Genes expected to be absent, or expressed at a notably low level, in these cells, and whose absence supports the assignment of this cell annotation.
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Rationale
PECAM1, PLVAP and CLDN5 used to define the vascular endothelial population, further refined by ACKR1 and SELP for vascular endothelial venous cells as supported by literature. Differential expression analysis was performed for each of the level2 cell types and here we report the top 10 markers as determined by one-vs-all negative binomial testing (non-redundant).
Inherited from level2
Set of Labels Description
This dataset generates a comprehensive Human Breast Cell Atlas (HBCA) using scRNA-seq of over 800,000 cells from 55 donors, identifying 41 cell subclusters across the epithelial (LASP, LHS, BMYO), immune (T cells, NK, B cells, macrophages), and stromal (fibroblast, endothelial, perivascular) compartments. To capture how key risk-modifying factors alter the homeostatic cellular composition of the breast, we assembled a cohort with broad donor diversity spanning a wide range of ages, parity statuses, and germline mutation backgrounds. By annotating at this resolution we could apply differential abundance testing to detect subcluster-level compositional shifts associated with each risk factor. This annotation set also serves as a standardised reference taxonomy, enabling harmonised cell-type comparisons across existing datasets where nomenclature had been inconsistent.
