Fig. 6: Advanced spatial analysis by STAIG reveals cancer-associated fibroblasts (CAF)-rich clusters in human Breast Cancer ST Data.

a Manual annotation of human breast cancer dataset based on the HE-stain image. b Clustering results with ARI and NMI by STAIG on human breast cancer dataset. Clustering results from other baseline methods are shown in Supplementary Fig. S16. c Differential Gene Expression (DGE) analysis of Cluster 3 versus other clusters. Each point represents a gene, the vertical axis represents the -log10 of the p-value and the horizontal axis represents the log2FoldChange (log2 FC). P-values were derived from a two-sided Wilcoxon rank-sum test. The significance thresholds were set at |log2FC| > 0.25 and p-value < 0.05. d Gene Ontology (GO) analysis for Cluster 3 versus other clusters. The vertical axis represents the GO terms, and the horizontal axis represents the -log10 of the p-value. GO enrichment analysis was performed using the one-sided hypergeometric test, and p-values were adjusted for multiple comparisons using the Benjamini-Hochberg method. e Violin plots and the visualization of expression of CAF marker genes (COL6A1, COL1A2, VIM, PDGFRB, S100A4) in Cluster 3 (n = 166 spots) versus other clusters (n = 3632 spots). The vertical axis represents gene expression levels. Each violin represents the distribution of expression for a particular gene, with the width indicating frequency. The central white dot denotes the median expression level, the thick black bar within each violin represents the interquartile range (IQR; 25th to 75th percentile), and the thin black line (whiskers) extends to 1.5 × IQR from the 25th and 75th percentiles, capturing the data range excluding outliers. Data represent biological replicates (individual spots).