This data was generated by Pass CG et al. (2023), re-processed by HPA (see methods) and simplified for global overview
SINGLE CELL TYPE - SKELETAL MUSCLEi
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
Myonuclei (type I)
c-1
Myonuclei (type I)
c-2
Myonuclei (type I)
c-3
Myonuclei (type I)
c-4
Myonuclei (type I)
c-5
Myonuclei (type I)
c-6
Myonuclei (type I)
c-7
Myonuclei (type IIa)
c-8
Myonuclei (denervated)
c-9
Fibro-adipogenic progenitor
c-10
Myonuclei (type IIx)
c-11
Myonuclei (type I)
c-12
Myonuclei (denervated)
c-13
Myonuclei (type IIa)
c-14
Myosatellite cells
c-15
Myonuclei (type I)
c-16
Macrophages
c-17
Myonuclei (denervated)
c-18
Capillary endothelial cells
c-19
Adipocytes
c-20
Vascular smooth muscle cell
c-21
Myonuclei (NMJ associated)
c-22
Pericytes
c-23
Arterial endothelial cells
c-24
T-cells
c-25
Venous endothelial cells
c-26
NK-cells & T-cells
c-27
Mast cells
Show allShow less
This data was generated by Pass CG et al. (2023), re-processed by HPA (see methods) and simplified for global overview
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.
SINGLE CELL TYPE
Max-norm
Z-score
Fraction of highest expression (≥1 nTPM)
log2(nTPM+1) z-score
We use cookies to enhance the usability of our website. If you continue, we'll assume that you are happy to receive all cookies. More information. Don't show this again.
The Human Protein Atlas project is funded
