Extended Data Fig. 2: Evidence of gene expression similarity between spatial neighbors.

a, Cosine similarity of gene expression profiles for 250 cells paired with all their neighbors in the TISSUE spatial graph compared to pairings with randomly drawn cells across all eleven spatial transcriptomics datasets. The boxplot corresponds to the quartiles of the cosine similarity measurements. The center line corresponds to median cosine similarity, which was strictly higher in the neighbor-paired comparisons than the random-paired comparisons across all datasets. Whiskers span up to 1.5 times the interquartile range of the metrics and values outside this range are shown as dots. Abbreviations are as follows: hippocampus (Hipp.) primary visual cortex (VISP), prefrontal cortex (PC), middle temporal gyrus (MTG), somatosensory cortex (SC), gastrulation (Gast.), U-2 OS cell line (U2OS). b, Scatter plots of the cosine similarities of gene expression profiles for 250 cells paired with their neighbors for either the training gene set or the test gene set determined by random train-test split of all genes (50% train, 50% test). Shown are cosine similarity pairs for 10 train-test splits for the two benchmark spatial transcriptomics datasets with the most measured genes.