On the top, protein expression in current human tissue, based on all annotated cell types, is reported with the units not detected (n), low (l), medium (m) and high (h). Underneath, protein expression in each annotated cell type are reported using the same units. Protein expression data is based on knowledge-based annotation. For genes where more than one antibody has been used, a collective score is set. If knowledge-based annotation could not be performed for a gene, no data is displayed here. View antibody staining data further down this page.
No data
RNA expressioni
A summary of mRNA expression data available for current tissue based on several datasets. The mRNA expression levels in human tissues are based on RNA-seq data generated by the Human Protein Atlas HPA, Genotype-Tissue Expression GTEx portal and CAGE data generated by the FANTOM5 consortium. Consensus normalized expression levels for human tissues was created by combining the data from HPA and GTEx datasets. The mRNA expression levels in pig brain are based on RNA-seq data generated by the Human Protein Atlas, and for mouse brain HPA data and in situ hybridization generated by the Allen brain atlas dataset are reported.
Scroll down to view mRNA expression data in more detail.
HPA Brain:
1.2
nTPM
FANTOM5:
0.0
Scaled Tags Per Million
Macaque:
3.8
nTPM
Mouse:
0.5
nTPM
Rat:
1.1
nTPM
Pig:
1.0
nTPM
MIDBRAIN - SINGLE NUCLEI RNA EXPRESSIONi
RNA expression in the single nuclei cluster types identified in this brain region visualized by a UMAP plot (top) and a bar chart (to the right).
- 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 two the right. 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. There are 3 options for cell intensities: 1) Intensity, which color the individual cells according to % of max (log2(read_count+1)/log2(max(read_count)+1)*100) in five different bins (<1%,<25%,<50%,<75%,≥75%) 2) Interval, which color the individual cells according to fixed interval of read count (0,1,2-4,5-9,>10) 3) Hexagon, which color the hexagon on average read count of all cells inside the hexagon
- The BAR CHART shows RNA expression (nTPM) in each cluster type. 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.
SINGLE NUCLEI BRAIN - MIDBRAIN, NEURONSi
RNA expression in the single nuclei cluster types identified in this brain region visualized by a UMAP plot (top) and a bar chart (to the right).
- 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 two the right. 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. There are 3 options for cell intensities: 1) Intensity, which color the individual cells according to % of max (log2(read_count+1)/log2(max(read_count)+1)*100) in five different bins (<1%,<25%,<50%,<75%,≥75%) 2) Interval, which color the individual cells according to fixed interval of read count (0,1,2-4,5-9,>10) 3) Hexagon, which color the hexagon on average read count of all cells inside the hexagon
- The BAR CHART shows RNA expression (nTPM) in each cluster type. 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-1
Inhibitory (GAD1/2) RORB+ K
c-2
Excitatory (VGLUT1) ETV1+ Z...
c-3
Inhibitory (GAD1/2) RORB+ K
c-4
Inhibitory (GAD1/2) RORB+ K
c-5
Unassigned
c-6
Tectum Excitatory (VGLUT2)
c-7
Inhibitory (GAD1/2)
c-8
Inhibitory (GAD1/2) TFAP2B+
c-9
Excitatory (VGLUT2)
c-10
Excitatory (VGLUT2)
c-11
Tectum Inhibitory (GAD1/2)
c-12
Excitatory (VGLUT2) TFAP2B+
c-13
Excitatory (VGLUT2)
c-14
Excitatory (VGLUT2)
c-15
Tectum Excitatory (VGLUT2)
c-16
Excitatory (VGLUT2)
c-17
Inhibitory (GAD1/2)
c-18
Excitatory (VGLUT2)
c-19
Inhibitory (GAD1/2)
c-20
Inhibitory (GAD1/2)
c-21
Excitatory (VGLUT2)
c-22
Excitatory (VGLUT2)
c-23
Inhibitory (GAD1/2) TFAP2B+
c-24
Inhibitory (GAD1/2)
c-25
Excitatory (VGLUT2) CRH+ CA...
c-26
Inhibitory (GAD1/2) SST+
c-27
Inhibitory (GAD1/2) NPY+
c-28
Inhibitory (GAD1/2) RORB+ K
c-29
Excitatory (VGLUT2) TFAP2B+
c-30
Excitatory (VGLUT2)
c-31
Dopaminergic TH+ LMX1A+ SLC...
c-32
Inhibitory (GAD1/2) PVALB+
c-33
Tegmentum Excitatory (VGLUT...
c-34
Excitatory (VGLUT2) LMX1A+
c-35
Tegmentum Inhibitory (GAD2)...
c-36
TPH2+
c-37
Inhibitory (GAD1/2) CXCL14+
c-38
Excitatory (VGLUT1) SATB2+
c-39
Inhibitory (GAD1/2) RORB+ K
c-40
Excitatory (VGLUT2) MEIS2+
c-41
Inhibitory (GAD1/2) TFAP2B+
c-42
Excitatory (VGLUT2)
c-43
Excitatory (VGLUT1)
c-44
SN Monoaminergic Inhibitory...
c-45
Inhibitory (GAD1/2)
c-46
Excitatory (VGLUT1) GRP+
c-47
Inhibitory (GAD1/2) PVALB+ ...
c-48
Excitatory (VGLUT1)
c-49
Inhibitory (GAD1/2) LAMP5+
c-50
Excitatory (VGLUT2) KIT+
c-51
Excitatory (VGLUT1) SLC5A7+
c-52
Inhibitory (GAD1/2) NOS1+ G...
