Fig. 6: scNiche reveals tumor niches characterized with distinct phenotypes from human TBNC dataset.

a The enrichment scores of each cell type in each tumor-enriched niche across 19 mixed subtype samples and 15 compartmentalized subtype samples. The enrichment scores are calculated among 7 tumor-enriched niches, and the p-value is calculated with the one-sided Mann-Whitney U test (*p ≤ 0.05; **p ≤ 0.01; ***p ≤ 0.001; ****p ≤ 0.0001). b Three representative tumor-enriched niches exhibit heterogeneity in the type of cells infiltrated and the degree of infiltration. Each cell is colored by the niche labels (left) and the cell type labels (right). c The average expression levels of tumor-related proteins of tumor cells in Niche 5 and Niche 11 in each sample. For Niche 5 (or Niche 11), only samples with a proportion of that niche exceeding 5% are considered. The p-value is calculated with the two-sided Mann-Whitney U test. Data are presented as boxplots (minima, 25th percentile, median, 75th percentile, and maxima). n = 7 (8) samples for Niche 5 (Niche 11). d The proportions of Niche 5 and Niche 11 in each sample. Only samples with a proportion of Niche 5 (or Niche 11) exceeding 5% are shown. The average expression levels of HLA1 and HLA-DR of tumor cells in Niche 9 and other tumor-enriched niches in each sample (e) and the proportions of tumor cells, immune cells, and stromal cells in Niche 9 and other tumor-enriched niches in each sample (f). For Niche 9 (or other tumor-enriched niches), only samples with a proportion of that niche exceeding 5% are considered. The p-value is calculated with the two-sided Mann-Whitney U test. Data are presented as boxplots (minima, 25th percentile, median, 75th percentile, and maxima). n = 8 (32) samples for Niche 9 (other tumor-enriched niches). The average expression levels of SMA and Vimentin of tumor cells in Niche 3 and other tumor-enriched niches in each sample (g) and the proportions of tumor cells, immune cells, and stromal cells in Niche 3 and other tumor-enriched niches in each sample (h). For Niche 3 (or other tumor-enriched niches), only samples with a proportion of that niche exceeding 5% are considered. The p-value is calculated with the two-sided Mann-Whitney U test. Data are presented as boxplots (minima, 25th percentile, median, 75th percentile, and maxima). n = 10 (29) samples for Niche 3 (other tumor-enriched niches). Source data are provided as a Source Data file.