Single cell type - PTPN3 - The Human Protein Atlas

PTPN3

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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.	PTPN3
Gene descriptionⁱ Full gene name according to HGNC.	Protein tyrosine phosphatase non-receptor type 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Enzymes 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.	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.	Glandular & Luminal cells - Unknown function (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 (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.	0.55
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, Ependymal cell)
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 (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, Ependymal cell)

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

PTPN3 is part of cluster 37 Glandular & Luminal cells - Unknown function with confidenceⁱ 1
334 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.
GCOM1	GCOM1, MYZAP-POLR2M combined locus	0.5419	37
PATJ	PATJ crumbs cell polarity complex component	0.5390	37
SMYD2	SET and MYND domain containing 2	0.4860	24
MARVELD2	MARVEL domain containing 2	0.4762	37
CDH1	Cadherin 1	0.4761	37
F11R	F11 receptor	0.4760	37
ILDR1	Immunoglobulin like domain containing receptor 1	0.4752	37
SHH	Sonic hedgehog signaling molecule	0.4746	37
ARHGAP8	Rho GTPase activating protein 8	0.4745	45
LMO7	LIM domain 7	0.4713	72
C3orf52	Chromosome 3 open reading frame 52	0.4670	45
OCLN	Occludin	0.4649	37
SLC6A12	Solute carrier family 6 member 12	0.4634	37
MET	MET proto-oncogene, receptor tyrosine kinase	0.4600	37
TSPAN12	Tetraspanin 12	0.4557	3

Adipocytes	0.4 nTPM
Breast	0.7 nTPM
Adipose tissue	0.2 nTPM

Alveolar cells type 1	23.8 nTPM
Lung	23.8 nTPM

Alveolar cells type 2	25.7 nTPM
Lung	25.7 nTPM

Astrocytes	0.6 nTPM
Brain	0.6 nTPM

B-cells	0.3 nTPM
Lung	1.3 nTPM
Adipose tissue	1.2 nTPM
Salivary gland	0.6 nTPM
Stomach	0.4 nTPM
Thymus	0.3 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
Spleen	0.0 nTPM

Ciliated cells	22.0 nTPM
Bronchus	29.7 nTPM
Endometrium	24.1 nTPM
Lung	17.6 nTPM
Fallopian tube	16.7 nTPM

Club cells	22.4 nTPM
Bronchus	27.2 nTPM
Lung	24.2 nTPM
Prostate	16.0 nTPM

Endothelial cells	3.5 nTPM
Breast	22.8 nTPM
Tongue	4.6 nTPM
Salivary gland	4.2 nTPM
Heart muscle	4.0 nTPM
Thymus	3.4 nTPM
Pancreas	2.6 nTPM
Prostate	2.6 nTPM
Liver	2.5 nTPM
Endometrium	2.5 nTPM
Lung	2.4 nTPM
Skin	1.9 nTPM
Testis	1.8 nTPM
Placenta	1.7 nTPM
Esophagus	1.4 nTPM
Skeletal muscle	1.3 nTPM
Vascular	1.1 nTPM
Ovary	0.9 nTPM
Fallopian tube	0.5 nTPM

Enteroendocrine cells	16.5 nTPM
Small intestine	24.0 nTPM
Rectum	13.4 nTPM
Colon	12.1 nTPM

Fibroblasts	1.9 nTPM
Heart muscle	9.7 nTPM
Vascular	3.5 nTPM
Skin	3.1 nTPM
Lung	2.9 nTPM
Prostate	2.0 nTPM
Pancreas	1.5 nTPM
Salivary gland	1.5 nTPM
Thymus	1.5 nTPM
Placenta	1.4 nTPM
Liver	1.2 nTPM
Esophagus	0.9 nTPM
Breast	0.9 nTPM
Skeletal muscle	0.3 nTPM
Adipose tissue	0.2 nTPM
Fallopian tube	0.2 nTPM
Stomach	0.0 nTPM

Granulocytes	2.2 nTPM
Tongue	4.9 nTPM
Fallopian tube	1.3 nTPM
Lung	0.5 nTPM

Intestinal goblet cells	16.5 nTPM
Small intestine	20.5 nTPM
Rectum	19.4 nTPM
Colon	9.6 nTPM

Lymphatic endothelial cells	29.8 nTPM
Fallopian tube	43.3 nTPM
Ovary	16.4 nTPM

Macrophages	0.7 nTPM
Endometrium	2.5 nTPM
Prostate	2.4 nTPM
Pancreas	2.1 nTPM
Tongue	2.1 nTPM
Salivary gland	1.6 nTPM
Kidney	0.9 nTPM
Vascular	0.8 nTPM
Skeletal muscle	0.6 nTPM
Fallopian tube	0.4 nTPM
Lung	0.3 nTPM
Breast	0.3 nTPM
Testis	0.0 nTPM
Skin	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Thymus	0.0 nTPM

Paneth cells	14.5 nTPM
Rectum	22.1 nTPM
Colon	14.5 nTPM
Small intestine	6.9 nTPM

Basal keratinocytes	8.6 nTPM
Skin	8.9 nTPM
Tongue	8.4 nTPM

Basal prostatic cells	17.9 nTPM
Prostate	17.9 nTPM

Basal respiratory cells	16.9 nTPM
Bronchus	16.9 nTPM

Basal squamous epithelial cells	6.2 nTPM
Esophagus	6.2 nTPM

Plasma cells	0.5 nTPM
Fallopian tube	2.6 nTPM
Liver	1.0 nTPM
Thymus	0.1 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Salivary gland	0.0 nTPM

