This data was generated by Siletti K et al. (2023), re-processed by HPA (see methods) and simplified for global overview
SINGLE CELL TYPE - BRAIN NEURONSi
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
Cerebellar granular cells V...
c-1
Cortical superficial intrat...
c-2
Hippocampal excitatory VGLU...
c-3
Midbrain inhibitory (PCP4+ ...
c-4
Medium spiny neurons GAD1/G...
c-5
Medium spiny neurons GAD1/G...
c-6
Dentate gyrus excitatory VG...
c-7
Cortex/hippocampus CGE Inte...
c-8
Medium spiny neurons GAD1/G...
c-9
Medium spiny neurons GAD1/G...
c-10
Mammillary/tuberal excitato...
c-11
Cerebellar granular cells V...
c-12
Cortex/hippocampus CGE Inte...
c-13
Supraoptic nucleus/POA unas...
c-14
Cortex/hippocampus MGE Inte...
c-15
Cortex/hippocampus MGE Inte...
c-16
Eccentric medium spiny neur...
c-17
Midbrain excitatory VGLUT2 ...
c-18
Hypothalamus unassigned
c-19
Cortical deep projecting ex...
c-20
Cerebellar granular cells V...
c-21
Cerebellar basket/stellate ...
c-22
Cortical intermediate excit...
c-23
Midbrain excitatory
c-24
Cortiex/hippocampus superfi...
c-25
Dentate gyrus excitatory VG...
c-26
Cortical intermediate intra...
c-27
Medium spiny neurons GAD1/G...
c-28
Midbrain inhibitory
c-29
Midbrain inhibitory (CALB2+
c-30
Midbrain/hypothalamic excit...
c-31
Cortical superficial intrat...
c-32
Tectum excitatory VGLUT2
c-33
Septal nuclei inhibitory
c-34
Hypothalamic inhibitory (LH
c-35
Cortex/hippocampus LAMP5-LH...
c-36
Midbrain unassigned
c-37
Midbrain/hypothalamic excit...
c-38
Mammillary body unassigned
c-39
Tectum inhibitory
c-40
Basal ganglia MGE Interneur...
c-41
Hippocampal excitatory VGLU...
c-42
Basal ganglia MGE Interneur...
c-43
Dentate gyrus excitatory VG...
c-44
Cortical superficial intrat...
c-45
Midbrain/hypothalamus unass...
c-46
Hypothalamic inhibitory (RO
c-47
Midbrain excitatory VGLUT2 ...
c-48
Midbrain inhibitory (CALB2+...
c-49
Basal striatal-projecting c...
c-50
Mammillary body excitatory ...
c-51
Midbrain/hippocampus excita...
c-52
Midbrain excitatory VGLUT2 ...
c-53
Midbrain inhibitory
c-54
Cortical deep projecting ex...
c-55
Midbrain/hypothalamus unass...
c-56
Hippocampal excitatory VGLU...
c-57
Midbrain/hypothalamic excit...
c-58
Midbrain/hypothalamic inhib...
c-59
Tuberal hypothalamus excita...
c-60
Midbrain excitatory VGLUT2
c-61
Hypothalamic/SN HIST monoam...
c-62
Cortex/hippocampus MGE Inte...
c-63
Hypothalamic excitatory VGL
c-64
Hypothalamic AVP magnocellu...
c-65
Hippocampal excitatory VGLU...
c-66
Deep cerebellar nuclei inte...
c-67
Cortex/hippocampus MGE Inte...
c-68
Basal cortical-projecting c...
c-69
Deep cerebellar nuclei exci...
c-70
Cortex/hippocampus excitato...
c-71
Cerebellar unipolar brush c...
c-72
Deep cerebellar nuclei proj...
c-73
Tegmentum excitatory VGLUT2...
c-74
Tegmentum inhibitory (BCL11...
c-75
Hippocampal excitatory VGLU...
c-76
Hypothalamic OXT magnocellu...
c-77
Midbrain/hypothalamic dopam...
c-78
Midbrain/Hypothalamic hista...
c-79
Supraoptic nucleus inhibito...
c-80
Hypothalamic parvocellular ...
c-81
Midbrain dopaminergic
c-82
Supraoptic nucleus inhibito...
c-83
Hippocampus unasigned (BHLH...
c-84
Tegmentum excitatory VGLUT1...
c-85
Midbrain serotonergic
c-86
GPi unasigned
c-87
POA/BNST inhibitory (SST+ V...
c-88
Cerebellar golgi cells
c-89
Cortex/hippocampus unassign...
c-90
Septal nuclei excitatory VG...
c-91
Mammillary body excitatory ...
c-92
Superior colliculus choline...
c-93
GPe inhibitory (CUX2+)
c-94
Cerebellar purkinje cells
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This data was generated by Siletti K et al. (2023), re-processed by HPA (see methods) and simplified for global overview
SINGLE CELL TYPE - BRAIN NON-NEURONSi
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
Bergmann glia
c-1
Choroid plexus epithelial c...
c-2
Oligodendrocyte progenitor ...
c-3
Microglia
c-4
Astrocytes
c-5
Oligodendrocytes
c-6
Fibroblasts
c-7
Ependymal cells
c-8
Oligodendrocyte progenitor ...
c-9
Microglia
c-10
Oligodendrocytes
c-11
Astrocytes
c-12
Oligodendrocytes
c-13
Astrocytes
c-14
Capillary endothelial cells
c-15
Immature oligodendrocytes (...
c-16
Immature oligodendrocytes
c-17
Pericytes
c-18
T-cells
c-19
Choroid plexus epithelial c...
c-20
Ependymal cells
c-21
Fibroblasts
c-22
Arterial endothelial cells
c-23
Venous endothelial cells
c-24
NK-cells
c-25
Vascular smooth muscle cell
c-26
Macrophages
c-27
Monocytes
c-28
Microglia
c-29
Astrocytes
c-30
Oligodendrocytes
c-31
B-cells
Show allShow less
This data was generated by Siletti K 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 - BRAIN NEURONS
SINGLE CELL TYPE - BRAIN NON-NEURONS
Max-norm
Z-score
Fraction of highest expression (≥1 nTPM)
log2(nTPM+1) z-score
Max-norm
Z-score
Fraction of highest expression (≥1 nTPM)
log2(nTPM+1) z-score
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The Human Protein Atlas project is funded
