of each factor for each dimension—compartments, cells, and gene pairs. Only the top 5 associated gene pairs for each factor are shown. D Top examples of compartment-specific colocalized gene pairs. Black scale bars denote 10 μm