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. 2022 Oct 17;50(22):e131. doi: 10.1093/nar/gkac901

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© The Author(s) 2022. 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 License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 4. — DeepST can dissect spatial domains from cancer tissue at a finer level. (A) Visium spatial transcriptomics data of a breast cancer sample annotated by pathologists. IDC, invasive ductal carcinoma; DCIS, ductal carcinoma in situ; LCIS, lobular carcinoma in situ; tumor edge; healthy region. (B) Spatial domains identified by DeepST on human breast cancer (Block A, Section 1) with domains= 10 and domains= 20. (C) Spatial domains were identified without a priori knowledge by DeepST. (D) Heatmap of Pearson correlation coefficient between domains (domains= 10). (E) Expression of TFF1 and ABCC11 with regional annotation on left (top); Violin plots of the two genes(bottom). (F) Differential expression analysis among domains 1, 2 and 4. Spatial location of domains 1, 2 and 4 (left); Volcano graph of DEGs between domains 1 and 4 (domains= 10) (middle); CPB1 and CRISP3 express differentially between domains 1 and 4 (purple) (right). (G) Gene ontology enrichment analysis of the DEGs between domains 1 and 4. Red denotes pathway with upregulated genes in domain 1; blue is the opposite. (H) Visualizations of the DEGs (|log fold change|2) between domains 1 and 4 with k= 10. T-test on the means of two independent domains. (I) Stacked violin plot show expression of all domains on the top three DEGs of domains 6, 2, 13, 1 and 8. (J) H&E of human breast cancer sample annotated by Agoko's telepathology platform. (K) Visium spatial transcriptomics with spatial domains generated by DeepST.

Inline graphic — DeepST can dissect spatial domains from cancer tissue at a finer level. (A) Visium spatial transcriptomics data of a breast cancer sample annotated by pathologists. IDC, invasive ductal carcinoma; DCIS, ductal carcinoma in situ; LCIS, lobular carcinoma in situ; tumor edge; healthy region. (B) Spatial domains identified by DeepST on human breast cancer (Block A, Section 1) with domains= 10 and domains= 20. (C) Spatial domains were identified without a priori knowledge by DeepST. (D) Heatmap of Pearson correlation coefficient between domains (domains= 10). (E) Expression of TFF1 and ABCC11 with regional annotation on left (top); Violin plots of the two genes(bottom). (F) Differential expression analysis among domains 1, 2 and 4. Spatial location of domains 1, 2 and 4 (left); Volcano graph of DEGs between domains 1 and 4 (domains= 10) (middle); CPB1 and CRISP3 express differentially between domains 1 and 4 (purple) (right). (G) Gene ontology enrichment analysis of the DEGs between domains 1 and 4. Red denotes pathway with upregulated genes in domain 1; blue is the opposite. (H) Visualizations of the DEGs (|log fold change|2) between domains 1 and 4 with k= 10. T-test on the means of two independent domains. (I) Stacked violin plot show expression of all domains on the top three DEGs of domains 6, 2, 13, 1 and 8. (J) H&E of human breast cancer sample annotated by Agoko's telepathology platform. (K) Visium spatial transcriptomics with spatial domains generated by DeepST.