Explore the expression profiles in single cell types

CNN1 - Prostate

TSPY2 - Testis

This section contains Single Cell Type information based on single cell RNA sequencing (scRNAseq) data from 25 human tissues and peripheral blood mononuclear cells (PBMCs), together with in-house generated immunohistochemically stained tissue sections visualizing the corresponding spatial protein expression patterns. The scRNAseq analysis was based on publicly available genome-wide expression data and comprises all protein-coding genes in 444 individual cell type clusters corresponding to 15 different cell type groups. 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. The genes expressed in each of the cell types can be explored in interactive UMAP plots and bar charts, with links to corresponding immunohistochemical stainings in human tissues.

More information about the specific content and the generation and analysis of the data in the section can be found on the Methods Summary.

Learn about:

  • mRNA and protein expression in single cell types
  • if a gene is enriched in a particular cell type (specificity)
  • which genes have a similar expression profile across cell types (expression cluster)



The RNA data was used to cluster genes according to their expression across single cell types. The clustering of 18965 genes expressed in single cell types resulted in 68 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 a 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


Classification of all protein-coding genes based on single cell type-specific expression, determining the number of genes elevated (cell type/group enriched, cell type enhanced) in a particular cell type compared to all other cell types.

Cell type group Cell type EnrichedGroup
Glandular epithelial cells Basal respiratory cells 527257289
Club cells 553240298
Ionocytes 914125148
Respiratory ciliated cells 18153546717
Gastric mucus-secreting cells 2236292350
Proximal enterocytes 4195682818
Paneth cells 649398453
Distal enterocytes 350603656
Intestinal goblet cells 1726260303
Exocrine glandular cells 2721268316
Basal prostatic cells 222212236
Prostatic glandular cells 723172202
Breast glandular cells 828209245
Breast myoepithelial cells 126205232
Endometrial ciliated cells 10132484626
Glandular and luminal cells 428404436
Squamous epithelial cells Basal keratinocytes 232248282
Suprabasal keratinocytes 2944319392
Basal squamous epithelial cells 126256283
Squamous epithelial cells 1940298357
Specialized epithelial cells Alveolar cells type 1 1263394469
Alveolar cells type 2 1669383468
Ductal cells 216220238
Hepatocytes 156114581851
Cholangiocytes 324155182
Proximal tubular cells 45100762907
Distal tubular cells 2340553616
Collecting duct cells 1224280316
Urothelial cells 324366393
Sertoli cells 643285334
Granulosa cells 2345428496
Endocrine cells Enteroendocrine cells 2740201268
Pancreatic endocrine cells 934354397
Leydig cells 040281321
Theca cells 1034295339
Neuronal cells Excitatory neurons 2245916592140
Inhibitory neurons 3046515322027
Cone photoreceptor cells 17104618739
Rod photoreceptor cells 2496536656
Bipolar cells 26112563701
Horizontal cells 2085522627
Glial cells Astrocytes 372139331183
Oligodendrocyte precursor cells 2235112191592
Oligodendrocytes 9021112901591
Microglial cells 16129633778
Muller glia cells 2263393478
Germ cells Spermatogonia 26148411585
Spermatocytes 3735810021397
Early spermatids 156106717692992
Late spermatids 9398415102587
Trophoblast cells Cytotrophoblasts 3103552658
Syncytiotrophoblasts 45132743920
Extravillous trophoblasts 26106703835
Endothelial cells Endothelial cells 465262331
Muscle cells Cardiomyocytes 170110610890
Skeletal myocytes 2954250333
Smooth muscle cells 249319370
Adipocytes Adipocytes 1781525623
Pigment cells Melanocytes 1432157203
Mesenchymal cells Fibroblasts 845408461
Hepatic stellate cells 1362277352
Peritubular cells 241322365
Endometrial stromal cells 318317338
Undifferentiated cells Undifferentiated cells 019194213
Blood & immune cells T-cells 62101321484
B-cells 2060261341
Plasma cells 13461379574
NK-cells 568389462
Granulocytes 2663311400
Monocytes 1174429514
Macrophages 11100445556
Hofbauer cells 16117593726
Kupffer cells 273403478
Dendritic cells 492476572
Langerhans cells 1554422491
Erythroid cells 4534358437