The single cell type resource - Explore the expression profiles in single cell types



CNN1 - Prostate


TSPY2 - Testis

This part of the Single cell resource contains Single cell type information based on single cell RNA sequencing (scRNAseq) data from 31 human tissues including peripheral blood mononuclear cells (PBMCs). The data is linked to in-house generated immunohistochemically stained tissue sections presented in the Tissue resource 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 557 individual cell type clusters corresponding to 15 different cell type groups, and 81 different cell types. 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 can be found on the Methods Summary. A cluster comparison between the HPA pipeline and Tabula Sapiens can be found here.

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 SINGLE CELL TYPE PROTEOMESi

SINGLE CELL TYPE EXPRESSIONi

The RNA data was used to cluster genes according to their expression across single cell types. The clustering of 19203 genes expressed in single cell types resulted in 80 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


SINGLE CELL TYPE SUMMARYi


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
enriched
EnhancedTotal
elevated
Glandular epithelial cells Ciliated cells 3298404534
Basal respiratory cells 323271297
Club cells 220155177
Ionocytes 235232269
Mucus glandular cells 37142152
Serous glandular cells 2628185239
Gastric mucus-secreting cells 2556368449
Proximal enterocytes 4895741884
Paneth cells 736349392
Distal enterocytes 644624674
Intestinal goblet cells 1436301351
Exocrine glandular cells 2521153199
Basal prostatic cells 821176205
Prostatic glandular cells 1920228267
Breast glandular cells 715133155
Breast myoepithelial cells 315152170
Glandular and luminal cells 1025307342
Secretory cells 511134150
Squamous epithelial cells Basal keratinocytes 040254294
Suprabasal keratinocytes 6066416542
Basal squamous epithelial cells 034321355
Squamous epithelial cells 144370415
Specialized epithelial cells Alveolar cells type 1 629300335
Alveolar cells type 2 1030205245
Salivary duct cells 16119126
Ductal cells 113172186
Hepatocytes 148123578849
Cholangiocytes 532173210
Proximal tubular cells 32102587721
Distal tubular cells 1326327366
Collecting duct cells 620200226
Mesothelial cells 826215249
Sertoli cells 929259297
Granulosa cells 519230254
Endocrine cells Enteroendocrine cells 1844224286
Pancreatic endocrine cells 727168202
Leydig cells 039292331
Neuronal cells Excitatory neurons 2443517952254
Inhibitory neurons 2444816622134
Cone photoreceptor cells 25103527655
Rod photoreceptor cells 2696630752
Bipolar cells 2094585699
Horizontal cells 1195673779
Glial cells Astrocytes 312249961251
Oligodendrocyte precursor cells 2033912631622
Oligodendrocytes 7822013321630
Microglial cells 10137659806
Muller glia cells 2056373449
Schwann cells 1129322362
Germ cells Spermatogonia 20126382528
Spermatocytes 4934810181415
Early spermatids 149104918553053
Late spermatids 25998717322978
Oocytes 981348211053
Trophoblast cells Cytotrophoblasts 157368426
Syncytiotrophoblasts 5086651787
Extravillous trophoblasts 2769583679
Endothelial cells Endothelial cells 259288349
Lymphatic endothelial cells 846286340
Muscle cells Cardiomyocytes 54106571731
Skeletal myocytes 80108321509
Smooth muscle cells 237336375
Adipocytes Adipocytes 1162412485
Pigment cells Melanocytes 1830212260
Mesenchymal cells Fibroblasts 533365403
Peritubular cells 137350388
Endometrial stromal cells 321248272
Ovarian stromal cells 127220248
Undifferentiated cells Undifferentiated cells 317206226
Blood & immune cells T-cells 80101323504
B-cells 1343292348
Plasma cells 16261413636
NK-cells 1777433527
Granulocytes 1948297364
Monocytes 2064798882
Macrophages 089414503
Hofbauer cells 1179436526
Kupffer cells 378384465
Dendritic cells 1229421462
Langerhans cells 1655540611
Erythroid cells 4035359434