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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 NUCLEI BRAIN - MIDBRAIN, NON-NEURONALi
RNA expression in the single nuclei cluster types identified in this brain region visualized by a UMAP plot (top) and a bar chart (to the right).
- 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 two the right. 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. There are 3 options for cell intensities: 1) Intensity, which color the individual cells according to % of max (log2(read_count+1)/log2(max(read_count)+1)*100) in five different bins (<1%,<25%,<50%,<75%,≥75%) 2) Interval, which color the individual cells according to fixed interval of read count (0,1,2-4,5-9,>10) 3) Hexagon, which color the hexagon on average read count of all cells inside the hexagon
- The BAR CHART shows RNA expression (nTPM) in each cluster type. 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-1
Oligodendrocytes
c-2
Oligodendrocytes
c-3
Microglia
c-4
Oligodendrocytes
c-5
Oligodendrocyte progenitor ...
c-6
Astrocytes
c-7
Oligodendrocytes
c-8
Oligodendrocytes
c-9
Oligodendrocytes
c-10
Oligodendrocytes
c-11
Oligodendrocytes
c-12
Astrocytes
c-13
Fibroblasts
c-14
NK-cells & T-cells
c-15
Macrophages
c-16
Ependymal cells
c-17
Capillary endothelial cells
c-18
Pericytes
c-19
Oligodendrocyte progenitor ...
c-20
Immature oligodendrocytes
c-21
Vascular smooth muscle cell
c-22
Oligodendrocyte progenitor ...
c-23
B-cells & Monocytes doublet
c-24
Arterial endothelial cells
c-25
CD44+ Mural cells
c-26
Bergmann glia
c-27
Oligodendrocytes & Lymphocy
c-28
Macrophages & Monocytes
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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
MIDBRAIN - Annotated protein expression
Pending normal tissue analysis
MIDBRAIN - HPA Brain RNA-seq
Max subtype nTPMi
Max subtype nTPM is the value for the subtype with the largest average nTPM across the subtype samples.
1.2
Sample id
Sample description
nTPM
Cuneiform nucleus nTPM: 1.2
2219
Male, age 76, both hemispheres
4.9
2019
Male, age 18, unknown
1.2
1870
Female, age 42, unknown
1.0
2666
Male, age 74, left hemisphere
0.9
1830
Male, age 51, unknown
0.8
1833
Male, age 53, unknown
0.8
2828
Female, age 72, unknown
0.7
2586
Male, age 75, left hemisphere
0.6
2411
Female, age 72, unknown
0.5
1827
Male, age 72, unknown
0.4
Dorsal raphe nucleus nTPM: 0.5
1828
Male, age 53, unknown
0.6
2016
Female, age 72, unknown
0.6
2298
Female, age 72, unknown
0.6
2047
Male, age 72, unknown
0.4
2750
Male, age 76, both hemispheres
0.4
Inferior colliculus nTPM: 0.7
1848
Female, age 42, unknown
0.9
1890
Male, age 53, unknown
0.8
2849
Male, age 72, unknown
0.7
2097
Female, age 72, unknown
0.4
Median raphe nucleus nTPM: 0.5
2220
Male, age 76, midline
0.5
Periaquaductal grey, anterior nTPM: 0.3
1947
Male, age 18, unknown
0.4
1795
Male, age 51, unknown
0.3
2502
Female, age 75, unknown
0.2
Periaquaductal grey, dorsal nTPM: 0.4
1831
Male, age 72, unknown
0.6
2464
Female, age 72, unknown
0.4
2850
Male, age 76, both hemispheres
0.4
1840
Male, age 53, unknown
0.2
Periaquaductal grey, lateral nTPM: 0.3
2053
Male, age 18, unknown
0.4
2140
Male, age 76, both hemispheres
0.3
2272
Male, age 74, both hemispheres
0.3
Pretectal area nTPM: 0.4
1815
Male, age 53, unknown
0.8
1817
Female, age 42, unknown
0.7
2007
Male, age 72, unknown
0.7
1816
Male, age 51, unknown
0.6
2825
Male, age 18, unknown
0.5
2224
Female, age 72, unknown
0.4
1944
Female, age 72, unknown
0.3
2407
Male, age 75, both hemispheres
0.3
2316
Male, age 76, right hemisphere
0.2
2667
Female, age 75, unknown
0.2
2273
Male, age 74, both hemispheres
0.0
Red nucleus nTPM: 0.8
2769
Male, age 72, unknown
1.1
1821
Female, age 72, unknown
1.0
1954
Female, age 42, unknown
1.0
1904
Male, age 53, unknown
0.9
2588
Male, age 74, left hemisphere
0.9
1865
Male, age 51, unknown
0.8
2725
Female, age 75, unknown
0.8
2227
Male, age 72, unknown
0.7
