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Patch-level analysis reveals subcellular heterogeneity in spatial transcriptomic profiles (A) Transcript location and patch correlation of genes in fibroblast. The scatterplot shows the location of transcripts of the labeled genes. The heatmap shows the patch correlation between the labeled genes. (B) Transcript location and patch correlation of genes in U2-OS. The scatterplot shows the location of transcripts of the labeled genes. The heatmap shows the patch correlation between the labeled genes. Several differences in patch correlation between the two cells are shown, such as PRPF8-IGF2R, TPR-LRP1, and PRPF8-PRKCA. (C) SRRM2 and PRPF8 visualization in fibroblast and U2-OS. The gene pair presents similar patch correlations in both cells. (D) PRPF8 and IGF2R visualization in fibroblast and U2-OS. The gene pair presents opposite patch correlations. (E) Boxplot of patch correlations between SRRM2-PRPF8 and PRPF8-IGF2R in fibroblast and U2-OS. p values: **: 0.001 < p < 0.01, ****: p <= 0.0001
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Image-based spatial omics methods such as fluorescence in situ hybridization (FISH) generate molecular profiles of single cells at single-molecule resolution. Current spatial transcriptomics methods focus on the distribution of single genes. However, the spatial proximity of RNA transcripts can play an important role in cellular function. We demons...
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... TNC-FLNC, PRPF8-COL5A1, and THBS1-MALAT1 all have negative proximity scores. However, because of the nearest-neighbor approach of studying gene neighborhoods, the detected proximity relationship can be affected by the varying number of genes studied ( Figure S2). Further analysis indicated that the mean and standard deviation of proximity score between the same pairs of genes were not significantly different when the number of genes studied was changed. ...
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... common 84 genes in the two MERFISH datasets were compared. Cells of different types present distinct patch correlations between the same set of genes (Figures 2A and 2B; Data S1). For example, the patch correlations between SRRM2 and PRPF8 are similar between fibroblast and U2-OS cells (Fig- ure 2C). ...
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... of different types present distinct patch correlations between the same set of genes (Figures 2A and 2B; Data S1). For example, the patch correlations between SRRM2 and PRPF8 are similar between fibroblast and U2-OS cells (Fig- ure 2C). However, the patch correlations between PRPF8 and IGF2R are different between fibroblast and U2-OS. ...
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... the patch correlations between PRPF8 and IGF2R are different between fibroblast and U2-OS. The two genes have a negative correlation in fibroblast shown by R = À0.33, and a positive correlation in U2-OS shown by R = 0:38 ( Figure 2D). When comparing the patch correlation of both cell populations, both SRRM2-PRPF8 and IGF2R-PRPF8 pairs show significant differences ( Figure 2E). ...
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... two genes have a negative correlation in fibroblast shown by R = À0.33, and a positive correlation in U2-OS shown by R = 0:38 ( Figure 2D). When comparing the patch correlation of both cell populations, both SRRM2-PRPF8 and IGF2R-PRPF8 pairs show significant differences ( Figure 2E). Therefore, the two genes are more likely to locate in the same subcellular patch in U2-OS than in fibroblast. ...
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