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:
248.8
nTPM
FANTOM5:
177.2
Scaled Tags Per Million
Macaque:
152.7
nTPM
Mouse:
342.6
nTPM
Rat:
277.0
nTPM
Pig:
174.3
nTPM
THALAMUS - 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 - THALAMUS, 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
Unassigned
c-2
Inhibitory (GAD1/2) RORB+ K
c-3
Inhibitory (GAD1/2) RORB+ K
c-4
Inhibitory (GAD1/2) RORB+ K
c-5
Inhibitory (GAD1/2) RORB+ K
c-6
Excitatory (VGLUT2) CALB2+
c-7
Inhibitory (GAD1/2) RORB+ K
c-8
Inhibitory (GAD1/2) RORB+ K
c-9
Excitatory (VGLUT2) PVALB+ ...
c-10
Inhibitory (GAD1/2) RORB+ K
c-11
Inhibitory (GAD1/2) RORB+ K
c-12
Posterior thalamic Excitato...
c-13
Inhibitory (GAD1/2) RORB+ K...
c-14
Excitatory (VGLUT2) PVALB+
c-15
Posterior thalamic Excitato...
c-16
Excitatory (VGLUT2) PVALB+ ...
c-17
Inhibitory (GAD1/2) RORB+ K
c-18
Excitatory (VGLUT2) PVALB+ ...
c-19
Excitatory (VGLUT2)
c-20
Excitatory (VGLUT2) PVALB+
c-21
Inhibitory (GAD1/2) ESR1+ S...
c-22
Excitatory (VGLUT2) PVALB+ ...
c-23
Posterior thalamic Excitato...
c-24
Inhibitory (GAD1/2) ESR1+
c-25
Inhibitory (GAD1/2) CXCL14+...
c-26
Inhibitory (GAD1/2) PENK+ L...
c-27
Inhibitory (GAD1/2) RORB+ K
c-28
Epithalamic Excitatory (VGL...
c-29
Excitatory (VGLUT2)
c-30
Excitatory (VGLUT2) PVALB+ ...
c-31
Excitatory (VGLUT2)
c-32
Excitatory (VGLUT2) PVALB+
c-33
Inhibitory (GAD1/2) RORB+ K
c-34
Excitatory (VGLUT2) PVALB+ ...
c-35
Inhibitory (GAD1/2) SST+
c-36
Cholinergic Excitatory (VGL...
c-37
Excitatory (VGLUT2)
c-38
Excitatory (VGLUT2)
c-39
Excitatory (VGLUT2)
c-40
Inhibitory (GAD1/2) CXCL14+...
c-41
Inhibitory (GAD1/2) RXFP1+ ...
c-42
Excitatory (VGLUT2)
c-43
Excitatory (VGLUT2)
c-44
Inhibitory (GAD1/2) ETV1+ T...
c-45
Excitatory (VGLUT2) CALB2+
c-46
Inhibitory (GAD1/2) RORB+ K
c-47
Excitatory (VGLUT1)
c-48
Inhibitory (GAD1/2) TAC1+
c-49
Excitatory (VGLUT2) NOS1+
c-50
Parvocellular CRH+ AVP+ OXT
c-51
Excitatory (VGLUT1) ETV1+ Z...
c-52
Unassigned
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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 - THALAMUS, 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
Oligodendrocytes
c-4
Oligodendrocytes
c-5
Oligodendrocytes
c-6
Oligodendrocyte progenitor ...
c-7
Oligodendrocytes
c-8
Microglia
c-9
Oligodendrocytes
c-10
Astrocytes
c-11
Astrocytes
c-12
Astrocytes (CD44+)
c-13
Oligodendrocytes
c-14
Fibroblasts
c-15
Oligodendrocytes
c-16
Pericytes
c-17
Vascular endothelial cells
c-18
Ependymal cells
c-19
Lymphocytes
c-20
Astrocytes (GABRB1+ GABRA2+
c-21
Vascular smooth muscle cell
c-22
Macrophages
c-23
Oligodendrocyte progenitor ...
c-24
Fibroblasts (BNC2+)
c-25
Monocytes
c-26
Immature oligodendrocytes
c-27
Choroid plexus epithelial c...
c-28
Oligodendrocyte progenitor ...
c-29
OPCs & Fibroblast doublets
c-30
Leukocytes
c-31
Oligodendrocyte progenitor ...
Show allShow less
This data was generated by Siletti K et al. (2023), re-processed by HPA (see methods) and simplified for global overview
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.
152.7
Macaque sample
Sample description
nTPM
Habenula nTPM: 65.7
Samples: 1
Max nTPM: 65.7
Min nTPM: 65.7
Sample A
65.7
Lateral thalamic nuclei nTPM: 152.7
Samples: 2
Max nTPM: 171.9
Min nTPM: 133.5
Sample A
171.9
Sample B
133.5
Thalamus nTPM: 126.4
Samples: 2
Max nTPM: 142.4
Min nTPM: 110.4
Sample A
142.4
Sample B
110.4
THALAMUS - 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.
174.3
Pig sample
Sample description
nTPM
Thalamus nTPM: 174.3
Samples: 3
Max nTPM: 207.1
Min nTPM: 126.8
Sample A
Female
188.9
Sample C
Male
207.1
Sample D
Male
126.8
THALAMUS - 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.
342.6
Mouse sample
Sample description
nTPM
Thalamus nTPM: 342.7
Samples: 4
Max nTPM: 358.6
Min nTPM: 319.7
Sample A
319.7
Sample B
355.6
Sample C
358.6
Sample D
336.7
THALAMUS - Rat RNA-seq
Max subtype nTPMi
Max subtype nTPM is the value for the subtype with the largest average nTPM across the subtype samples.
277.0
Rat sample
Sample description
nTPM
Thalamus nTPM: 277.0
Samples: 4
Max nTPM: 285.1
Min nTPM: 255.2
Sample A
255.2
Sample A
283.4
Sample A
284.4
Sample A
285.1
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