Single cell type - TLR5 - The Human Protein Atlas

TLR5

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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.	TLR5
Gene descriptionⁱ Full gene name according to HGNC.	Toll like receptor 5
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Human disease related genes
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.	4

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.	Macrophages - Innate immune response (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 (Mucus glandular 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.	0.62
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 enriched (Central nervous system macrophage)
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.	Group enriched (classical monocyte, intermediate monocyte, neutrophil, myeloid DC, non-classical monocyte)
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 (Mucus glandular 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 enriched (Central nervous system macrophage)

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: Group enriched (classical monocyte, intermediate monocyte, neutrophil, myeloid DC, non-classical monocyte)
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

TLR5 is part of cluster 58 Macrophages - Innate immune response with confidenceⁱ 1
420 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.
P2RY13	Purinergic receptor P2Y13	0.6791	58
OGFRL1	Opioid growth factor receptor like 1	0.6295	58
SLC37A2	Solute carrier family 37 member 2	0.6162	58
TLR1	Toll like receptor 1	0.6151	74
SIRPB2	Signal regulatory protein beta 2	0.6069	29
CD14	CD14 molecule	0.5817	58
ALPK1	Alpha kinase 1	0.5811	74
TLR2	Toll like receptor 2	0.5702	29
EGR2	Early growth response 2	0.5657	58
CEACAM4	CEA cell adhesion molecule 4	0.5645	74
CLEC4E	C-type lectin domain family 4 member E	0.5580	29
GGTA1	Glycoprotein alpha-galactosyltransferase 1 (inactive)	0.5511	75
ITGAM	Integrin subunit alpha M	0.5457	58
ZNF117	Zinc finger protein 117	0.5441	74
CREG1	Cellular repressor of E1A stimulated genes 1	0.5421	58

IMMUNE CELLS

TLR5 is part of cluster 38 Monocytes & Neutrophils - Degranulation with confidenceⁱ 1
501 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.
CARD16	Caspase recruitment domain family member 16	1.0000	38
SQOR	Sulfide quinone oxidoreductase	1.0000	38
LTA4H	Leukotriene A4 hydrolase	0.9762	38
NUP58	Nucleoporin 58	0.9762	38
HADHB	Hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit beta	0.9762	38
PRAM1	PML-RARA regulated adaptor molecule 1	0.9762	38
RIN2	Ras and Rab interactor 2	0.9762	38
CFP	Complement factor properdin	0.9762	38
USP4	Ubiquitin specific peptidase 4	0.9762	38
PRLR	Prolactin receptor	0.9762	38
MVP	Major vault protein	0.9762	38
HIPK3	Homeodomain interacting protein kinase 3	0.9762	38
THOC5	THO complex subunit 5	0.9762	38
TOM1	Target of myb1 membrane trafficking protein	0.9762	38
PSEN1	Presenilin 1	0.9762	38

Adipocytes	1.1 nTPM
Breast	1.8 nTPM
Adipose tissue	0.4 nTPM

Alveolar cells type 1	0.7 nTPM
Lung	0.7 nTPM

Alveolar cells type 2	8.5 nTPM
Lung	8.5 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	0.7 nTPM
Esophagus	5.9 nTPM
Lung	1.3 nTPM
Salivary gland	0.9 nTPM
Thymus	0.4 nTPM
Lymph node	0.3 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Adipose tissue	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Ciliated cells	10.0 nTPM
Endometrium	13.2 nTPM
Bronchus	12.3 nTPM
Lung	11.2 nTPM
Fallopian tube	3.3 nTPM

Club cells	26.3 nTPM
Bronchus	28.0 nTPM
Lung	25.8 nTPM
Prostate	25.1 nTPM

Endothelial cells	2.1 nTPM
Breast	7.9 nTPM
Heart muscle	7.2 nTPM
Salivary gland	3.8 nTPM
Tongue	3.3 nTPM
Pancreas	2.6 nTPM
Prostate	2.1 nTPM
Esophagus	1.8 nTPM
Endometrium	1.3 nTPM
Thymus	1.3 nTPM
Vascular	1.2 nTPM
Ovary	1.2 nTPM
Placenta	1.1 nTPM
Testis	0.9 nTPM
Fallopian tube	0.8 nTPM
Lung	0.7 nTPM
Skeletal muscle	0.6 nTPM
Skin	0.4 nTPM
Liver	0.0 nTPM