2785
Male, age 18, unknown
0.7
2823
Male, age 76, right hemisphere
0.7
2503
Female, age 72, unknown
0.5
2584
Male, age 75, left hemisphere
0.4
Substantia nigra nTPM: 0.7
1889
Female, age 72, unknown
0.8
2409
Female, age 72, unknown
0.8
2583
Male, age 75, right hemisphere
0.8
2665
Male, age 74, both hemispheres
0.8
1916
Female, age 42, unknown
0.7
1851
Male, age 51, unknown
0.6
1941
Male, age 53, unknown
0.6
2590
Female, age 75, unknown
0.6
2241
Male, age 72, unknown
0.5
2699
Male, age 18, unknown
0.4
Superior colliculus nTPM: 0.5
2668
Female, age 75, unknown
0.9
2087
Female, age 72, unknown
0.8
1839
Male, age 51, unknown
0.6
1995
Male, age 72, unknown
0.6
1913
Female, age 42, unknown
0.5
2587
Male, age 74, left hemisphere
0.5
2664
Male, age 75, both hemispheres
0.5
1796
Male, age 53, unknown
0.4
2261
Male, age 18, unknown
0.4
1895
Male, age 76, right hemisphere
0.3
Ventral tegmental area nTPM: 0.5
1915
Female, age 42, unknown
0.8
2218
Male, age 76, both hemispheres
0.6
1942
Male, age 51, unknown
0.5
2021
Male, age 53, unknown
0.5
2410
Female, age 72, unknown
0.5
2223
Female, age 72, unknown
0.3
MIDBRAIN - FANTOM5 CAGEi
RNA expression in human tissues obtained through Cap Analysis of Gene Expression (CAGE) generated by the FANTOM5 project are reported as Scaled Tags Per Million.
Max subtype Scaled Tags Per Millioni
Max subtype Scaled Tags Per Million is the value for the subtype with the largest average Scaled Tags Per Million across the subtype samples.
Max subtype nTPM is the value for the subtype with the largest average nTPM across the subtype samples.
3.8
Macaque sample
Sample description
nTPM
Substantia nigra nTPM: 1.6
Samples: 1
Max nTPM: 1.6
Min nTPM: 1.6
Sample A
1.6
Midbrain nTPM: 3.8
Samples: 1
Max nTPM: 3.8
Min nTPM: 3.8
Sample A
3.8
Superior colliculi nTPM: 1.3
Samples: 1
Max nTPM: 1.3
Min nTPM: 1.3
Sample A
1.3
MIDBRAIN - Pig RNA-seqi
RNA-seq data obtained from pig brain is reported as nTPM. Normal distribution across the dataset is visualized with box plots, shown as median and 25th and 75th percentiles. Points are displayed as outliers if they are above or below 1.5 times the interquartile range. nTPM values of the individual samples are presented next to the box plot.
Max subtype nTPMi
Max subtype nTPM is the value for the subtype with the largest average nTPM across the subtype samples.
1.0
Pig sample
Sample description
nTPM
Substantia nigra nTPM: 0.8
Samples: 3
Max nTPM: 1.2
Min nTPM: 0.4
Sample A
Female
0.9
Sample B
Female
0.4
Sample C
Male
1.2
Midbrain nTPM: 1.0
Samples: 3
Max nTPM: 1.4
Min nTPM: 0.7
Sample B
Female
0.9
Sample C
Male
0.7
Sample D
Male
1.4
Periaqueductal gray nTPM: 0.8
Samples: 3
Max nTPM: 0.9
Min nTPM: 0.7
Sample B
Female
0.7
Sample C
Male
0.7
Sample D
Male
0.9
Superior colliculi nTPM: 0.9
Samples: 4
Max nTPM: 1.1
Min nTPM: 0.7
Sample A
Female
1.1
Sample B
Female
0.8
Sample C
Male
0.9
Sample D
Male
0.7
MIDBRAIN - Mouse RNA-seqi
RNA-seq data obtained from mouse brain is reported as nTPM. Normal distribution across the dataset is visualized with box plots, shown as median and 25th and 75th percentiles. Points are displayed as outliers if they are above or below 1.5 times the interquartile range. nTPM values of the individual samples are presented next to the box plot.
Max subtype nTPMi
Max subtype nTPM is the value for the subtype with the largest average nTPM across the subtype samples.
0.5
Mouse sample
Sample description
nTPM
Midbrain nTPM: 0.6
Samples: 4
Max nTPM: 0.7
Min nTPM: 0.4
Sample A
0.6
Sample B
0.5
Sample C
0.4
Sample D
0.7
MIDBRAIN - Rat RNA-seq
Max subtype nTPMi
Max subtype nTPM is the value for the subtype with the largest average nTPM across the subtype samples.
1.1
Rat sample
Sample description
nTPM
Midbrain nTPM: 1.1
Samples: 4
Max nTPM: 1.2
Min nTPM: 1.0
Sample A
1.0
Sample A
1.1
Sample A
1.2
Sample A
1.1
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The Human Protein Atlas project is funded
