Single cell type - NPTXR - The Human Protein Atlas

NPTXR

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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.	NPTXR
Gene descriptionⁱ Full gene name according to HGNC.	Neuronal pentraxin receptor
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Plasma proteins
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.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	1

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.	Neurons - Neuronal signaling (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 (Inhibitory neurons, Excitatory neurons, Oligodendrocyte precursor cells, Cardiomyocytes)
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.	0.74
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 (Thalamic excitatory)
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.	Not detected in immune cells
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 (Inhibitory neurons, Excitatory neurons, Oligodendrocyte precursor cells, Cardiomyocytes)

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 (Thalamic excitatory)

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: Not detected in immune cells
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

NPTXR is part of cluster 69 Neurons - Neuronal signaling with confidenceⁱ 1
331 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.
CELF6	CUGBP Elav-like family member 6	0.7975	69
PROP1	PROP paired-like homeobox 1	0.7801	69
PTPRO	Protein tyrosine phosphatase receptor type O	0.7759	69
CCK	Cholecystokinin	0.7545	34
APBA1	Amyloid beta precursor protein binding family A member 1	0.7455	69
GALNTL6	Polypeptide N-acetylgalactosaminyltransferase like 6	0.7365	69
SYT16	Synaptotagmin 16	0.7293	69
HTR1E	5-hydroxytryptamine receptor 1E	0.7289	69
GRIN1	Glutamate ionotropic receptor NMDA type subunit 1	0.7224	69
CNR1	Cannabinoid receptor 1	0.7209	69
CHRM3	Cholinergic receptor muscarinic 3	0.7187	34
DACH2	Dachshund family transcription factor 2	0.7143	69
CACNA1D	Calcium voltage-gated channel subunit alpha1 D	0.7006	69
PNMA6F	PNMA family member 6F	0.6943	69
CHRFAM7A	CHRNA7 (exons 5-10) and FAM7A (exons A-E) fusion	0.6881	69

Adipocytes	5.2 nTPM
Adipose tissue	6.3 nTPM
Breast	4.1 nTPM

Alveolar cells type 1	0.3 nTPM
Lung	0.3 nTPM

Alveolar cells type 2	0.3 nTPM
Lung	0.3 nTPM

Astrocytes	9.0 nTPM
Brain	9.0 nTPM

B-cells	0.2 nTPM
Salivary gland	0.6 nTPM
Lymph node	0.5 nTPM
Thymus	0.5 nTPM
Spleen	0.4 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM

Ciliated cells	1.9 nTPM
Fallopian tube	2.9 nTPM
Bronchus	2.1 nTPM
Endometrium	1.7 nTPM
Lung	0.9 nTPM

Club cells	5.3 nTPM
Prostate	7.3 nTPM
Lung	6.5 nTPM
Bronchus	2.2 nTPM

Endothelial cells	5.7 nTPM
Vascular	12.1 nTPM
Prostate	12.0 nTPM
Thymus	10.9 nTPM
Salivary gland	9.3 nTPM
Pancreas	7.8 nTPM
Tongue	7.6 nTPM
Fallopian tube	7.5 nTPM
Heart muscle	6.8 nTPM
Skin	5.5 nTPM
Lung	5.3 nTPM
Ovary	3.9 nTPM
Testis	3.1 nTPM
Skeletal muscle	2.8 nTPM
Esophagus	2.6 nTPM
Liver	2.5 nTPM
Placenta	1.7 nTPM
Endometrium	1.4 nTPM
Breast	0.0 nTPM

Enteroendocrine cells	2.3 nTPM
Small intestine	3.4 nTPM
Rectum	3.4 nTPM
Colon	0.1 nTPM

