Single cell type - NPTX1 - The Human Protein Atlas

NPTX1

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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.	NPTX1
Gene descriptionⁱ Full gene name according to HGNC.	Neuronal pentraxin 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	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.	Secreted, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	2

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 (Cone photoreceptor cells, Excitatory neurons, Late spermatids, Horizontal 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.	0.89
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 (Deep-layer corticothalamic and 6b, Deep-layer intratelencephalic)
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
Extracellular locationⁱ A possible secretion of the protein was predicted based on N-terminal signal sequence (signal peptide) predictions and transmembrane region predictions, and subsequently annotated for its local or systemic secretion based on literature, function, and protein and RNA expression data.	Protein predicted to be secreted

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 (Cone photoreceptor cells, Excitatory neurons, Late spermatids, Horizontal 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 (Deep-layer corticothalamic and 6b, Deep-layer intratelencephalic)

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

NPTX1 is part of cluster 34 Neurons - Neuronal signaling with confidenceⁱ 1
518 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.
XKR7	XK related 7	0.6503	69
NOS1AP	Nitric oxide synthase 1 adaptor protein	0.6273	34
SV2B	Synaptic vesicle glycoprotein 2B	0.6121	34
MAP6	Microtubule associated protein 6	0.6002	66
ANKRD33B	Ankyrin repeat domain 33B	0.5955	66
HS3ST4	Heparan sulfate-glucosamine 3-sulfotransferase 4	0.5915	34
WDR17	WD repeat domain 17	0.5901	34
DIRAS2	DIRAS family GTPase 2	0.5854	34
RALYL	RALY RNA binding protein like	0.5822	34
ADAMTSL1	ADAMTS like 1	0.5660	34
MAP2	Microtubule associated protein 2	0.5659	69
SH3GL2	SH3 domain containing GRB2 like 2, endophilin A1	0.5652	34
ASIC2	Acid sensing ion channel subunit 2	0.5650	34
PHF24	PHD finger protein 24	0.5546	34
GALNT9	Polypeptide N-acetylgalactosaminyltransferase 9	0.5503	34

Adipocytes	1.0 nTPM
Breast	1.6 nTPM
Adipose tissue	0.4 nTPM

Alveolar cells type 1	0.2 nTPM
Lung	0.2 nTPM

Alveolar cells type 2	0.1 nTPM
Lung	0.1 nTPM

Astrocytes	7.7 nTPM
Brain	7.7 nTPM

B-cells	0.1 nTPM
Adipose tissue	0.8 nTPM
Spleen	0.5 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM

Ciliated cells	0.2 nTPM
Lung	0.4 nTPM
Endometrium	0.3 nTPM
Bronchus	0.0 nTPM
Fallopian tube	0.0 nTPM

Club cells	0.1 nTPM
Bronchus	0.1 nTPM
Prostate	0.1 nTPM
Lung	0.0 nTPM

Endothelial cells	1.2 nTPM
Esophagus	7.3 nTPM
Vascular	3.7 nTPM
Endometrium	2.6 nTPM
Pancreas	2.6 nTPM
Salivary gland	1.2 nTPM
Prostate	1.0 nTPM
Fallopian tube	1.0 nTPM
Breast	0.9 nTPM
Placenta	0.6 nTPM
Skin	0.2 nTPM
Tongue	0.2 nTPM
Heart muscle	0.1 nTPM
Skeletal muscle	0.1 nTPM
Thymus	0.1 nTPM
Testis	0.0 nTPM
Liver	0.0 nTPM
Lung	0.0 nTPM
Ovary	0.0 nTPM

Enteroendocrine cells	0.1 nTPM
Colon	0.3 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Fibroblasts	0.5 nTPM
Fallopian tube	2.0 nTPM
Esophagus	1.2 nTPM
Pancreas	0.8 nTPM
Prostate	0.7 nTPM
Skeletal muscle	0.6 nTPM
Lung	0.6 nTPM
Breast	0.6 nTPM
Skin	0.4 nTPM
Adipose tissue	0.1 nTPM
Salivary gland	0.1 nTPM
Thymus	0.1 nTPM
Heart muscle	0.0 nTPM
Liver	0.0 nTPM
Placenta	0.0 nTPM
Stomach	0.0 nTPM
Vascular	0.0 nTPM

Granulocytes	1.7 nTPM
Tongue	4.9 nTPM
Fallopian tube	0.2 nTPM
Lung	0.0 nTPM

Intestinal goblet cells	0.2 nTPM
Colon	0.5 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Lymphatic endothelial cells	0.0 nTPM
Fallopian tube	0.1 nTPM
Ovary	0.0 nTPM

Macrophages	0.3 nTPM
Pancreas	2.1 nTPM
Breast	1.8 nTPM
Adipose tissue	0.3 nTPM
Skeletal muscle	0.2 nTPM
Prostate	0.2 nTPM
Thymus	0.2 nTPM
Fallopian tube	0.1 nTPM
Testis	0.0 nTPM
Kidney	0.0 nTPM
Endometrium	0.0 nTPM
Skin	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Salivary gland	0.0 nTPM
Tongue	0.0 nTPM
Vascular	0.0 nTPM

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

Bipolar cells	10.2 nTPM
Eye	10.2 nTPM

Cone photoreceptor cells	236.2 nTPM
Eye	236.2 nTPM

Early spermatids	2.7 nTPM
Testis	2.7 nTPM

Plasma cells	0.0 nTPM
Liver	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM
Fallopian tube	0.0 nTPM

Schwann cells	0.1 nTPM
Adipose tissue	0.4 nTPM
Esophagus	0.0 nTPM
Vascular	0.0 nTPM

