Single cell type - TLR3 - The Human Protein Atlas

TLR3

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Pathway

GENERAL INFORMATIONⁱ General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.
Gene nameⁱ Official gene symbol, which is typically a short form of the gene name, according to HGNC.	TLR3
Gene descriptionⁱ Full gene name according to HGNC.	Toll like receptor 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	CD markers Disease related genes Human disease related genes Potential drug targets Transporters
Predicted locationⁱ All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions. Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached. Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s). The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location.	Membrane, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	6

HUMAN PROTEIN ATLAS INFORMATIONⁱ Summary of RNA expression and protein localization based on data generated within the Human Protein Atlas project.
Single cell type expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity.	Early spermatids - Spermatogenesis (mainly)
Single cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected.	Cell type enhanced (Early spermatids, Schwann cells)
Tau specificity scoreⁱ Tau specificity score is a numerical indicator of the specificity of the gene expression across cells or tissues. The value ranges from 0 and 1, where 0 indicates identical expression across all cells/tissue types, while 1 indicates expression in a single cell/tissue type.	0.64
Brain cluster specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell cluster types based on snRNA-seq data from brain samples. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. "cell type" refer to one of the 34 cluster names used to summarize the 2.5 million cells included in the brain cell representation.	Cell type enhanced (Central nervous system macrophage, Fibroblast)
Immune cell specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected.	Immune cell enhanced (memory CD8 T-cell, gdT-cell)
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); neXtProt protein existence (neXtProt evidence);and a Human Protein Atlas antibody- or RNA based score (HPA evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable.	Evidence at protein level

ASSAYSⁱ

SINGLE CELL TYPESⁱ A summary of normalized single cell RNA (nTPM) from all single cell types. Color-coding is based on cell type groups, each consisting of cell types with functional features in common.
Single cell types RNA single cell type specificity: Cell type enhanced (Early spermatids, Schwann cells)

TISSUE CELL TYPEⁱ The tissue cell type section provides a cell type specificity prediction for all protein coding genes. More information on the data available can be found here and a description of the analysis here.
	Core cell typesⁱ The core cell type table displays data for a panel of eight cell types that are found in many tissues. Colored dots indicate that the selected gene has core cell type specificity in the indicated tissue. Grey dots indicate that cell type is present within that tissue, but the selected gene is not predicted to be enriched there. Category Alphabetical Enrichment Tissue specific cell typesⁱ This plot shows the enrichment score of the selected gene in all non-core cell types found within the profiled tissues, allowing comparisons between different cell types within different tissues. An enlarged symbol indicates classification of the gene as cell type enriched in the corresponding cell type.

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Cell type enhanced (Central nervous system macrophage, Fibroblast)

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
HPA datasetⁱ The resulting transcript expression values calculated as nTPM, resulting from the internal normalization pipeline for 18 immune cell types and total peripheral blood mononuclear cells (PBMC). Lineage Expression Alphabetical Immune cell type specificity: Immune cell enhanced (memory CD8 T-cell, gdT-cell)
Monaco datasetⁱ The transcript expression values (nTPM) resulting from the internal normalization pipeline are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SINGLE CELL TYPE

TLR3 is part of cluster 21 Early spermatids - Spermatogenesis with confidenceⁱ 1
337 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
ENSG00000269825	Novel zinc finger protein	0.5652	21
CEP152	Centrosomal protein 152	0.5387	21
SLC35A5	Solute carrier family 35 member A5	0.5380	21
AKNAD1	AKNA domain containing 1	0.5335	21
JRKL	JRK like	0.5293	21
PKHD1	PKHD1 ciliary IPT domain containing fibrocystin/polyductin	0.5088	21
KBTBD7	Kelch repeat and BTB domain containing 7	0.5064	21
MMAA	Metabolism of cobalamin associated A	0.4825	21
CALR3	Calreticulin 3	0.4819	13
AGAP9	ArfGAP with GTPase domain, ankyrin repeat and PH domain 9	0.4806	21
KATNA1	Katanin catalytic subunit A1	0.4758	21
PDCL2	Phosducin like 2	0.4717	21
PLPP6	Phospholipid phosphatase 6	0.4701	21
TRIM17	Tripartite motif containing 17	0.4696	21
TXNDC2	Thioredoxin domain containing 2	0.4689	21

IMMUNE CELLS

TLR3 is part of cluster 1 T-cells - Unknown function with confidenceⁱ 0.79
202 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
TRGV3	T cell receptor gamma variable 3	1.0000	1
SORBS3	Sorbin and SH3 domain containing 3	1.0000	1
ANKEF1	Ankyrin repeat and EF-hand domain containing 1	0.9762	1
TMEM67	Transmembrane protein 67	0.9762	1
HDAC11	Histone deacetylase 11	0.9762	33
GFI1	Growth factor independent 1 transcriptional repressor	0.9762	1
SPEF2	Sperm flagellar 2	0.9762	1
GLB1L2	Galactosidase beta 1 like 2	0.9762	1
ETNK2	Ethanolamine kinase 2	0.9762	1
KIF21A	Kinesin family member 21A	0.9762	1
STAT4	Signal transducer and activator of transcription 4	0.9762	1
TSPAN15	Tetraspanin 15	0.9762	1
LRFN3	Leucine rich repeat and fibronectin type III domain containing 3	0.9762	1
BFSP1	Beaded filament structural protein 1	0.9762	1
WNT1	Wnt family member 1	0.9762	1

