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.
h
m
l
n
Endothelial cells:
Not detected
Glial cells:
Not detected
Neuronal cells:
Not detected
Neuropil:
Not detected
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.
Consensus:
0.1
nTPM
HPA:
0.1
nTPM
HPA Brain:
2.1
nTPM
HPA PFC Brain:
0.0
nTPM
CEREBRAL CORTEX - 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 - CEREBRAL CORTEX, 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
Excitatory (VGLUT1) CUX2+
c-2
Inhibitory (GAD1/2) LHX6+ T...
c-3
Inhibitory (GAD1/2) CXCL14+...
c-4
Inhibitory (GAD1/2) LHX6+ T...
c-5
Inhibitory (GAD1/2) CXCL14+
c-6
Excitatory (VGLUT1) FOXP2+
c-7
Excitatory (VGLUT1) CUX2+
c-8
Excitatory (VGLUT1)
c-9
Inhibitory (GAD1/2) LHX6+ T...
c-10
Inhibitory (GAD1/2) CXCL14+...
c-11
Inhibitory (GAD1/2) CXCL14+...
c-12
Excitatory (VGLUT1) FOXP2+
c-13
Excitatory (VGLUT1) FOXP2+
c-14
Excitatory (VGLUT1) CUX2+
c-15
Excitatory (VGLUT1) FOXP2+
c-16
Inhibitory (GAD1/2) CXCL14+...
c-17
Excitatory (VGLUT1/2)
c-18
Excitatory (VGLUT1) FOXP2+
c-19
Excitatory (VGLUT1/2) CUX2+
c-20
Inhibitory (GAD1/2) LAMP5+ ...
c-21
Excitatory (VGLUT1) FOXP2+
c-22
Inhibitory (GAD1/2) CXCL14+
c-23
Excitatory (VGLUT1) FOXP2+
c-24
Excitatory (VGLUT1) SOX5+
c-25
Excitatory (VGLUT1) CUX2+
c-26
Excitatory (VGLUT1) FOXP2+
c-27
Excitatory (VGLUT1) CUX2+
c-28
Excitatory (VGLUT1) CUX2+
c-29
Excitatory (VGLUT1/2) CUX2+
c-30
Inhibitory (GAD1/2) LHX6+ T...
c-31
Excitatory (VGLUT1/2) CUX2+
c-32
Inhibitory (GAD1) LHX6+ KIT...
c-33
Excitatory (VGLUT1) FOXP2+
c-34
Inhibitory (GAD1/2) RXFP1+ ...
c-35
Inhibitory (GAD1/2) PENK+ D...
c-36
Inhibitory (GAD1/2) LHX6+ T...
c-37
Excitatory (VGLUT1)
c-38
Excitatory (VGLUT1)
c-39
Excitatory (VGLUT1) FOXP2+
c-40
Excitatory (VGLUT1) FOXP2+
c-41
Excitatory (VGLUT1/2) CUX2+
c-42
Excitatory (VGLUT1/2)
c-43
Excitatory (VGLUT1/2)
c-44
Inhibitory (GAD1/2) NOS1+ S...
c-45
Unassigned
c-46
Excitatory (VGLUT1) CUX2+
c-47
Inhibitory (GAD1/2) LHX6+ E...
c-48
Excitatory (VGLUT1/2) FOXP2...
c-49
Excitatory (VGLUT1) FOXP2+
Show allShow less
This data was generated by Siletti K et al. (2023), re-processed by HPA (see methods) and simplified for global overview
SINGLE NUCLEI BRAIN - CEREBRAL CORTEX, 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
Oligodendrocyte progenitor ...
c-4
Oligodendrocytes
c-5
Astrocytes
c-6
Astrocytes
c-7
Microglia
c-8
Oligodendrocyte progenitor ...
c-9
Oligodendrocytes
c-10
Oligodendrocytes
c-11
Astrocytes
c-12
Astrocytes
c-13
Astrocytes
c-14
Microglia
c-15
Vascular endothelial cells
c-16
Fibroblasts
c-17
Oligodendrocytes (CNTN1+)
c-18
Macrophages
c-19
Immature oligodendrocytes
c-20
Oligodendrocyte progenitor ...
c-21
Pericytes
c-22
Lymphocytes
c-23
Fibroblasts
c-24
Vascular smooth muscle cell
c-25
Astrocytes
c-26
Oligodendrocyte progenitor ...
c-27
Fibroblasts (BNC2+ TRPM3+)
c-28
Fibroblasts (BNC2+ KCNMA1+ ...
c-29
Pericytes
c-30
Fibroblasts
c-31
Macrophages & Lymphocytes
Show allShow less
This data was generated by Siletti K et al. (2023), re-processed by HPA (see methods) and simplified for global overview
CEREBRAL CORTEX - Antibody stainingi
Antibody staining in the annotated cell types in the current human tissue is reported as not detected, low, medium, or high, based on conventional immunohistochemistry profiling in selected tissues. This score is based on the combination of the staining intensity and fraction of stained cells. Each image is clickable and will lead to virtual microscopy that enables deeper exploration of all samples and also displays staining intensity scores, fraction scores and subcellular localization as well as patient and tissue information for each sample.
Ascending and descending describe two types of gradient, based on difference in staining intensity between enterocytes in crypts and apical enterocytes.
Ascending - the staining intensity is stronger in apical enterocytes (towards the lumen) compared to enterocytes in the crypts (gland based)
Descending - the staining is weaker in apical enterocytes compared to enterocytes in crypts
Antibody HPA067855
Endothelial cells
Not detected
Glial cells
Not detected
Neuronal cells
Not detected
Neuropil
Not detected
CEREBRAL CORTEX - HPA RNA-seqi
The RNA-seq details section shows detailed information about the individual samples used for the transcript profiling and results of the RNA-seq analysis.
Information about each individual sample is listed below, including gender, age, a tissue section image and estimated fractions of cell types. nTPM (normalized transcripts per million) values give a quantification of the gene abundance which is comparable between different genes and samples.
Average nTPMi
Max subtype nTPM is the value for the subtype with the largest average nTPM across the subtype samples.
0.1
Male, age 5
Cerebral cortex sample 48 nTPM: 0.1
Female, age 40
Cerebral cortex sample 105 nTPM: 0.2
Cell types%
Neuronal cells:
35
Glial cells and endothelial cells:
65
Male, age 70
Cerebral cortex sample 106 nTPM: 0
Cell types%
Neuronal cells:
35
Glial cells and endothelial cells:
65
CEREBRAL CORTEX - 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.
We use cookies to enhance the usability of our website. If you continue, we'll assume that you are happy to receive all cookies. More information. Don't show this again.