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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
B-cells
c-1
Corneal apical cells
c-2
T-cells (CD4+)
c-3
Venous ECs
c-4
B-cells
c-5
Rod photoreceptor cells
c-6
Corneal suprabasal epitheli...
c-7
T-cells (CD8+)
c-8
Fibroblasts
c-9
Conjunctival epithelial cel
c-10
B-cells
c-11
Conjunctival epithelial cel
c-12
Conjunctival epithelial cel
c-13
T-cells
c-14
Conjunctival epithelial cel
c-15
Fibroblasts
c-16
Conjunctival epithelial cel
c-17
Plasma cells
c-18
Resident macrophages
c-19
T-cells (CD4+)
c-20
Conjunctival epithelial cel
c-21
Corneal basal epithelial ce
c-22
Vascular smooth muscle cell
c-23
Limbal epithelial cells
c-24
Fibroblasts
c-25
Capillary ECs
c-26
T-cells (CD4+)
c-27
T-cells (CD8+)
c-28
Lymphatic endothelial cells
c-29
Monocytes
c-30
NK-cells
c-31
M2-like macrophages
c-32
Conjunctival Melaonocytes
c-33
Arterial ECs
c-34
NK-T-cells
c-35
Neutrophils
c-36
Transitional M2-like macrop...
c-37
Müller glia
c-38
Mast cells
c-39
B-cells
c-40
Pericytes
c-41
Serous acinar cells
c-42
Uveal Melanocytes
c-43
Mixed cell types
c-44
Corneal Fibroblasts
c-45
Bipolar cells
c-46
Conjunctival goblet cells
c-47
Schwann cells
c-48
Amacrine cells
c-49
Cone photoreceptor cells
c-50
Retinal pigment epithelia
c-51
Oligodendrocytes
c-52
Horizontal cells
SINGLE CELL TYPE - RETINAi
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
Rod photoreceptor cells
c-1
Müller glia
c-2
Rod photoreceptor cells
c-3
Rod photoreceptor cells
c-4
Rod photoreceptor cells
c-5
Rod photoreceptor cells
c-6
ON bipolar cells
c-7
Müller glia
c-8
Rod bipolar cells
c-9
OFF bipolar cells
c-10
Müller glia
c-11
Rod photoreceptor cells
c-12
OFF bipolar cells
c-13
Amacrine cells
c-14
Rod bipolar cells
c-15
Horizontal cells
c-16
Glycinergic amacrine cells
c-17
OFF bipolar cells
c-18
Cone photoreceptor cells
c-19
Rod bipolar cells
c-20
OFF bipolar cells
c-21
Rod bipolar cells
c-22
OFF bipolar cells
c-23
ON bipolar cells
c-24
ON bipolar cells
c-25
ON bipolar cells
c-26
Amacrine cells (SLC18A2+)
c-27
Glycinergic horizontal-like...
c-28
Starbust amacrine cells (Ch...
c-29
Retinal ganglion cells
c-30
Astrocytes
c-31
Microglia
c-32
Mural & Epithelial cells
SINGLE CELL TYPE TABULA SAPIENS - EYEi
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
Conjunctival epithelial cel
c-1
Monocyte
c-2
Microglial cell
c-3
Eye photoreceptor cell
c-4
Muller cell
c-5
Fibroblast
c-6
T cell
c-7
Limbal stem cell
c-8
Retinal blood vessel endoth...
c-9
Epithelial cell of lacrimal...
c-10
Corneal keratocyte
c-11
B cell
c-12
Retinal pigment epithelial ...
c-13
Corneal epithelial cell
c-14
Limbal stromal cell
c-15
Melanocyte
c-16
Retinal bipolar neuron
c-17
Dendritic cell
c-18
Plasma cell
c-19
Lacrimal gland functional u...
c-20
Macrophage
c-21
Erythroid lineage cell
c-22
Radial glial cell
c-23
Ocular surface cell
c-24
Cd8-positive, alpha-beta t ...
c-25
Endothelial cell
c-26
Retina horizontal cell
c-27
Ciliary body
c-28
Cd4-positive, alpha-beta t ...
c-29
Mast cell
c-30
Adipocyte
c-31
Retinal ganglion cell
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
