Article Extended Data Fig. 4 | Spatially resolved transcriptome profiling of TDLN myeloid cells. ( a ) GSEA testing the enrichment of indicated transcriptional signatures (as detected by whole-transcriptome GeoMx DSP) for DCs, comparing paracortex stage III cells from recurrence (R) versus disease-free (DF) patients with melanoma. Dot size indicates the adjusted P value; dot colour indicates normalized enrichment scores (NES). ( b ) Scaled average gene expression levels of selected DEGs on the basis of association with the indicated protein groups or functions. ( c ) Heat map with scaled (Z-score) RNA expression levels DEGs ( P < 0.05) between TDLN paracortex DCs from DF and R patients with stage III melanoma. Columns represent individual patients; associations with published tumour-associated phenotypic signatures are indicated. ( d ) Enrichment of biological pathways among DEGs ( P < 0.05) upregulated in R versus DF DCs. ( e ) GSEA testing the enrichment of indicated transcriptional signatures (as detected by whole-transcriptome GeoMx DSP) for macrophages (Mac), comparing paracortex stage III cells from recurrence (R) versus disease- free (DF) patients with melanoma. Dot size indicates the adjusted P value; dot colour indicates normalized enrichment scores (NES). ( f ) Scaled average gene expression levels of selected DEGs on the basis of association with the indicated protein groups or functions. ( g ) Heat map with scaled (Z-score) RNA expression levels for DEGs ( P < 0.05) between TDLN paracortex macrophages from DF and R patients with stage III melanoma. Columns represent individual patients; associations with published tumour-associated phenotypic signatures are indicated. ( h ) Enrichment of biological pathways among all DEGs ( P < 0.05) upregulated in R versus DF macrophages. P values were calculated using a LMM ( c , g ), hypergeometric test and Benjamini–Hochberg procedure as implemented by Metascape ( c , f ) or weighted Kolmogorov–Smirnov-like running-sum statistic, as implemented by GSEA ( a , d ).