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:
1.0
nTPM
FANTOM5:
0.0
Scaled Tags Per Million
HIPPOCAMPAL FORMATION - 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 - HIPPOCAMPAL FORMATION, 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
Dentate gyrus excitatory
c-2
CA1-3 Excitatory (VGLUT1) K
c-3
Inhibitory (GAD1/2) CXCL14+...
c-4
CA1-3 Excitatory (VGLUT1) K
c-5
Dentate gyrus excitatory (V...
c-6
Inhibitory (GAD1/2) LHX6+ T...
c-7
Inhibitory (GAD1/2) LHX6+ T...
c-8
CA1-3 Excitatory (VGLUT1) K
c-9
Dentate gyrus excitatory (V...
c-10
Dentate gyrus excitatory (V...
c-11
Dentate gyrus excitatory (V...
c-12
Dentate gyrus excitatory (V...
c-13
Inhibitory (GAD1/2) LAMP5+ ...
c-14
CA1-3 Excitatory (VGLUT1) K
c-15
Inhibitory (GAD1/2) CXCL14+...
c-16
CA1-3 Excitatory (VGLUT1) K
c-17
CA1-3 Excitatory (VGLUT1) K
c-18
CA1-3 Excitatory (VGLUT1) K
c-19
Dentate gyrus excitatory (V...
c-20
Inhibitory (GAD1/2) CXCL14+
c-21
Inhibitory (GAD1/2) CXCL14+
c-22
CA1-3 Excitatory (VGLUT1)
c-23
Excitatory (VGLUT1) FOXP2+
c-24
CA4 Excitatory (VGLUT1) KIT
c-25
Dentate gyrus excitatory (V...
c-26
Excitatory (VGLUT1) FOXP2+
c-27
CA1-3 Excitatory (VGLUT1) K
c-28
Excitatory (VGLUT1) RXFP1+
c-29
CA4 Excitatory (VGLUT1) KIT
c-30
CA1-3 Excitatory (VGLUT1) K
c-31
Excitatory (VGLUT1) PCP4+ F...
c-32
CA1-3 Excitatory (VGLUT1) K
c-33
Excitatory (VGLUT1/2)
c-34
Excitatory (VGLUT1/2) CUX2+
c-35
CA1-3 Excitatory (VGLUT1)
c-36
Excitatory (VGLUT1) CUX2+
c-37
Excitatory (VGLUT1) RORB+ F...
c-38
Excitatory (VGLUT1) RXFP1+ ...
c-39
CA1-3 Excitatory (VGLUT1)
c-40
Excitatory (VGLUT1)
c-41
Dentate gyrus excitatory (V...
c-42
CA1-3 Excitatory (VGLUT1)
c-43
Excitatory (VGLUT1) SATB2+
c-44
CA4 Excitatory (VGLUT1) KIT
c-45
Atypical neuron SOX11+
c-46
CA4 Excitatory (VGLUT1) KIT
c-47
Inhibitory (GAD1) LHX6+
c-48
Excitatory (VGLUT1) RXFP1+
c-49
CA4 Excitatory (VGLUT1) KIT
c-50
Atypical neuron PLCB4+ CDH4
c-51
Unassigned
c-52
Inhibitory (GAD2) DRD2+ PPP...
c-53
Dentate gyrus excitatory (V...
c-54
Dentate gyrus excitatory (V...
c-55
Excitatory (VGLUT1) RXFP1+
c-56
Excitatory (VGLUT1) PCP4+ F...
