Fig. 5: HERGAST enhanced critical molecular signature with high accuracy. | Nature Communications

Fig. 5: HERGAST enhanced critical molecular signature with high accuracy.

From: Unveiling fine-scale spatial structures and amplifying gene expression signals in ultra-large ST slices with HERGAST

Fig. 5

a Reconstruction results of HERGAST based on zero-inflated Poisson distribution. The top panels are visualizations of the gene’s spatial expression. Numbers in the title are the Pearson correlation coefficients with ground truth expression. Bottom panels are distributions of gene expression in mark (highly expressed, in orange color) and non-mark area (lowly expressed, in blue color). Full results of various spatial pattern can be seen in Supplementary Fig. 15. Results based on zero-inflated negative binomial distribution can be seen in Supplementary Fig. 16. b Same as (a) but on negative control case. Negative control case based on zero-inflated negative binomial distribution can be seen in Supplementary Fig. 17. c Reconstruction results of lymph node markers in normal colon tissue. From left to right, panels are: H&E staining image of this sample containing manual annotation of lymph node areas; Clustering result of HERGAST; Original expression of the lymph node marker meta gene; Reconstructed expression of the lymph node marker meta gene. These same results are observed across 10 repeated experiments. d H&E image, and spatial clustering results of different methods in Xenium human breast cancer slice. These same results are observed across 10 repeated experiments. e The original and amplified spatial expression of ERBB2, ESR1, PGR, and EGFR in selected regions. Full spatial expression landscapes can be found in Supplementary Fig. 18. f Zoom-in view of the H&E image, original and amplified spatial expression of EGFR and ESR1 in selected corresponding red box regions in (e). More examples can be found in Supplementary Fig. 19.

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