The single cell type section - 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 29 human tissues and peripheral blood mononuclear cells (PBMCs). The data is linked to in-house generated immunohistochemically stained tissue sections presented in the Tissue section in order to visualize 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 536 individual cell type clusters corresponding to 15 different cell type groups. A specificity classification was performed to determine the number of genes elevated in these single cell types. 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 19212 genes expressed in single cell types resulted in 77 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 318268289
Club cells 219147168
Ionocytes 233233268
Respiratory ciliated cells 11132432575
Mucus glandular cells 36144153
Serous glandular cells 2430160214
Gastric mucus-secreting cells 2747372446
Proximal enterocytes 5297722871
Paneth cells 747335389
Distal enterocytes 549536590
Intestinal goblet cells 1339291343
Exocrine glandular cells 633210249
Basal prostatic cells 921175205
Prostatic glandular cells 1920226265
Breast glandular cells 710140157
Breast myoepithelial cells 313164180
Endometrial ciliated cells 2127424553
Glandular and luminal cells 329316348
Squamous epithelial cells Basal keratinocytes 040262302
Suprabasal keratinocytes 6064413537
Basal squamous epithelial cells 129322352
Squamous epithelial cells 142369412
Specialized epithelial cells Alveolar cells type 1 729306342
Alveolar cells type 2 1029193232
Salivary duct cells 17118126
Ductal cells 115168184
Hepatocytes 149119575843
Cholangiocytes 527176208
Proximal tubular cells 32105585722
Distal tubular cells 1330329372
Collecting duct cells 922206237
Thymic epithelial cells 825222255
Sertoli cells 1130272313
Granulosa cells 1444359417
Endocrine cells Enteroendocrine cells 1850212280
Pancreatic endocrine cells 829166203
Leydig cells 244293339
Theca cells 1026203239
Neuronal cells Excitatory neurons 2346017892272
Inhibitory neurons 2546616502141
Cone photoreceptor cells 24110518652
Rod photoreceptor cells 28101636765
Bipolar cells 21100577698
Horizontal cells 1199680790
Glial cells Astrocytes 352329891256
Oligodendrocyte precursor cells 2234912621633
Oligodendrocytes 8022713181625
Microglial cells 12148660820
Muller glia cells 2158385464
Schwann cells 1228332372
Germ cells Spermatogonia 27141397565
Spermatocytes 5436710171438
Early spermatids 128103917702937
Late spermatids 26599117443000
Trophoblast cells Cytotrophoblasts 162357420
Syncytiotrophoblasts 5392645790
Extravillous trophoblasts 2870582680
Endothelial cells Endothelial cells 468296368
Muscle cells Cardiomyocytes 57106579742
Skeletal myocytes 83111316510
Smooth muscle cells 434336374
Adipocytes Adipocytes 1072416498
Pigment cells Melanocytes 1831209258
Mesenchymal cells Fibroblasts 445352401
Peritubular cells 238354394
Endometrial stromal cells 320258281
Undifferentiated cells Undifferentiated cells 323222248
Blood & immune cells T-cells 75104322501
B-cells 1449294357
Plasma cells 16058447665
NK-cells 1680442538
Granulocytes 2042285347
Monocytes 474610688
Macrophages 193418512
Hofbauer cells 1092448550
Kupffer cells 488360452
Dendritic cells 1333430476
Langerhans cells 1651558625
Erythroid cells 4037366443