Table 3.

Immune microenvironment cellular fraction differences of imaging subtypes in the imaging-subtype discovery cohort. A BC-specific reference signature matrix developed from single-cell transcriptome data was used to estimate the relative proportion of 15 cell types in the bulk RNA-seq data. Then, the differences in the cellular fraction of imaging subtypes were assessed.

Cell Types	p-Value	Subtype 2-1	Subtype 3-1	Subtype 3-2
Malignant cells	0.166	0.141	0.517	0.67
Fibroblasts	5.11 × 10−6 *	2.58 × 10−6 *	0.031*	0.021 *
Proliferating T cells	1.18 × 10−5 *	1.06 × 10−5 *	0.001*	0.416
Cytotoxic T cells	NaN	NaN	NaN	NaN
Regulatory T cells	0.738	0.751	0.795	0.996
Naive-like T cells	0.408	1	0.504	0.464
Natural killer cells	0.408	1	0.504	0.464
Neutrophils	0.697	0.848	0.969	0.683
Plasma cells	0.241	0.218	0.759	0.565
Dendritic cells	0.408	0.504	1	0.464
Macrophages	0.011 *	0.013 *	0.773	0.059
Monocytes	0.8	0.911	0.976	0.788
Mast cells	0.408	0.504	1	0.464
B cells	0.704	0.896	0.679	0.91
Transitional T cells	0.884	0.892	0.996	0.923

Note: unless otherwise indicated, data are the p-value of ANOVA or Tukey’s test. * p-value for p-value < 0.05. NaN: Not a Number.