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:
1.1
nTPM
FANTOM5:
0.0
Scaled Tags Per Million
BASAL GANGLIA - 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 - BASAL GANGLIA, 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) PENK+ D...
c-2
Inhibitory (GAD1/2) DRD1+ T...
c-3
Inhibitory (GAD1/2) DRD1+ T...
c-4
Inhibitory (GAD1/2) PENK+ D...
c-5
Inhibitory (GAD1/2) PENK+ D...
c-6
Inhibitory (GAD1/2) DRD1+ T...
c-7
Inhibitory (GAD1/2) PENK+ D...
c-8
Inhibitory (GAD1/2) DRD1+ T...
c-9
Inhibitory (GAD1/2) DRD1+ T...
c-10
Inhibitory (GAD1/2)
c-11
Eccentric MSN Inhibitory (G...
c-12
Eccentric MSN Inhibitory (G...
c-13
Inhibitory (GAD1/2) PENK+ D...
c-14
Eccentric MSN Inhibitory (G...
c-15
Inhibitory (GAD1/2) LHX6+ E...
c-16
Inhibitory (GAD1/2) TAC3+
c-17
Inhibitory (GAD1/2) PENK+ D...
c-18
Inhibitory (GAD1/2) PENK+ D...
c-19
Inhibitory (GAD1/2)
c-20
Inhibitory (GAD1/2) DRD1+ T...
c-21
Excitatory (VGLUT1)
c-22
Inhibitory (GAD1/2) DRD1+
c-23
Inhibitory (GAD1/2) DRD1+ T...
c-24
Inhibitory (GAD1/2) PENK+ D...
c-25
Inhibitory (GAD1/2)
c-26
Inhibitory (GAD1/2) DRD1+ T...
c-27
Inhibitory (GAD1/2) DRD1+ T...
c-28
Inhibitory (GAD1/2)
c-29
Inhibitory (GAD1/2) CXCL14+...
c-30
Inhibitory (GAD1/2) LHX6+ T...
c-31
Inhibitory (GAD1/2) DRD1+ T...
c-32
Inhibitory (GAD1/2)
c-33
Inhibitory (GAD1/2) DRD1+ T...
c-34
Inhibitory (GAD1/2)
c-35
Inhibitory (GAD1/2) DRD1+
c-36
Inhibitory (GAD1/2) TAC1+
c-37
Inhibitory (GAD1/2)
c-38
Excitatory (VGLUT1)
c-39
Inhibitory (GAD1/2) TH+ PDY...
c-40
Inhibitory (GAD1/2) CXCL14+...
c-41
Inhibitory (GAD1) SST+ NPY+...
c-42
Unassigned
c-43
Inhibitory (GAD1/2) LAMP5+ ...
c-44
Excitatory (VGLUT1) RXFP1+
c-45
Cholinergic Inhibitory (GAD
c-46
Excitatory (VGLUT2) CALB2+
c-47
Excitatory (VGLUT2) CALB2+ ...
c-48
Inhibitory (GAD1/2) RORB+ K
c-49
Inhibitory (GAD1/2) TSHZ1+ ...
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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 - BASAL GANGLIA, 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
Astrocytes
c-6
Oligodendrocyte progenitor ...
c-7
Oligodendrocytes
c-8
Microglia
c-9
Choroid plexus epithelial c...
c-10
Astrocytes
c-11
Astrocytes
c-12
Astrocytes
c-13
Oligodendrocytes
c-14
Astrocytes
c-15
Oligodendrocytes
c-16
Fibroblasts
c-17
Choroid plexus epithelial c...
c-18
Microglia
c-19
Oligodendrocytes (TTR+)
c-20
Macrophages
c-21
Ependymal cells
c-22
Astrocytes (TTR+)
c-23
Lymphocytes
c-24
Pericytes
c-25
Oligodendrocytes (ROBO2+ NP
c-26
Oligodendrocyte progenitor ...
c-27
Vascular endothelial cells
c-28
Ependymal cells (TTR+)
c-29
Astrocytes
c-30
Oligodendrocyte progenitor ...
c-31
Vascular smooth muscle cell
c-32
Immature oligodendrocytes
c-33
Mixed OPCs & CP ECs
c-34
Mural cells
c-35
Immature oligodendrocytes
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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
BASAL GANGLIA - Annotated protein expression
Pending normal tissue analysis
BASAL GANGLIA - 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.
1.1
Sample id
Sample description
nTPM
Caudate nucleus nTPM: 1.0
2288
Male, age 75, left hemisphere
1.3
2289
Male, age 61, right hemisphere
1.2
1857
Female, age 85, left hemisphere
1.0
2846
Female, age 79, unknown
1.0
1854
Male, age 80, left hemisphere
0.9
2481
Female, age 94, left hemisphere
0.9
1781
Male, age 74, unknown
0.8
2290
Female, age 72, unknown
0.8
Globus pallidus, externus nTPM: 1.1
2646
Male, age 61, right hemisphere
1.3
1996
Male, age 80, right hemisphere
1.1
2395
Male, age 75, both hemispheres
1.1
2772
Female, age 79, unknown
1.0
2567
Female, age 72, unknown
0.9
Globus pallidus, internus nTPM: 1.1
2111
Female, age 85, right hemisphere
1.4
2566
Female, age 72, unknown
1.2
2037
Male, age 80, right hemisphere
1.1
2287
Male, age 75, right hemisphere
1.1
2778
Female, age 91, both hemispheres
1.1
1818
Male, age 74, unknown
1.0
2483
Female, age 94, right hemisphere
0.9
Nucleus accumbens nTPM: 1.0
2824
Male, age 61, right hemisphere
1.3
1783
Male, age 74, unknown
1.2
2732
Male, age 80, right hemisphere
1.2
1806
Female, age 85, left hemisphere
1.0
2698
Female, age 72, unknown
1.0
1856
Female, age 91, right hemisphere
0.9
2286
Male, age 75, left hemisphere
0.9
2391
Female, age 94, left hemisphere
0.8
Nucleus basalis of Meynert nTPM: 1.0
2569
Male, age 61, both hemispheres
1.1
2393
Male, age 80, right hemisphere
1.0
2821
Male, age 75, both hemispheres
1.0
2484
Female, age 94, left hemisphere
0.7
Nucleus of the diagonal band nTPM: 0.8
1979
Male, age 74, unknown
1.0
2195
Female, age 85, both hemispheres
0.9
2775
Male, age 80, right hemisphere
0.8
2029
Male, age 61, right hemisphere
0.6
1812
Female, age 91, both hemispheres
0.5
Putamen nTPM: 0.9
2489
Female, age 72, unknown
1.1
2647
Male, age 75, left hemisphere
1.0
1838
Male, age 80, right hemisphere
0.9
1937
Female, age 91, right hemisphere
0.9
2466
Female, age 79, unknown
0.9
2482
Female, age 94, left hemisphere
0.9
1829
Male, age 74, unknown
0.8
Septal nuclei nTPM: 0.9
2394
Male, age 61, left hemisphere
1.0
2629
Female, age 94, right hemisphere
1.0
2031
Female, age 72, unknown
0.9
2059
Female, age 85, both hemispheres
0.9
1960
Male, age 74, unknown
0.8
2009
Female, age 91, both hemispheres
0.8
2199
Male, age 80, right hemisphere
0.8
Stria terminalis, bed nucleus nTPM: 0.9
2201
Male, age 74, unknown
1.1
2486
Female, age 94, both hemispheres
1.0
1974
Female, age 91, both hemispheres
0.8
BASAL GANGLIA - 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.
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