Enteroendocrine cells	0.4 nTPM
Colon	1.2 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Fibroblasts	6.2 nTPM
Esophagus	15.0 nTPM
Adipose tissue	14.3 nTPM
Stomach	10.1 nTPM
Skin	9.1 nTPM
Skeletal muscle	8.9 nTPM
Salivary gland	6.1 nTPM
Thymus	6.0 nTPM
Breast	6.0 nTPM
Lung	5.5 nTPM
Vascular	5.3 nTPM
Heart muscle	5.2 nTPM
Fallopian tube	2.9 nTPM
Prostate	2.6 nTPM
Placenta	1.0 nTPM
Pancreas	0.4 nTPM
Liver	0.0 nTPM

Granulocytes	0.2 nTPM
Lung	0.5 nTPM
Fallopian tube	0.2 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	0.7 nTPM
Rectum	1.0 nTPM
Small intestine	0.8 nTPM
Colon	0.2 nTPM

Lymphatic endothelial cells	11.1 nTPM
Fallopian tube	16.6 nTPM
Ovary	5.5 nTPM

Macrophages	23.3 nTPM
Salivary gland	50.2 nTPM
Testis	49.0 nTPM
Prostate	44.9 nTPM
Skeletal muscle	28.1 nTPM
Adipose tissue	27.6 nTPM
Vascular	27.4 nTPM
Spleen	26.1 nTPM
Bone marrow	24.3 nTPM
Breast	24.3 nTPM
Thymus	23.5 nTPM
Fallopian tube	23.1 nTPM
Esophagus	19.3 nTPM
Tongue	16.6 nTPM
Lung	15.3 nTPM
Kidney	14.2 nTPM
Stomach	12.9 nTPM
Endometrium	8.6 nTPM
Skin	6.7 nTPM
Pancreas	0.0 nTPM

Paneth cells	0.1 nTPM
Rectum	0.2 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Basal prostatic cells	6.8 nTPM
Prostate	6.8 nTPM

Basal respiratory cells	18.2 nTPM
Bronchus	18.2 nTPM

Cholangiocytes	17.2 nTPM
Liver	17.2 nTPM

Collecting duct cells	19.4 nTPM
Kidney	19.4 nTPM

Plasma cells	1.0 nTPM
Salivary gland	5.8 nTPM
Fallopian tube	1.3 nTPM
Stomach	0.4 nTPM
Thymus	0.3 nTPM
Liver	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Schwann cells	1.7 nTPM
Vascular	5.2 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	12.8 nTPM
Salivary gland	25.6 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	4.1 nTPM
Salivary gland	14.0 nTPM
Skeletal muscle	9.6 nTPM
Tongue	5.1 nTPM
Breast	5.1 nTPM
Lung	4.7 nTPM
Ovary	4.5 nTPM
Adipose tissue	3.8 nTPM
Esophagus	3.6 nTPM
Thymus	3.1 nTPM
Prostate	3.0 nTPM
Vascular	2.7 nTPM
Fallopian tube	1.8 nTPM
Endometrium	1.7 nTPM
Skin	1.7 nTPM
Liver	1.3 nTPM
Placenta	0.5 nTPM

Suprabasal keratinocytes	10.8 nTPM
Tongue	20.9 nTPM
Skin	0.7 nTPM

T-cells	1.5 nTPM
Lymph node	7.4 nTPM
Salivary gland	5.0 nTPM
Kidney	3.5 nTPM
Thymus	2.7 nTPM
Spleen	2.6 nTPM
Skin	1.8 nTPM
Tongue	1.8 nTPM
PBMC	1.5 nTPM
Endometrium	1.1 nTPM
Prostate	1.1 nTPM
Lung	0.8 nTPM
Adipose tissue	0.5 nTPM
Fallopian tube	0.5 nTPM
Stomach	0.4 nTPM
Breast	0.4 nTPM
Colon	0.0 nTPM
Liver	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Vascular	0.0 nTPM

