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RNA expression in the single cell type clusters identified in this tissue visualized by a UMAP plot (top) and a bar chart (bottom).
- UMAP PLOT visualizes the cells in each cluster; where each dot corresponds to a cell. For each individual cell, mouseover reveals read count and which cluster the cell belongs to. Hovering over a cluster name will highlight the corresponding cluster in the bar chart below. There are 2 options for color schemes: 1) cell type color, which is based on cell type groups used in the Single cell type part of the Single cell resource and 2) cluster color, which assigns a unique color to each cluster.
The cells are colored according to % of max (log2(read_count+1)/log2(max(read_count)+1)*100) in five different bins (<1%,<25%,<50%,<75%,≥75%)
- The LEGEND shows RNA expression (nTPM) in each cell type cluster. Hovering over the cluster name reveals nTPM value and number of included cells. Hovering over a bar highlights the corresponding cluster in the UMAP plot above. Color-coding can be toggled on the top of the page, between 2 options: 1) cell type color, which is based on cell type groups used in the Single cell type part of the Single cell resource and 2) cluster color, which assigns a unique color to each cluster.
Cell type color
Cluster color
Colored according to cell type group
Colored according to clusters
Read count filter:0
Cluster filter:
Cluster
Cell type
Expression (nCPM)
c-0
Early acinar cells (SOX9+)
c-1
T-cells (CD8+)
c-2
Fibroblasts
c-3
Mature serous acinar cells
c-4
Memory B-cells
c-5
Early seromucous acinar cel
c-6
Naive B-cells
c-7
Duct cells
c-8
Venous endothelial cells
c-9
Basal epithelial cells
c-10
Seromucous acinar cells
c-11
Macrophages (TREM2+)
c-12
Fibroblasts
c-13
Macrophages (LYVE1+)
c-14
Early mucous acinar cells
c-15
Mature serous acinar cells
c-16
Naive T-cells (CD4+)
c-17
Mucous acinar cells (MUC19+
c-18
Neutrophils
c-19
Mucous acinar cells (MUC5B+
c-20
Cytotoxic T-cells (CD8+)
c-21
Regulatory T-cells (CD4+)
c-22
Plasma cells
c-23
Myoepithelial cells
c-24
Macrophages
c-25
NK-cells
c-26
Lymphatic endothelial cells
c-27
Capillary endothelial cells
c-28
Monocytes (FCN1+)
c-29
Vascular smooth muscle cell
c-30
Ionocytes
c-31
Fibroblasts (FN1+)
c-32
Arterial endothelial cells
c-33
Mast cells
c-34
Naive T-cells (CD8+)
c-35
Serous acinar cells (Mixed)
c-36
NKT-cells
c-37
Cycling immune cells
c-38
ILCs
c-39
Serous & Fibroblasts
c-40
Pericytes
c-41
Cycling epithelial cells
c-42
Fibroblasts (NGFR+)
c-43
Non-myelinated schwann cell
SINGLE CELL TYPE TABULA SAPIENS - SALIVARY GLANDi
RNA expression in the single cell type clusters identified in this tissue visualized by a UMAP plot and a bar chart. This window shows single cell expression data generated by the https://tabula-sapiens.sf.czbiohub.org/about#consortium, that also offers UMAP visualization and cell type clusters for each tissue sample: https://tabula-sapiens.sf.czbiohub.org/organs, here integrate offering easy comparison to the HPA cluster method of single cell types.
UMAP PLOT visualizes the cells in each cluster; where each dot corresponds to a cell. For each individual cell, mouseover reveals read count and which cluster the cell belongs to. Hovering over a cluster name will highlight the corresponding cluster in the bar chart below. There are 2 options for color schemes: 1) cell type color, which is based on cell type groups used in the Single cell type part of the Single cell resource and 2) cluster color, which assigns a unique color to each cluster.
The cells are colored according to % of max (log2(read_count+1)/log2(max(read_count)+1)*100) in five different bins (<1%,<25%,<50%,<75%,≥75%)
The LEGEND shows RNA expression (nTPM) in each cell type cluster. Hovering over the cluster name reveals nTPM value and number of included cells. Hovering over a bar highlights the corresponding cluster in the UMAP plot above. Color-coding can be toggled on the top of the page, between 2 options: 1) cell type color, which is based on cell type groups used in the Single cell type part of the Single cell resource and 2) cluster color, which assigns a unique color to each cluster.
Cell type color
Cluster color
Colored according to cell type group
Colored according to clusters
Read count filter:0
Cluster
Cell type
Expression (nCPM)
c-0
Acinar cell of salivary gla
c-1
Naive b cell
c-2
Memory b cell
c-3
Cd4-positive helper t cell
c-4
Pericyte cell
c-5
Nk cell
c-6
Fibroblast
c-7
Endothelial cell of lymphat...
c-8
Adventitial cell
c-9
B cell
c-10
Endothelial cell
c-11
Monocyte
c-12
Plasma cell
c-13
Duct epithelial cell
c-14
Basal cell
c-15
Cd8-positive, alpha-beta t ...
c-16
Neutrophil
c-17
T cell
c-18
Myoepithelial cell
c-19
Cd4-positive, alpha-beta t ...
c-20
Macrophage
c-21
Salivary gland cell
c-22
Ionocyte
CELL TYPE MARKERSi
The heatmap in this section shows expression of the currently selected gene (on top) and well-known cell type markers in the different single cell type clusters of this tissue. The panel on the left shows which cell type each marker is associated with. Color-coding is based on cell type groups, each consisting of cell types with functional features in common.
Hover the mouse-pointer over the individual data points (squares) to see nTPM level and Z-score. Clicking on a gene name redirects to the corresponding gene page.
Z-score is when you normalize a variable such that the standard deviation is 1 and the mean is 0. Thus, all the genes are easier to compare, as they have the same center and distribution.
The Human Protein Atlas project is funded
