The thyroid cell type enriched transcriptome

The main function of the thyroid gland is the regulation of the metabolic rate. It produces the thyroid hormones thyroxine (T4) and triiodothyronine (T3), which increase heart rate, respiration and gastrointestinal motility and stimulate carbohydrate and fat metabolism. The thyroid gland also produces calcitonin, a hormone that regulates blood calcium levels.

3017 genes were predicted to have cell type specificity in the thyroid.

  • 11 cell types profiled
  • 1013 very highly enriched genes
  • 971 highly enriched genes
  • 1033 moderately enriched genes

Thyroid cell type enriched transcriptome: Summary

Genes with predicted cell type specificity within thyroid 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 thyroid cell types.

Cell type Very highHighModerate Total enriched
Parafollicular cells 30 13 4 47
Thyroid glandular cells 718 548 332 1598
Mitotic cells (Thyroid) 33 25 11 69
Endothelial cells 8 25 37 70
Smooth muscle cells 15 32 39 86
Fibroblasts 11 126 326 463
Macrophages 45 32 40 117
Neutrophils 19 12 4 35
T-cells 35 119 196 350
Plasma cells 99 39 44 182
All cell types 10139711033 3017

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

Thyroid cell type enriched transcriptome: Illustrative examples

Parafollicular cells

Parafollicular cells, also known as clear cells, or C-cells, are a neuroendocrine cell found in the thyroid, whose main function is to produce and secrete calcitonin (CALCA), which helps to regulate calcium homeostasis. Other genes classified as having specificity in parafollicular cells include Dopa decarboxylase (DDC), an enzyme that catalyzes a range of different decarboxylation reactions.

CALCA - Thyroid


DDC - Thyroid


Thyroid glandular cells

Thyroid glandular cells, or follicular cells, are the major cell type in the thyroid gland, and regulate thyroid function including the production and secretion of thyroid hormones. The hormone triodothyronine (T3) is formed from thyroxine (T4), via the action of enzyme iodotyrosine deiodinase (IYD). Cystathionine Gamma-Lyase (CTH), a cytoplasmic enzyme, FKBP Prolyl Isomerase 5 (FKBP5), a member of the immunophilin protein family, which plays a role in immunoregulation, protein folding and trafficking, and Monoamine oxidase A gene (MAOA), a mitochondrial enzyme, were all classified as having specificity in glandular cells in the thyroid.

IYD - Thyroid


CTH - Thyroid


FKBP5 - Thyroid


MAOA - Thyroid