Undifferentiated cells	1.2 nTPM
Rectum	2.0 nTPM
Colon	0.7 nTPM
Small intestine	0.7 nTPM

Amygdala excitatory	2.0 nTPM
Thalamus	5.0 nTPM
Basal ganglia	2.3 nTPM
Hippocampus	1.4 nTPM
Amygdala	1.3 nTPM
Cerebral cortex	1.2 nTPM
Hypothalamus	1.1 nTPM

Astrocyte	2.6 nTPM
Midbrain	5.4 nTPM
Cerebellum	5.0 nTPM
Spinal cord	3.5 nTPM
Medulla oblongata	3.0 nTPM
Basal ganglia	2.6 nTPM
Pons	2.3 nTPM
Thalamus	2.3 nTPM
Amygdala	1.9 nTPM
Hypothalamus	1.1 nTPM
Cerebral cortex	0.6 nTPM
Hippocampus	0.5 nTPM

Bergmann glia	0.1 nTPM
Cerebellum	0.4 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	95.9 nTPM
Amygdala	118.4 nTPM
Hippocampus	101.1 nTPM
Cerebral cortex	100.9 nTPM
Hypothalamus	98.2 nTPM
Midbrain	98.1 nTPM
Cerebellum	96.1 nTPM
Thalamus	94.9 nTPM
Pons	90.0 nTPM
Basal ganglia	88.3 nTPM
Spinal cord	86.6 nTPM
Medulla oblongata	82.7 nTPM

Cerebellar inhibitory	0.7 nTPM
Cerebellum	1.2 nTPM
Pons	1.1 nTPM
Midbrain	0.6 nTPM
Medulla oblongata	0.4 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	2.8 nTPM
Hypothalamus	4.2 nTPM
Amygdala	3.4 nTPM
Cerebral cortex	3.2 nTPM
Hippocampus	2.7 nTPM
Basal ganglia	2.6 nTPM
Midbrain	2.3 nTPM
Thalamus	1.2 nTPM

Choroid plexus epithelial cell	0.9 nTPM
Medulla oblongata	1.8 nTPM
Basal ganglia	1.7 nTPM
Hippocampus	0.0 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	1.6 nTPM
Spinal cord	3.7 nTPM
Midbrain	3.4 nTPM
Thalamus	2.0 nTPM
Basal ganglia	1.6 nTPM
Cerebellum	1.6 nTPM
Hippocampus	1.6 nTPM
Hypothalamus	1.4 nTPM
Cerebral cortex	1.3 nTPM
Pons	0.9 nTPM
Amygdala	0.6 nTPM
Medulla oblongata	0.0 nTPM

Deep-layer corticothalamic and 6b	1.1 nTPM
Amygdala	1.1 nTPM
Cerebral cortex	1.1 nTPM
Hypothalamus	1.1 nTPM
Midbrain	1.1 nTPM
Hippocampus	1.0 nTPM
Basal ganglia	0.9 nTPM

Deep-layer intratelencephalic	1.0 nTPM
Hypothalamus	1.3 nTPM
Hippocampus	1.2 nTPM
Basal ganglia	0.9 nTPM
Amygdala	0.7 nTPM
Cerebral cortex	0.7 nTPM

Deep-layer near-projecting	2.4 nTPM
Hypothalamus	4.5 nTPM
Cerebral cortex	2.4 nTPM
Basal ganglia	2.0 nTPM
Hippocampus	2.0 nTPM
Amygdala	1.2 nTPM

Eccentric medium spiny neuron	3.0 nTPM
Thalamus	3.6 nTPM
Hippocampus	3.3 nTPM
Amygdala	2.9 nTPM
Cerebral cortex	2.8 nTPM
Hypothalamus	2.8 nTPM
Basal ganglia	2.7 nTPM

Endothelial cell	4.2 nTPM
Basal ganglia	9.3 nTPM
Cerebral cortex	5.8 nTPM
Spinal cord	5.2 nTPM
Hippocampus	4.8 nTPM
Midbrain	3.8 nTPM
Hypothalamus	3.7 nTPM
Pons	3.7 nTPM
Medulla oblongata	3.1 nTPM
Cerebellum	2.3 nTPM
Thalamus	2.3 nTPM
Amygdala	2.2 nTPM