The core fibroblast enriched transcriptome

Fibroblasts are spindle-shaped mesenchymal cells found in the interstitial spaces. They are the primary source of extracellular matrix proteins, which provide a tissue scaffold and play a key role in cell phenotype determination and function. Fibroblasts have an important role in wound healing, migrating to sites of damage following tissue injury, where they deposit new collagen and facilitate the healing process. Fibroblasts can be activated by a variety of biological signals that promote proliferation and cellular differentiation, for example into myofibroblasts which have increased matrix production.

In this section we detail the predicted core fibroblast transcriptome, highlighting genes classified as having predicted specificity in fibroblasts, or closely related mesenchymal cells, in multiple tissue types. Such genes could be useful general markers for fibroblasts across tissue beds, and are likely critical for fibroblast specific functions. These genes are sub-divided into 3 categories, based on the number of tissues in which they were independently classified as fibroblast enriched.


Fibroblasts were profiled in 14 of the tissues featured in the Tissue Cell section.

  • 9 genes predicted as enriched in fibroblasts in 75-100 % tissues
  • 54 genes predicted as enriched in fibroblasts in 50-75 % tissues
  • 159 genes predicted as enriched in fibroblasts in 25-50 % tissues


Protein expression of genes enriched in fibroblasts across tissue types

An example of a protein with enriched expression in fibroblasts across multiple tissue types is Microfibril Associated Protein 4 (MFAP4), an extracellular matrix protein that belongs to the fibrinogen-related protein superfamily. This protein is thought to be involved in cell adhesion, intercellular interactions and the assembly and/or maintenance of elastic fibers.


MFAP4 - Colon

MFAP4

MFAP4 - Breast

MFAP4

MFAP4 - Kidney

MFAP4

MFAP4 - Lung

MFAP4

MFAP4 - Prostate

MFAP4

MFAP4 - Skin

MFAP4

MFAP4 - Stomach

MFAP4

Another example of a protein with enriched expression in fibroblasts across multiple tissue types is Cadherin 11 (CDH11), a type II classical cadherin with a role in calcium-dependent cell-cell adhesion.


CDH11 - Kidney

CDH11

CDH11 - Lung

CDH11

CDH11 - Skeletal muscle

CDH11

CDH11 - Thyroid

CDH11


Genes with predicted specificity in fibroblasts in individual tissues

A summary table of all genes with predicted high enrichment in fibroblasts in profiled tissues is provided below. Identified genes are subdivided into 3 categories in each tissue, based on the difference between the enrichment score in fibroblasts, compared to the other cell types profiled (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: Genes predicted to be enriched in fibroblasts by tissue type

Tissue Very highHighModerate Total enriched
Adipose subcutaneous 25 112 103 240
Adipose visceral 11 56 284 351
Breast 23 75 140 238
Colon 0 5 37 42
Heart muscle 12 98 251 361
Kidney 4 65 214 283
Liver 52 111 153 316
Lung 28 64 164 256
Pancreas 0 12 60 72
Prostate 59 94 132 285
Skeletal muscle 0 53 285 338
Skin 10 45 161 210
Stomach 0 5 161 166
Thyroid 11 126 326 463