Extended Data Fig. 4: ASPEN analysis of 49 cell subsets and senescence-related gene signatures (related to Fig. 3).

a, Results from ASPEN analysis of the 49 cell subsets from the breast cancer scRNA-seq atlas dataset and Hallmark gene sets (Human MSigDB), yielding cell-specific age-related programs (ARPs) in TNBC (left) ER+ breast cancer (right). Cell type subsets (color coded by major cell type groups) are represented on x-axes and Hallmark pathways with at least one statistically significant cell type are on the y-axes. ARPs were manually grouped into biologically similar processes. b, Results from ASPEN for 29 cell types (x-axis) and senescence-associated pathways from the MSigDB curated (C2) and ontology (C5) gene sets (y-axis) in TNBC (left) and ER+ (right) breast cancer. Cell types are color coded by indicated major cell type groups. a,b, Bubble color indicates normalized enrichment score (NES) of age-associated GSEA analysis, with color intensity indicating magnitude of enrichment according to the indicated scale. Statistical significance of NES is determined at a threshold of adjusted p-value < 0.05, whereby significance must be achieved in both fgsea-derived permutation test and gage-derived two-sided Welch’s t-test–style parametric gene set test (see Methods). Red indicates significant enrichment in older donors; blue indicates significant enrichment in younger donors; white indicates not significant (NS); gray indicates cell types were present in <50% of donors and were excluded from analysis. Circle size indicates magnitude of Seurat-identified enrichment score correlation to age according to the scale. TNF = tumor necrosis factor, SIG = signaling, IFN = Interferon, RESP = response, SIGNAL = Signaling, REJECTN = rejection, OX PHOS = oxidative phosphorylation, METAB = metabolism, TGF = transforming growth factor, ESTRGN = estrogen, EMT = epithelial to mesenchymal transition, DN = down, UNFOLD PROT RESP = Unfolded Protein Response, CAF = cancer associated fibroblast, PVL = perivascular-like cells.