Single cell type - PTPN6 - The Human Protein Atlas

PTPN6

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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.	PTPN6
Gene descriptionⁱ Full gene name according to HGNC.	Protein tyrosine phosphatase non-receptor type 6
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.	7

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.	B-cells - B-cell 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 (Monocytes, B-cells, Hofbauer cells, Macrophages, Kupffer cells, Langerhans 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.	0.57
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 (Leukocyte, 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.	Low immune cell specificity
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 (Monocytes, B-cells, Hofbauer cells, Macrophages, Kupffer cells, Langerhans 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 (Leukocyte, 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: Low immune cell specificity
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

PTPN6 is part of cluster 73 B-cells - B-cell function with confidenceⁱ 1
195 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.
SCIMP	SLP adaptor and CSK interacting membrane protein	0.7853	73
LAPTM5	Lysosomal protein transmembrane 5	0.7775	73
CD37	CD37 molecule	0.7720	73
LAT2	Linker for activation of T cells family member 2	0.7452	73
LY86	Lymphocyte antigen 86	0.7339	73
POU2F2	POU class 2 homeobox 2	0.7115	73
RGS19	Regulator of G protein signaling 19	0.7072	29
CSK	C-terminal Src kinase	0.6911	73
ALOX5	Arachidonate 5-lipoxygenase	0.6899	58
CD52	CD52 molecule	0.6899	73
LYN	LYN proto-oncogene, Src family tyrosine kinase	0.6858	29
BTK	Bruton tyrosine kinase	0.6822	30
RCSD1	RCSD domain containing 1	0.6710	73
ATG16L2	Autophagy related 16 like 2	0.6674	74
CD72	CD72 molecule	0.6550	73

IMMUNE CELLS

PTPN6 is part of cluster 29 Non-specific - Unknown function with confidenceⁱ 0.89
401 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.
BMF	Bcl2 modifying factor	0.9524	25
SIGLEC16	Sialic acid binding Ig like lectin 16	0.9524	29
EPN1	Epsin 1	0.9286	25
CLCN7	Chloride voltage-gated channel 7	0.9286	29
CNPPD1	Cyclin Pas1/PHO80 domain containing 1	0.9286	40
SOWAHD	Sosondowah ankyrin repeat domain family member D	0.9286	29
POLD4	DNA polymerase delta 4, accessory subunit	0.9286	29
PSEN2	Presenilin 2	0.9286	25
ZNF580	Zinc finger protein 580	0.9048	29
DYNAP	Dynactin associated protein	0.9048	29
PWWP2B	PWWP domain containing 2B	0.9048	29
HSPA4	Heat shock protein family A (Hsp70) member 4	0.9048	29
CCDC24	Coiled-coil domain containing 24	0.9048	29
MED22	Mediator complex subunit 22	0.9048	29
LMO2	LIM domain only 2	0.9048	25

Adipocytes	8.5 nTPM
Breast	13.9 nTPM
Adipose tissue	3.0 nTPM

Alveolar cells type 1	8.5 nTPM
Lung	8.5 nTPM

Alveolar cells type 2	11.1 nTPM
Lung	11.1 nTPM

Astrocytes	0.6 nTPM
Brain	0.6 nTPM

B-cells	228.3 nTPM
Bone marrow	367.5 nTPM
Lymph node	312.9 nTPM
Thymus	296.3 nTPM
PBMC	292.5 nTPM
Spleen	265.8 nTPM
Lung	264.3 nTPM
Stomach	232.8 nTPM
Kidney	228.8 nTPM
Salivary gland	196.2 nTPM
Liver	169.1 nTPM
Esophagus	153.4 nTPM
Skin	123.7 nTPM
Adipose tissue	65.4 nTPM

Ciliated cells	17.8 nTPM
Lung	28.2 nTPM
Bronchus	20.4 nTPM
Endometrium	11.7 nTPM
Fallopian tube	10.9 nTPM

Club cells	22.7 nTPM
Lung	34.0 nTPM
Bronchus	17.2 nTPM
Prostate	17.0 nTPM

Dendritic cells	50.2 nTPM
PBMC	71.9 nTPM
Adipose tissue	28.4 nTPM

Endothelial cells	5.1 nTPM
Liver	10.1 nTPM
Tongue	8.2 nTPM
Pancreas	7.8 nTPM
Skeletal muscle	7.8 nTPM
Esophagus	6.5 nTPM
Placenta	5.7 nTPM
Prostate	5.6 nTPM
Lung	5.4 nTPM
Skin	5.0 nTPM
Thymus	4.7 nTPM
Heart muscle	4.4 nTPM
Vascular	4.4 nTPM
Testis	4.3 nTPM
Salivary gland	4.2 nTPM
Ovary	2.7 nTPM
Endometrium	2.5 nTPM
Fallopian tube	1.4 nTPM
Breast	0.9 nTPM

