The immune cell section - Expression profiles in human immune cells


The Immune Cell section contains single cell information on genome-wide RNA expression profiles of human protein-coding genes covering various B- and T-cells, monocytes, granulocytes and dendritic cells. The transcriptomics analysis covers 18 cell types isolated with cell sorting and includes classification based on specificity, distribution and expression cluster across all immune cells. More information about the specific content and the generation and analysis of the data in the section can be found in the Methods Summary.

Learn about:

  • if a gene is enriched in a particular immune cell type (specificity)
  • which genes have a similar expression profile across the immune cells (expression cluster)
  • the catalogue of genes elevated in each of the immune cell types

Hematopoietic Stem Cell Common Lymphoid Progenitor Common Myeloid Progenitor Mastcells Myeloblasts Erythrocytes Platelets Lymphocytes NK-cells B-cells T-cells Granulocytes Monocytes Dendritic Cells
Classical monocyte
Intermediate monocyte
Non-classical monocyte
Myeloid DC
Plasmacytoid DC
Memory B-cell
Naive B-cell
MAIT T-cell
Memory CD4 T-cell
Memory CD8 T-cell
Naive CD4 T-cell
Naive CD8 T-cell

The genome-wide RNA expression profiles of human protein-coding genes in 18 single cell immune cell types are presented covering various B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells. The RNA expression for each gene with a classification based on the RNA expression of individual cell types across the 18 cell types is presented as well as a classification based on the main cell lineage types. This classification is based on the same principal used for the tissue-based classification resulting in the annotation of each gene according to cell type specificity (cell type enriched, group enriched, cell type enhanced and low cell type specificity) and cell type distribution (detected in single, few, many or all cell types). The cell type specific protein-coding genes are highlighted and genome-wide differential analysis of the expression profiles between the different cell lineages and cell types are presented.


The RNA data is used to cluster genes according to their expression across immune cells. The clustering of 14634 genes expressed in immune cells resulted in 52 expression clusters, which have been manually annotated to describe common features in terms of function and specificity. The result of the cluster analysis is presented as an UMAP based on gene expression, where each cluster has been summarized as colored areas containing most of the cluster genes.

Go to interactive expression cluster page


All protein-coding genes have been classified according to the immune cell expression into genes elevated in at least one of the immune cells. In the figure, the number of cell lineage-elevated genes with highest expression in blood or lymphoid tissues is shown to the left and the cell lineage-enriched genes with highest expression in blood or lymphoid tissues to the right. All blood cell specific categories can be found here.


In the figure, the number of genes enriched in maximum 3 immune cell types are displayed. Click on the numbers or cell type names to obtain the corresponding list of genes.