Fibroblasts	2.1 nTPM
Prostate	5.3 nTPM
Fallopian tube	5.3 nTPM
Pancreas	4.7 nTPM
Heart muscle	3.0 nTPM
Stomach	2.9 nTPM
Vascular	2.3 nTPM
Salivary gland	1.8 nTPM
Liver	1.2 nTPM
Breast	1.2 nTPM
Skin	1.0 nTPM
Thymus	1.0 nTPM
Esophagus	0.9 nTPM
Lung	0.9 nTPM
Placenta	0.8 nTPM
Skeletal muscle	0.5 nTPM
Adipose tissue	0.3 nTPM

Granulocytes	0.7 nTPM
Fallopian tube	1.5 nTPM
Lung	0.5 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Lymphatic endothelial cells	0.5 nTPM
Fallopian tube	0.9 nTPM
Ovary	0.0 nTPM

Macrophages	0.4 nTPM
Salivary gland	2.2 nTPM
Prostate	1.9 nTPM
Skin	1.1 nTPM
Endometrium	0.6 nTPM
Vascular	0.5 nTPM
Breast	0.5 nTPM
Adipose tissue	0.3 nTPM
Lung	0.2 nTPM
Thymus	0.2 nTPM
Tongue	0.2 nTPM
Fallopian tube	0.2 nTPM
Testis	0.0 nTPM
Kidney	0.0 nTPM
Pancreas	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

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

Basal prostatic cells	5.1 nTPM
Prostate	5.1 nTPM

Bipolar cells	7.0 nTPM
Eye	7.0 nTPM

Plasma cells	0.8 nTPM
Fallopian tube	1.9 nTPM
Salivary gland	1.8 nTPM
Liver	1.5 nTPM
Stomach	0.8 nTPM
Thymus	0.5 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Schwann cells	3.8 nTPM
Vascular	11.5 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	1.7 nTPM
Salivary gland	3.5 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	4.7 nTPM
Vascular	13.5 nTPM
Prostate	7.9 nTPM
Fallopian tube	7.1 nTPM
Endometrium	6.7 nTPM
Salivary gland	6.2 nTPM
Thymus	6.2 nTPM
Liver	5.5 nTPM
Tongue	4.8 nTPM
Lung	3.5 nTPM
Breast	3.4 nTPM
Skeletal muscle	2.9 nTPM
Ovary	2.8 nTPM
Skin	1.3 nTPM
Esophagus	1.2 nTPM
Placenta	1.1 nTPM
Adipose tissue	0.4 nTPM

T-cells	2.9 nTPM
Thymus	11.0 nTPM
Salivary gland	5.7 nTPM
Adipose tissue	4.3 nTPM
Prostate	4.0 nTPM
Vascular	4.0 nTPM
Fallopian tube	3.7 nTPM
Lymph node	3.2 nTPM
Lung	3.2 nTPM
Breast	2.9 nTPM
Liver	2.1 nTPM
Skin	2.1 nTPM
Skeletal muscle	1.9 nTPM
Spleen	1.9 nTPM
Tongue	1.9 nTPM
PBMC	1.8 nTPM
Endometrium	1.7 nTPM
Bone marrow	1.7 nTPM
Stomach	1.7 nTPM
Colon	1.0 nTPM
Kidney	0.9 nTPM
Esophagus	0.0 nTPM

Undifferentiated cells	0.4 nTPM
Colon	0.6 nTPM
Small intestine	0.4 nTPM
Rectum	0.1 nTPM

Amygdala excitatory	181.9 nTPM
Hypothalamus	366.4 nTPM
Amygdala	181.0 nTPM
Hippocampus	176.5 nTPM
Basal ganglia	165.4 nTPM
Cerebral cortex	148.8 nTPM
Thalamus	53.1 nTPM

Astrocyte	17.7 nTPM
Cerebral cortex	23.4 nTPM
Cerebellum	23.1 nTPM
Hypothalamus	21.4 nTPM
Amygdala	18.9 nTPM
Hippocampus	17.5 nTPM
Midbrain	17.5 nTPM
Pons	16.6 nTPM
Thalamus	15.7 nTPM
Spinal cord	14.5 nTPM
Medulla oblongata	12.9 nTPM
Basal ganglia	12.7 nTPM

