TUSCAN: Tumor segmentation and classification analysis in spatial transcriptomics

doi:10.1371/journal.pcbi.1014058

TUSCAN: Tumor segmentation and classification analysis in spatial transcriptomics

Fig 3

Tumor clone analysis of human breast cancer.

(A) Spatial visualization of three tumor clones and normal tissue sections. (B) Heatmap of the estimated CNPs of tumor spots. Clonal classifications were determined by consensus clustering. (C) CNV burden calculated as the number of genes with extreme expression levels relative to the normal group. CNV_gain: . CNV_loss: . (D) Spatially variable features across three tumor clones. Top to bottom: clone 1 vs. clones 2 and 3; clone 2 vs. clones 1 and 3; clone 3 vs. clones 1 and 2. (E) Differential expression analysis of three tumor clones and normal cells. (F) GSEA of three tumor clones. Human hallmark gene sets from the Molecular Signatures Database (MSigDB) were used as the reference.

doi: https://doi.org/10.1371/journal.pcbi.1014058.g003