The undifferentiated cell-specific proteome

Undifferentiated cells are found in the entire body and are responsible for the renewal of the different cell types comprising our organs. In this analysis, we describe undifferentiated cells of the intestines. They include stem cells, transit-amplifying cells (TA) and progenitor/precursors cells. Transcriptome analysis shows that 57% (n=11150) of all human proteins (n=19670) are detected in undifferentiated cells and 205 of these genes show an elevated expression in any undifferentiated cells compared to other cell type groups.

  • 205 elevated genes
  • 2 enriched genes
  • 37 group enriched genes
  • Main function: Cell renewal

The undifferentiated cell transcriptome

The scRNA-seq-based undifferentiated cell transcriptome can be analyzed with regard to specificity, illustrating the number of genes with elevated expression in each specific undifferentiated cell type compared to other cell types (Table 1). Genes with an elevated expression are divided into three subcategories:

  • Cell type enriched: At least four-fold higher mRNA level in a certain cell type compared to any other cell type.
  • Group enriched: At least four-fold higher average mRNA level in a group of 2-10 cell types compared to any other cell type.
  • Cell type enhanced: At least four-fold higher mRNA level in a cell certain cell type compared to the average level in all other cell types.

Table 1. Number of genes in the subdivided specificity categories of elevated expression in undifferentiated cells.

Cell type Cell type enrichedGroup enrichedCell type enhancedTotal elevated
Undifferentiated cells 2 37 166 205

Undifferentiated cell function

Undifferentiated cells of the intestines are located in the crypts (base) of the intestinal epithelium. They include stem cells, transit-amplifying cells (TA) and progenitor/precursor cells. The main characteristics of all stem cells are to generate more of themselves (self-renewal) and to differentiate into specific types of mature cells. When a stem cell divides, it generates one stem cell and one so-called daughter cell. This daughter cell proliferates rapidly to form a population of TA-cells. TA-cells give rise to progenitor/precursor cells, which in turn have the ability to differentiate into specific mature cells. In the case of the intestine, undifferentiated cells are responsible for the replenishment of all cell types of the epithelium: enterocytes, mucus-secreting cells (goblets cells), Paneth cells and intestinal neuroendocrine cells. In most adult mammals, almost the entire intestinal epithelium is replaced every 2-6 days.

The histology of organs that contain undifferentiated cells, including interactive images, is described in the Protein Atlas Histology Dictionary.


Here, the protein-coding genes expressed in undifferentiated cells are described and characterized.

The transcript profiling was based on publicly available genome-wide expression data from scRNA-seq experiments covering 13 different normal tissues, as well as analysis of human peripheral blood mononuclear cells (PBMCs). All datasets (unfiltered read counts of cells) were clustered separately using louvain clustering and the clusters obtained were gathered at the end, resulting in a total of 192 different cell type clusters. The clusters were then manually annotated based on a survey of known tissue and cell type-specific markers. The scRNA-seq data from each cluster of cells was aggregated to average normalized protein-coding transcripts per million (pTPM) and the normalized expression value (nTPM) across all protein-coding genes. A specificity and distribution classification was performed to determine the number of genes elevated in these single cell types, and the number of genes detected in one, several or all cell types, respectively.

It should be noted that since the analysis was limited to datasets from 13 organs only, not all human cell types are represented. Furthermore, some cell types are present only in low amounts, or identified only in mixed cell clusters, which may affect the results and bias the cell type specificity.

Relevant links and publications

UhlĂ©n M et al., Tissue-based map of the human proteome. Science (2015)
PubMed: 25613900 DOI: 10.1126/science.1260419

Fagerberg L et al., Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Mol Cell Proteomics. (2014)
PubMed: 24309898 DOI: 10.1074/mcp.M113.035600

Parikh K et al., Colonic epithelial cell diversity in health and inflammatory bowel disease. Nature. (2019)
PubMed: 30814735 DOI: 10.1038/s41586-019-0992-y

Wang Y et al., Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine. J Exp Med. (2020)
PubMed: 31753849 DOI: 10.1084/jem.20191130