Schwann cells	0.5 nTPM
Vascular	1.6 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	9.0 nTPM
Salivary gland	13.6 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	6.0 nTPM
Prostate	14.0 nTPM
Salivary gland	12.3 nTPM
Esophagus	10.8 nTPM
Skin	8.3 nTPM
Ovary	8.1 nTPM
Breast	6.1 nTPM
Vascular	6.0 nTPM
Endometrium	5.2 nTPM
Tongue	5.1 nTPM
Liver	4.7 nTPM
Thymus	4.6 nTPM
Placenta	2.4 nTPM
Lung	2.4 nTPM
Fallopian tube	2.4 nTPM
Adipose tissue	1.8 nTPM
Skeletal muscle	1.2 nTPM

Suprabasal keratinocytes	18.2 nTPM
Skin	20.6 nTPM
Tongue	15.8 nTPM

T-cells	0.8 nTPM
Endometrium	2.8 nTPM
Prostate	2.6 nTPM
Colon	1.9 nTPM
Tongue	1.7 nTPM
Salivary gland	1.3 nTPM
Kidney	0.9 nTPM
Skeletal muscle	0.8 nTPM
Lung	0.8 nTPM
Vascular	0.8 nTPM
Skin	0.7 nTPM
Fallopian tube	0.7 nTPM
Liver	0.6 nTPM
Lymph node	0.6 nTPM
PBMC	0.3 nTPM
Thymus	0.3 nTPM
Spleen	0.2 nTPM
Stomach	0.2 nTPM
Breast	0.2 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

Undifferentiated cells	14.5 nTPM
Small intestine	18.0 nTPM
Rectum	16.4 nTPM
Colon	9.1 nTPM

Amygdala excitatory	40.5 nTPM
Cerebral cortex	76.4 nTPM
Hippocampus	65.4 nTPM
Amygdala	61.5 nTPM
Hypothalamus	19.8 nTPM
Basal ganglia	16.0 nTPM
Thalamus	3.6 nTPM

Astrocyte	9.5 nTPM
Spinal cord	35.6 nTPM
Pons	13.6 nTPM
Thalamus	10.9 nTPM
Medulla oblongata	10.7 nTPM
Cerebellum	10.6 nTPM
Hypothalamus	7.0 nTPM
Hippocampus	6.1 nTPM
Midbrain	4.9 nTPM
Basal ganglia	2.6 nTPM
Amygdala	1.5 nTPM
Cerebral cortex	1.2 nTPM

Bergmann glia	8.2 nTPM
Pons	12.9 nTPM
Cerebellum	7.4 nTPM
Medulla oblongata	4.3 nTPM

Central nervous system macrophage	2.1 nTPM
Thalamus	13.9 nTPM
Cerebral cortex	2.0 nTPM
Hippocampus	1.5 nTPM
Amygdala	1.4 nTPM
Basal ganglia	1.1 nTPM
Medulla oblongata	0.8 nTPM
Midbrain	0.7 nTPM
Pons	0.5 nTPM
Cerebellum	0.4 nTPM
Hypothalamus	0.4 nTPM
Spinal cord	0.3 nTPM

Cerebellar inhibitory	2.8 nTPM
Medulla oblongata	4.6 nTPM
Pons	4.3 nTPM
Cerebellum	2.8 nTPM
Midbrain	2.5 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	15.5 nTPM
Thalamus	24.4 nTPM
Midbrain	16.8 nTPM
Hippocampus	15.0 nTPM
Amygdala	14.2 nTPM
Hypothalamus	14.2 nTPM
Basal ganglia	13.2 nTPM
Cerebral cortex	10.6 nTPM

Choroid plexus epithelial cell	57.7 nTPM
Basal ganglia	113.1 nTPM
Hippocampus	47.1 nTPM
Medulla oblongata	40.4 nTPM
Thalamus	30.1 nTPM

Committed oligodendrocyte precursor	10.3 nTPM
Thalamus	79.7 nTPM
Medulla oblongata	9.0 nTPM
Basal ganglia	8.2 nTPM
Amygdala	5.1 nTPM
Spinal cord	3.7 nTPM
Cerebral cortex	1.9 nTPM
Cerebellum	1.6 nTPM
Hippocampus	1.6 nTPM
Hypothalamus	1.4 nTPM
Pons	0.9 nTPM
Midbrain	0.8 nTPM

Deep-layer corticothalamic and 6b	13.0 nTPM
Cerebral cortex	17.7 nTPM
Basal ganglia	15.6 nTPM
Amygdala	14.4 nTPM
Midbrain	11.1 nTPM
Hippocampus	11.0 nTPM
Hypothalamus	8.4 nTPM

Deep-layer intratelencephalic	43.4 nTPM
Hypothalamus	47.1 nTPM
Hippocampus	46.5 nTPM
Cerebral cortex	45.0 nTPM
Amygdala	41.1 nTPM
Basal ganglia	37.3 nTPM

Deep-layer near-projecting	1.2 nTPM
Hippocampus	1.6 nTPM
Hypothalamus	1.5 nTPM
Amygdala	1.1 nTPM
Cerebral cortex	0.9 nTPM
Basal ganglia	0.7 nTPM

Eccentric medium spiny neuron	9.8 nTPM
Amygdala	21.4 nTPM
Hippocampus	16.6 nTPM
Cerebral cortex	11.2 nTPM
Thalamus	4.9 nTPM
Hypothalamus	2.8 nTPM
Basal ganglia	2.0 nTPM

Endothelial cell	3.4 nTPM
Thalamus	17.5 nTPM
Medulla oblongata	6.2 nTPM
Basal ganglia	2.8 nTPM
Midbrain	2.8 nTPM
Cerebellum	2.3 nTPM
Spinal cord	1.7 nTPM
Cerebral cortex	1.3 nTPM
Pons	1.2 nTPM
Amygdala	1.1 nTPM
Hippocampus	1.0 nTPM
Hypothalamus	0.0 nTPM