The breast cell type enriched transcriptome

The primary function of the breast is to provide milk for newborn babies, and mainly consists of a mixture of glandular and adipose tissue. Glandular tissue is arranged in a branching ductal structure, terminating in alveoli, with adipocytes filling the interstitial space. Both males and females have breast tissue, although only data from female breast tissue is analyzed here.

2093 genes were predicted to have cell type specificity in the breast.

  • 11 cell types profiled
  • 617 very highly enriched genes
  • 570 highly enriched genes
  • 917 moderately enriched genes

Breast cell type enriched transcriptome: Summary

Genes with predicted cell type specificity within breast are detailed in Table 1. Identified genes are subdivided into 3 specificity categories, based on the difference between the enrichment score in the corresponding cell type, compared to the other cell types profiled in the tissue (see Methods Summary page for details):

  • Predicted specificity: ´Very high´ - Differential score vs. other profiled cell types within the tissue >0.35
  • Predicted specificity: ´High´ - Differential score vs. other profiled cell types within the tissue >0.25
  • Predicted specificity: ´Moderate´ - Differential score vs. other profiled cell types within the tissue >0.15

Table 1. Number of genes in each specificity category in the breast cell types.

Cell type Very highHighModerate Total enriched
Breast glandular cells 1 30 250 270
Breast glandular cells (progenitors) 3 5 20 28
Breast myoepithelial cells 0 6 60 66
Adipocytes (Breast) 316 170 124 610
Endothelial cells 89 98 101 288
Smooth muscle cells 0 4 27 31
Fibroblasts 23 75 140 238
Macrophages 51 35 41 127
T-cells 13 70 125 208
Plasma cells 121 77 29 227
All cell types 617570917 2093

Figure 1. Bar plot of the number of enriched genes in the cell types of the breast, divided by specificity category

Breast cell type enriched transcriptome: Illustrative examples

Breast glandular cells

Glandular cells of the breast, sometimes called luminal cells, line the alveoli and lumen of the glandular tissue, and secrete the majority of proteins and substances that make up milk. In non-lactating women these cells are usually inactive, and are activated by hormonal changes that occur during pregnancy and childbirth in order to promote lactation. Genes classified as having specificity in breast glandular cells include the gluconeogenesis regulator and tumor suppressor Fructose-bisphosphatase 1 (FBP1), as well as proteins with unknown function such as SH3 Domain Containing 21 (SH3D21) and Transmembrane protein 45B (TMEM45B) .

FBP1 - Breast


SH3D21 - Breast


TMEM45B - Breast


Breast glandular cells (progenitor)

Glandular progenitor cells are a distinct, long lived subset of breast glandular cells that have the ability to generate novel glandular cells, to both expand the glandular population during pregnancy, as well as maintaining homeostasis during other periods. Genes classified as having specificity in glandular progenitor cells include Calmodulin like protein 5 (CALML5), a calcium binding protein thought to be involved in terminal differentiation of cells, and Pleckstrin homology like domain family A member 1 (PHLDA1), a regulator of translation and apoptosis.

CALML5 - Breast


PHLDA1 - Breast


Breast myoepithelial cells

Myoepithelial cells, or basal cells, lie underneath the glandular cells, and express many smooth muscle proteins. Myoepithelial cells have contractile ability and can constrict to expel the milk from the ducts and out of the body via the nipple. Myoepithelial cells also help regulate the proliferation and differentiation of glandular cells. Genes classified as having specificity in myoepithelial cells include structural proteins such as Keratin 14 (KRT14), as well as Anoctamin 1 (ANO1), a chloride channel with a diverse range of cellular functions including cell proliferation, survival, secretion, and migration as well as playing a role in the contraction of smooth muscle proteins.

KRT14 - Breast


ANO1 - Breast



The main function of adipocytes is to store energy in the form of fat and release it between meals, however they also function as endocrine tissue, secreting several growth factors, hormones and inflammatory mediators. During pregnancy and lactation, adipocytes of the breast provide lipids to the glandular cells for milk production, and are also the source of several hormones secreted into the milk. Genes classified as having specificity in Adipocytes include Perilipin 4 (PLIN4), which coats stored lipid droplets to protect them from lipases, as well as Acetyl-CoA carboxylase beta (ACACB), which plays a central role in fatty acid metabolism.

PLIN4 - Breast


ACACB - Breast