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 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 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 557 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 SINGLE CELL TYPE PROTEOMESⁱ


Glandular epithelial cells		Squamous epithelial cells
Specialized epithelial cells		Endocrine cells
Neuronal cells		Glial cells
Germ cells		Trophoblast cells
Endothelial cells		Muscle cells
Mesenchymal cells		Adipocytes
Pigment cells	Blood & immune cells	Undifferentiated cells

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	Enriched	Group enriched	Enhanced	Total elevated
Glandular epithelial cells	Ciliated cells	32	98	404	534
	Basal respiratory cells	3	23	271	297
	Club cells	2	20	155	177
	Ionocytes	2	35	232	269
	Mucus glandular cells	3	7	142	152
	Serous glandular cells	26	28	185	239
	Gastric mucus-secreting cells	25	56	368	449
	Proximal enterocytes	48	95	741	884
	Paneth cells	7	36	349	392
	Distal enterocytes	6	44	624	674
	Intestinal goblet cells	14	36	301	351
	Exocrine glandular cells	25	21	153	199
	Basal prostatic cells	8	21	176	205
	Prostatic glandular cells	19	20	228	267
	Breast glandular cells	7	15	133	155
	Breast myoepithelial cells	3	15	152	170
	Glandular and luminal cells	10	25	307	342
	Secretory cells	5	11	134	150
Squamous epithelial cells	Basal keratinocytes	0	40	254	294
	Suprabasal keratinocytes	60	66	416	542
	Basal squamous epithelial cells	0	34	321	355
	Squamous epithelial cells	1	44	370	415
Specialized epithelial cells	Alveolar cells type 1	6	29	300	335
	Alveolar cells type 2	10	30	205	245
	Salivary duct cells	1	6	119	126
	Ductal cells	1	13	172	186
	Hepatocytes	148	123	578	849
	Cholangiocytes	5	32	173	210
	Proximal tubular cells	32	102	587	721
	Distal tubular cells	13	26	327	366
	Collecting duct cells	6	20	200	226
	Mesothelial cells	8	26	215	249
	Sertoli cells	9	29	259	297
	Granulosa cells	5	19	230	254
Endocrine cells	Enteroendocrine cells	18	44	224	286
	Pancreatic endocrine cells	7	27	168	202
	Leydig cells	0	39	292	331
Neuronal cells	Excitatory neurons	24	435	1795	2254
	Inhibitory neurons	24	448	1662	2134
	Cone photoreceptor cells	25	103	527	655
	Rod photoreceptor cells	26	96	630	752
	Bipolar cells	20	94	585	699
	Horizontal cells	11	95	673	779
Glial cells	Astrocytes	31	224	996	1251
	Oligodendrocyte precursor cells	20	339	1263	1622
	Oligodendrocytes	78	220	1332	1630
	Microglial cells	10	137	659	806
	Muller glia cells	20	56	373	449
	Schwann cells	11	29	322	362
Germ cells	Spermatogonia	20	126	382	528
	Spermatocytes	49	348	1018	1415
	Early spermatids	149	1049	1855	3053
	Late spermatids	259	987	1732	2978
	Oocytes	98	134	821	1053
Trophoblast cells	Cytotrophoblasts	1	57	368	426
	Syncytiotrophoblasts	50	86	651	787
	Extravillous trophoblasts	27	69	583	679
Endothelial cells	Endothelial cells	2	59	288	349
	Lymphatic endothelial cells	8	46	286	340
Muscle cells	Cardiomyocytes	54	106	571	731
	Skeletal myocytes	80	108	321	509
	Smooth muscle cells	2	37	336	375
Adipocytes	Adipocytes	11	62	412	485
Pigment cells	Melanocytes	18	30	212	260
Mesenchymal cells	Fibroblasts	5	33	365	403
	Peritubular cells	1	37	350	388
	Endometrial stromal cells	3	21	248	272
	Ovarian stromal cells	1	27	220	248
Undifferentiated cells	Undifferentiated cells	3	17	206	226
Blood & immune cells	T-cells	80	101	323	504
	B-cells	13	43	292	348
	Plasma cells	162	61	413	636
	NK-cells	17	77	433	527
	Granulocytes	19	48	297	364
	Monocytes	20	64	798	882
	Macrophages	0	89	414	503
	Hofbauer cells	11	79	436	526
	Kupffer cells	3	78	384	465
	Dendritic cells	12	29	421	462
	Langerhans cells	16	55	540	611
	Erythroid cells	40	35	359	434