Bergmann glia	7.7 nTPM
Pons	12.9 nTPM
Cerebellum	5.9 nTPM
Medulla oblongata	4.3 nTPM

Central nervous system macrophage	7.7 nTPM
Cerebral cortex	15.2 nTPM
Hippocampus	13.0 nTPM
Hypothalamus	10.6 nTPM
Amygdala	9.5 nTPM
Medulla oblongata	6.5 nTPM
Thalamus	6.4 nTPM
Cerebellum	5.5 nTPM
Midbrain	5.1 nTPM
Basal ganglia	4.7 nTPM
Pons	4.7 nTPM
Spinal cord	3.8 nTPM

Cerebellar inhibitory	19.6 nTPM
Spinal cord	24.7 nTPM
Midbrain	22.1 nTPM
Pons	19.1 nTPM
Medulla oblongata	16.4 nTPM
Cerebellum	15.4 nTPM

Cge interneuron	214.9 nTPM
Hypothalamus	404.9 nTPM
Basal ganglia	218.9 nTPM
Amygdala	218.4 nTPM
Cerebral cortex	175.5 nTPM
Thalamus	169.2 nTPM
Hippocampus	166.8 nTPM
Midbrain	150.7 nTPM

Choroid plexus epithelial cell	5.4 nTPM
Hippocampus	13.9 nTPM
Medulla oblongata	2.7 nTPM
Thalamus	2.7 nTPM
Basal ganglia	2.3 nTPM

Committed oligodendrocyte precursor	26.9 nTPM
Hypothalamus	56.0 nTPM
Amygdala	50.7 nTPM
Hippocampus	37.0 nTPM
Cerebral cortex	28.5 nTPM
Cerebellum	25.4 nTPM
Midbrain	23.5 nTPM
Basal ganglia	23.0 nTPM
Thalamus	22.5 nTPM
Pons	11.5 nTPM
Spinal cord	11.0 nTPM
Medulla oblongata	6.5 nTPM

Deep-layer corticothalamic and 6b	18.4 nTPM
Hippocampus	39.8 nTPM
Hypothalamus	35.8 nTPM
Amygdala	11.4 nTPM
Cerebral cortex	10.7 nTPM
Midbrain	7.8 nTPM
Basal ganglia	4.7 nTPM

Deep-layer intratelencephalic	175.4 nTPM
Hypothalamus	416.2 nTPM
Hippocampus	133.7 nTPM
Amygdala	124.3 nTPM
Cerebral cortex	107.0 nTPM
Basal ganglia	95.6 nTPM

Deep-layer near-projecting	85.3 nTPM
Hypothalamus	171.9 nTPM
Amygdala	84.9 nTPM
Cerebral cortex	75.0 nTPM
Hippocampus	50.4 nTPM
Basal ganglia	44.5 nTPM

Eccentric medium spiny neuron	45.3 nTPM
Amygdala	55.8 nTPM
Hippocampus	53.5 nTPM
Cerebral cortex	49.7 nTPM
Hypothalamus	47.1 nTPM
Thalamus	39.8 nTPM
Basal ganglia	26.1 nTPM

Endothelial cell	6.7 nTPM
Amygdala	19.0 nTPM
Hippocampus	14.7 nTPM
Hypothalamus	12.4 nTPM
Cerebral cortex	8.3 nTPM
Medulla oblongata	6.2 nTPM
Cerebellum	3.1 nTPM
Basal ganglia	2.8 nTPM
Thalamus	2.8 nTPM
Pons	1.9 nTPM
Spinal cord	1.7 nTPM
Midbrain	0.9 nTPM

Ependymal cell	14.4 nTPM
Hypothalamus	22.3 nTPM
Midbrain	21.0 nTPM
Amygdala	18.8 nTPM
Hippocampus	18.4 nTPM
Thalamus	14.2 nTPM
Basal ganglia	10.7 nTPM
Pons	10.2 nTPM
Medulla oblongata	10.1 nTPM
Spinal cord	3.8 nTPM