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

Smooth muscle cells	0.8 nTPM
Breast	5.3 nTPM
Skin	3.4 nTPM
Fallopian tube	1.3 nTPM
Skeletal muscle	1.2 nTPM
Endometrium	1.1 nTPM
Salivary gland	0.5 nTPM
Ovary	0.3 nTPM
Placenta	0.2 nTPM
Thymus	0.1 nTPM
Vascular	0.1 nTPM
Liver	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Tongue	0.0 nTPM

T-cells	0.3 nTPM
Breast	1.4 nTPM
Skin	1.1 nTPM
Skeletal muscle	1.1 nTPM
Endometrium	0.5 nTPM
Liver	0.3 nTPM
Adipose tissue	0.3 nTPM
Lymph node	0.2 nTPM
Salivary gland	0.2 nTPM
PBMC	0.1 nTPM
Bone marrow	0.1 nTPM
Thymus	0.1 nTPM
Tongue	0.1 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
Esophagus	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Vascular	0.0 nTPM
Fallopian tube	0.0 nTPM

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

Amygdala excitatory	155.8 nTPM
Hypothalamus	260.1 nTPM
Hippocampus	198.1 nTPM
Amygdala	178.1 nTPM
Cerebral cortex	139.2 nTPM
Basal ganglia	134.5 nTPM
Thalamus	25.0 nTPM

Astrocyte	3.1 nTPM
Hypothalamus	7.7 nTPM
Cerebral cortex	7.4 nTPM
Amygdala	7.1 nTPM
Spinal cord	3.9 nTPM
Hippocampus	3.4 nTPM
Medulla oblongata	1.3 nTPM
Basal ganglia	1.1 nTPM
Pons	0.6 nTPM
Cerebellum	0.5 nTPM
Midbrain	0.5 nTPM
Thalamus	0.4 nTPM

Bergmann glia	6.6 nTPM
Medulla oblongata	12.8 nTPM
Cerebellum	4.2 nTPM
Pons	2.9 nTPM

Central nervous system macrophage	3.0 nTPM
Cerebral cortex	12.9 nTPM
Amygdala	6.6 nTPM
Hippocampus	5.3 nTPM
Hypothalamus	3.2 nTPM
Cerebellum	1.3 nTPM
Medulla oblongata	1.1 nTPM
Spinal cord	0.9 nTPM
Pons	0.7 nTPM
Basal ganglia	0.6 nTPM
Thalamus	0.4 nTPM
Midbrain	0.3 nTPM

Cerebellar inhibitory	33.0 nTPM
Pons	45.7 nTPM
Midbrain	37.0 nTPM
Medulla oblongata	34.8 nTPM
Cerebellum	25.5 nTPM
Spinal cord	22.0 nTPM

Cge interneuron	8.0 nTPM
Hypothalamus	16.6 nTPM
Amygdala	9.1 nTPM
Cerebral cortex	7.0 nTPM
Thalamus	6.7 nTPM
Hippocampus	6.1 nTPM
Midbrain	5.7 nTPM
Basal ganglia	4.9 nTPM

Choroid plexus epithelial cell	1.5 nTPM
Hippocampus	5.5 nTPM
Medulla oblongata	0.4 nTPM
Basal ganglia	0.1 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	9.8 nTPM
Hypothalamus	32.8 nTPM
Amygdala	24.8 nTPM
Cerebral cortex	13.9 nTPM
Hippocampus	11.1 nTPM
Medulla oblongata	10.3 nTPM
Pons	8.0 nTPM
Basal ganglia	3.3 nTPM
Midbrain	1.7 nTPM
Cerebellum	1.6 nTPM
Thalamus	0.5 nTPM
Spinal cord	0.0 nTPM

Deep-layer corticothalamic and 6b	234.2 nTPM
Hypothalamus	363.3 nTPM
Midbrain	268.5 nTPM
Cerebral cortex	226.5 nTPM
Hippocampus	217.9 nTPM
Amygdala	199.0 nTPM
Basal ganglia	130.1 nTPM

Deep-layer intratelencephalic	202.0 nTPM
Hypothalamus	349.8 nTPM
Amygdala	197.1 nTPM
Hippocampus	177.7 nTPM
Cerebral cortex	164.1 nTPM
Basal ganglia	121.5 nTPM

Deep-layer near-projecting	154.9 nTPM
Hypothalamus	245.1 nTPM
Amygdala	178.3 nTPM
Cerebral cortex	137.5 nTPM
Basal ganglia	108.4 nTPM
Hippocampus	105.4 nTPM

Eccentric medium spiny neuron	38.6 nTPM
Basal ganglia	65.7 nTPM
Thalamus	55.8 nTPM
Hypothalamus	45.0 nTPM
Cerebral cortex	28.3 nTPM
Hippocampus	21.1 nTPM
Amygdala	15.4 nTPM

Endothelial cell	4.3 nTPM
Amygdala	13.4 nTPM
Cerebral cortex	11.5 nTPM
Hypothalamus	7.4 nTPM
Hippocampus	5.8 nTPM
Cerebellum	3.9 nTPM
Medulla oblongata	3.1 nTPM
Thalamus	1.1 nTPM
Basal ganglia	0.9 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM

Ependymal cell	2.7 nTPM
Amygdala	11.9 nTPM
Hippocampus	3.8 nTPM
Medulla oblongata	2.0 nTPM
Basal ganglia	1.8 nTPM
Hypothalamus	1.8 nTPM
Midbrain	1.3 nTPM
Pons	1.2 nTPM
Thalamus	0.4 nTPM
Spinal cord	0.0 nTPM