Adipocytes	12.7 nTPM
Adipose tissue	15.4 nTPM
Breast	9.9 nTPM

Alveolar cells type 1	18.5 nTPM
Lung	18.5 nTPM

Alveolar cells type 2	18.9 nTPM
Lung	18.9 nTPM

Astrocytes	0.3 nTPM
Brain	0.3 nTPM

B-cells	1.8 nTPM
Skin	20.3 nTPM
Lung	2.7 nTPM
Thymus	0.4 nTPM
Bone marrow	0.2 nTPM
Salivary gland	0.2 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Ciliated cells	6.2 nTPM
Bronchus	9.2 nTPM
Endometrium	7.7 nTPM
Fallopian tube	4.6 nTPM
Lung	3.1 nTPM

Club cells	11.6 nTPM
Prostate	15.0 nTPM
Bronchus	13.6 nTPM
Lung	6.4 nTPM

Endothelial cells	6.8 nTPM
Prostate	12.0 nTPM
Heart muscle	11.9 nTPM
Skeletal muscle	11.1 nTPM
Lung	11.0 nTPM
Salivary gland	9.5 nTPM
Vascular	9.0 nTPM
Thymus	8.6 nTPM
Endometrium	8.2 nTPM
Esophagus	7.3 nTPM
Ovary	6.1 nTPM
Tongue	6.0 nTPM
Fallopian tube	6.0 nTPM
Skin	3.9 nTPM
Liver	3.8 nTPM
Placenta	3.4 nTPM
Testis	3.1 nTPM
Breast	0.9 nTPM
Pancreas	0.0 nTPM

Enteroendocrine cells	1.5 nTPM
Colon	2.7 nTPM
Rectum	1.7 nTPM
Small intestine	0.0 nTPM

Fibroblasts	9.9 nTPM
Adipose tissue	23.4 nTPM
Heart muscle	22.2 nTPM
Skeletal muscle	18.4 nTPM
Esophagus	12.9 nTPM
Salivary gland	11.3 nTPM
Vascular	10.9 nTPM
Thymus	9.0 nTPM
Stomach	8.6 nTPM
Fallopian tube	7.4 nTPM
Prostate	7.3 nTPM
Skin	7.1 nTPM
Liver	5.9 nTPM
Lung	5.0 nTPM
Breast	5.0 nTPM
Pancreas	1.9 nTPM
Placenta	1.4 nTPM

Granulocytes	2.1 nTPM
Tongue	4.9 nTPM
Lung	1.0 nTPM
Fallopian tube	0.4 nTPM

Intestinal goblet cells	9.4 nTPM
Small intestine	16.7 nTPM
Rectum	9.0 nTPM
Colon	2.5 nTPM

Lymphatic endothelial cells	3.3 nTPM
Fallopian tube	6.5 nTPM
Ovary	0.0 nTPM

Macrophages	4.9 nTPM
Prostate	21.5 nTPM
Salivary gland	14.2 nTPM
Breast	10.7 nTPM
Endometrium	7.4 nTPM
Esophagus	6.4 nTPM
Tongue	5.8 nTPM
Fallopian tube	5.3 nTPM
Adipose tissue	4.6 nTPM
Skeletal muscle	4.4 nTPM
Bone marrow	3.0 nTPM
Testis	2.5 nTPM
Vascular	2.5 nTPM
Kidney	1.8 nTPM
Skin	1.1 nTPM
Lung	1.1 nTPM
Thymus	0.8 nTPM
Pancreas	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	5.9 nTPM
Rectum	10.7 nTPM
Colon	3.6 nTPM
Small intestine	3.5 nTPM

Basal respiratory cells	8.0 nTPM
Bronchus	8.0 nTPM

Basal squamous epithelial cells	8.9 nTPM
Esophagus	8.9 nTPM

Cholangiocytes	7.6 nTPM
Liver	7.6 nTPM

Collecting duct cells	11.7 nTPM
Kidney	11.7 nTPM

Plasma cells	0.8 nTPM
Salivary gland	3.1 nTPM
Fallopian tube	1.9 nTPM
Liver	0.5 nTPM
Stomach	0.4 nTPM
Spleen	0.2 nTPM
Thymus	0.1 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

Schwann cells	36.0 nTPM
Esophagus	59.9 nTPM
Adipose tissue	39.8 nTPM
Vascular	8.4 nTPM

Serous glandular cells	8.2 nTPM
Tongue	8.8 nTPM
Salivary gland	7.7 nTPM

Smooth muscle cells	4.2 nTPM
Lung	8.2 nTPM
Adipose tissue	6.5 nTPM
Liver	6.4 nTPM
Tongue	5.7 nTPM
Breast	4.8 nTPM
Salivary gland	4.4 nTPM
Placenta	3.9 nTPM
Vascular	3.9 nTPM
Fallopian tube	3.5 nTPM
Thymus	3.4 nTPM
Ovary	3.4 nTPM
Skin	3.2 nTPM
Skeletal muscle	2.8 nTPM
Esophagus	2.4 nTPM
Prostate	2.4 nTPM
Endometrium	1.7 nTPM