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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 - HIPPOCAMPAL FORMATION, 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
Oligodendrocyte progenitor ...
c-2
Oligodendrocytes
c-3
Oligodendrocytes
c-4
Microglia
c-5
Oligodendrocytes
c-6
Oligodendrocytes
c-7
Astrocytes
c-8
Astrocytes
c-9
Astrocytes
c-10
Astrocytes
c-11
Oligodendrocytes (TTR+)
c-12
Oligodendrocytes
c-13
Astrocytes
c-14
Ependymal cells
c-15
Astrocytes
c-16
Astrocytes (TTR+)
c-17
Oligodendrocyte progenitor ...
c-18
Vascular endothelial cells
c-19
Microglia (AIF1+)
c-20
Fibroblasts
c-21
Microglia (TTR+)
c-22
Immature oligodendrocytes
c-23
Pericytes
c-24
Macrophages
c-25
Lymphocytes
c-26
Choroid plexus epithelial c...
c-27
Macrophages and B-cells
c-28
Oligodendrocyte progenitor ...
c-29
Vascular smooth muscle cell
c-30
Doublets
c-31
Macrophages
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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
HIPPOCAMPAL FORMATION - Annotated protein expression
Pending normal tissue analysis
HIPPOCAMPAL FORMATION - HPA Brain Stereo-seq
HIPPOCAMPAL FORMATION - 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.
1.0
Sample id
Sample description
nTPM
Dentate gyrus nTPM: 1.0
2246
Female, age 85, both hemispheres
1.1
2530
Female, age 94, left hemisphere
1.1
2528
Male, age 74, both hemispheres
1.0
2531
Female, age 67, both hemispheres
1.0
1927
Female, age 91, both hemispheres
0.8
2010
Male, age 76, both hemispheres
0.8
Entorhinal gyrus nTPM: 0.8
1787
Male, age 76, left hemisphere
1.0
2764
Male, age 80, right hemisphere
1.0
2117
Female, age 91, right hemisphere
0.9
2686
Male, age 75, right hemisphere
0.8
1938
Female, age 85, left hemisphere
0.7
2613
Female, age 94, left hemisphere
0.6
Hippocampus, CA1 nTPM: 0.9
2045
Male, age 76, both hemispheres
1.2
2082
Female, age 91, right hemisphere
1.0
1873
Female, age 85, both hemispheres
0.8
2527
Male, age 74, both hemispheres
0.7
2749
Male, age 80, left hemisphere
0.6
Hippocampus, CA2 nTPM: 0.8
2249
Male, age 74, both hemispheres
1.0
2437
Female, age 94, left hemisphere
1.0
1940
Female, age 85, left hemisphere
0.9
1963
Male, age 80, left hemisphere
0.8
1892
Male, age 76, both hemispheres
0.7
2113
Female, age 91, right hemisphere
0.6
Hippocampus, CA3 nTPM: 0.9
2620
Female, age 94, left hemisphere
1.2
2861
Female, age 67, both hemispheres
1.2
2137
Male, age 80, left hemisphere
0.8
2436
Male, age 74, both hemispheres
0.8
1867
Male, age 76, both hemispheres
0.7
1891
Female, age 85, both hemispheres
0.7
Parahippocampal cortex nTPM: 0.9
1990
Female, age 91, right hemisphere
1.1
2532
Female, age 72, left hemisphere
1.1
2018
Male, age 76, both hemispheres
1.0
2250
Female, age 67, right hemisphere
0.9
2692
Male, age 74, both hemispheres
0.9
2622
Female, age 67, right hemisphere
0.8
2693
Female, age 94, both hemispheres
0.8
1850
Male, age 80, both hemispheres
0.7
1933
Female, age 85, both hemispheres
0.7
2245
Female, age 91, both hemispheres
0.7
Perirhinal gyrus nTPM: 0.9
1794
Male, age 80, right hemisphere
1.0
1847
Female, age 91, left hemisphere
1.0
2848
Male, age 76, right hemisphere
0.9
1841
Female, age 85, right hemisphere
0.7
2521
Female, age 94, right hemisphere
0.7
Subiculum nTPM: 1.0
2438
Female, age 94, left hemisphere
1.2
2619
Male, age 74, both hemispheres
1.2
2042
Male, age 76, both hemispheres
1.0
2729
Female, age 91, right hemisphere
1.0
1977
Female, age 85, both hemispheres
0.9
1901
Male, age 80, both hemispheres
0.8
HIPPOCAMPAL FORMATION - 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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