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. 2021 Feb 22;49(10):e55. doi: 10.1093/nar/gkab095

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© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 3. — Identification of morphologic markers and functional terms in prostate cancer data (P3.3 and P2.4). (A) Spatial mapping of the PC1 and PC5 image latents in P3.3 tissue. The PC values in each spot are visualized using colormaps. The maximum and minimum values of the colormap represent two standard deviations above and below the mean value, respectively. Spatial mapping of the top 4 genes showing the greatest contrast in (B) PC1 and (C) PC5 image latent space. The top genes are presented in descending order of |log₂RC| (FDR < 0.05). The normalized gene expression level in each spot is visualized using colormaps. The maximum and minimum values of the colormap represent two standard deviations above and below the mean expression, respectively. Gene ontology (GO) analysis was performed in P3.3 tissue for (D) PC1 and (E) PC5 SPADE genes showing positive or negative association with PC image latent. The top 3 positive or negative GO terms for each subcategory, biological process (BP), cellular component (CC), and molecular function (MF), are exhibited in the left and right panel, respectively. The number of overlapping genes is expressed as the size of the dot, and the Benjamini–Hochberg adjusted P-value is exhibited with a colormap. (F) Spatial mapping of the PC2 image latent in P2.4 tissue. The PC values in each spot are visualized using a colormap. The maximum and minimum values of the colormap represent two standard deviations above and below the mean value, respectively. (G) Spatial mapping of the top 4 genes showing the greatest contrast in PC2 image latent space. The top genes are presented in descending order of |log₂RC| (FDR < 0.05) in the top and bottom rows. (H) The GO analysis was implemented in P2.4 tissue for PC2 SPADE genes presenting a positive or negative association with PC2 image latent. The top 3 positive or negative GO terms for each subcategory, BP, CC and MF, are exhibited in the left and right panel, respectively. The number of overlapping genes is expressed as the size of the dot, and the Benjamini-Hochberg adjusted P-value is exhibited with a colormap.