T-cells	1.8 nTPM
Vascular	3.2 nTPM
Skeletal muscle	3.0 nTPM
Endometrium	2.9 nTPM
Bone marrow	2.8 nTPM
Esophagus	2.4 nTPM
Prostate	2.2 nTPM
Tongue	2.1 nTPM
Adipose tissue	2.0 nTPM
Breast	2.0 nTPM
Colon	1.9 nTPM
Kidney	1.8 nTPM
PBMC	1.8 nTPM
Skin	1.8 nTPM
Spleen	1.7 nTPM
Lung	1.5 nTPM
Liver	1.2 nTPM
Fallopian tube	1.1 nTPM
Stomach	1.0 nTPM
Lymph node	0.6 nTPM
Salivary gland	0.6 nTPM
Thymus	0.4 nTPM

Undifferentiated cells	3.6 nTPM
Small intestine	5.5 nTPM
Rectum	3.3 nTPM
Colon	1.9 nTPM

Amygdala excitatory	0.1 nTPM
Cerebral cortex	0.2 nTPM
Amygdala	0.1 nTPM
Basal ganglia	0.1 nTPM
Hippocampus	0.1 nTPM
Hypothalamus	0.1 nTPM
Thalamus	0.0 nTPM

Astrocyte	1.5 nTPM
Basal ganglia	2.1 nTPM
Amygdala	1.9 nTPM
Cerebral cortex	1.8 nTPM
Cerebellum	1.6 nTPM
Hippocampus	1.6 nTPM
Midbrain	1.6 nTPM
Medulla oblongata	1.4 nTPM
Thalamus	1.4 nTPM
Hypothalamus	1.3 nTPM
Spinal cord	1.1 nTPM
Pons	1.0 nTPM

Bergmann glia	1.0 nTPM
Cerebellum	3.0 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	37.6 nTPM
Basal ganglia	43.7 nTPM
Medulla oblongata	43.5 nTPM
Spinal cord	42.4 nTPM
Hypothalamus	40.4 nTPM
Pons	40.2 nTPM
Thalamus	39.1 nTPM
Midbrain	38.9 nTPM
Amygdala	37.6 nTPM
Cerebellum	33.5 nTPM
Cerebral cortex	27.8 nTPM
Hippocampus	26.5 nTPM

Cerebellar inhibitory	0.0 nTPM
Cerebellum	0.1 nTPM
Pons	0.1 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	0.1 nTPM
Basal ganglia	0.1 nTPM
Hippocampus	0.1 nTPM
Hypothalamus	0.1 nTPM
Amygdala	0.0 nTPM
Cerebral cortex	0.0 nTPM
Midbrain	0.0 nTPM
Thalamus	0.0 nTPM

Choroid plexus epithelial cell	0.8 nTPM
Medulla oblongata	1.8 nTPM
Basal ganglia	1.4 nTPM
Hippocampus	0.0 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	0.2 nTPM
Pons	0.9 nTPM
Hippocampus	0.8 nTPM
Basal ganglia	0.5 nTPM
Thalamus	0.5 nTPM
Amygdala	0.0 nTPM
Cerebellum	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hypothalamus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Spinal cord	0.0 nTPM

Deep-layer corticothalamic and 6b	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	0.1 nTPM
Amygdala	0.1 nTPM
Basal ganglia	0.1 nTPM
Cerebral cortex	0.1 nTPM
Hippocampus	0.1 nTPM
Hypothalamus	0.0 nTPM

Deep-layer near-projecting	0.0 nTPM
Basal ganglia	0.1 nTPM
Cerebral cortex	0.1 nTPM
Amygdala	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM

Eccentric medium spiny neuron	0.1 nTPM
Amygdala	0.1 nTPM
Basal ganglia	0.1 nTPM
Cerebral cortex	0.1 nTPM
Hypothalamus	0.1 nTPM
Thalamus	0.1 nTPM
Hippocampus	0.0 nTPM

Endothelial cell	6.0 nTPM
Basal ganglia	9.3 nTPM
Cerebral cortex	9.0 nTPM
Spinal cord	8.6 nTPM
Pons	7.5 nTPM
Medulla oblongata	7.2 nTPM
Thalamus	5.6 nTPM
Hippocampus	5.1 nTPM
Cerebellum	4.6 nTPM
Midbrain	3.8 nTPM
Hypothalamus	2.5 nTPM
Amygdala	2.2 nTPM

Ependymal cell	1.6 nTPM
Spinal cord	3.8 nTPM
Pons	2.7 nTPM
Medulla oblongata	2.2 nTPM
Thalamus	1.6 nTPM
Basal ganglia	1.4 nTPM
Hippocampus	1.2 nTPM
Amygdala	0.6 nTPM
Midbrain	0.6 nTPM
Hypothalamus	0.0 nTPM