Enteroendocrine cells	25.4 nTPM
Small intestine	37.8 nTPM
Rectum	23.5 nTPM
Colon	14.9 nTPM

Fibroblasts	4.0 nTPM
Lung	13.7 nTPM
Placenta	11.4 nTPM
Liver	9.5 nTPM
Salivary gland	5.7 nTPM
Stomach	4.3 nTPM
Thymus	4.0 nTPM
Esophagus	3.7 nTPM
Prostate	3.3 nTPM
Breast	2.1 nTPM
Skin	1.9 nTPM
Vascular	1.7 nTPM
Pancreas	1.1 nTPM
Fallopian tube	0.6 nTPM
Skeletal muscle	0.4 nTPM
Adipose tissue	0.1 nTPM
Heart muscle	0.0 nTPM

Granulocytes	104.3 nTPM
Lung	215.3 nTPM
Fallopian tube	54.0 nTPM
Tongue	43.7 nTPM

Intestinal goblet cells	13.1 nTPM
Small intestine	16.5 nTPM
Colon	13.0 nTPM
Rectum	9.7 nTPM

Lymphatic endothelial cells	1.3 nTPM
Fallopian tube	2.6 nTPM
Ovary	0.0 nTPM

Macrophages	148.1 nTPM
Lung	335.1 nTPM
Bone marrow	264.5 nTPM
Kidney	261.1 nTPM
Pancreas	238.4 nTPM
Spleen	207.5 nTPM
Stomach	174.9 nTPM
Testis	130.2 nTPM
Skeletal muscle	127.0 nTPM
Thymus	123.6 nTPM
Esophagus	122.0 nTPM
Skin	108.1 nTPM
Fallopian tube	105.7 nTPM
Prostate	105.4 nTPM
Breast	99.5 nTPM
Tongue	97.3 nTPM
Adipose tissue	94.1 nTPM
Salivary gland	85.2 nTPM
Vascular	69.4 nTPM
Endometrium	64.6 nTPM

Basal prostatic cells	12.1 nTPM
Prostate	12.1 nTPM

Basal squamous epithelial cells	21.1 nTPM
Esophagus	21.1 nTPM

Collecting duct cells	5.8 nTPM
Kidney	5.8 nTPM

Cytotrophoblasts	25.9 nTPM
Placenta	25.9 nTPM

Paneth cells	17.3 nTPM
Rectum	20.2 nTPM
Small intestine	17.3 nTPM
Colon	14.5 nTPM

Plasma cells	60.9 nTPM
Liver	90.6 nTPM
Stomach	83.8 nTPM
Bone marrow	75.5 nTPM
Thymus	65.8 nTPM
Spleen	56.3 nTPM
Salivary gland	45.7 nTPM
Fallopian tube	43.7 nTPM
Esophagus	26.0 nTPM

Schwann cells	35.7 nTPM
Adipose tissue	107.0 nTPM
Esophagus	0.0 nTPM
Vascular	0.0 nTPM

Serous glandular cells	10.5 nTPM
Salivary gland	16.6 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	3.5 nTPM
Thymus	7.4 nTPM
Lung	7.1 nTPM
Skin	6.7 nTPM
Breast	5.3 nTPM
Liver	4.7 nTPM
Skeletal muscle	4.7 nTPM
Esophagus	3.6 nTPM
Tongue	3.6 nTPM
Salivary gland	3.5 nTPM
Endometrium	2.7 nTPM
Placenta	1.9 nTPM
Adipose tissue	1.3 nTPM
Ovary	1.3 nTPM
Prostate	1.2 nTPM
Vascular	0.9 nTPM
Fallopian tube	0.9 nTPM

T-cells	82.0 nTPM
Bone marrow	173.0 nTPM
Kidney	152.5 nTPM
Liver	140.3 nTPM
Stomach	124.7 nTPM
Spleen	109.7 nTPM
PBMC	106.6 nTPM
Lymph node	102.4 nTPM
Thymus	101.0 nTPM
Lung	91.3 nTPM
Esophagus	82.7 nTPM
Salivary gland	78.9 nTPM
Skin	74.3 nTPM
Breast	71.9 nTPM
Colon	64.3 nTPM
Vascular	53.9 nTPM
Tongue	50.8 nTPM
Skeletal muscle	44.6 nTPM
Prostate	38.4 nTPM
Endometrium	29.5 nTPM
Fallopian tube	19.7 nTPM
Adipose tissue	12.4 nTPM

Undifferentiated cells	14.7 nTPM
Small intestine	15.9 nTPM
Rectum	15.2 nTPM
Colon	12.9 nTPM

Amygdala excitatory	1.8 nTPM
Hypothalamus	3.0 nTPM
Basal ganglia	2.0 nTPM
Amygdala	1.6 nTPM
Hippocampus	1.5 nTPM
Thalamus	1.4 nTPM
Cerebral cortex	1.3 nTPM

Astrocyte	1.7 nTPM
Cerebellum	3.2 nTPM
Hippocampus	2.0 nTPM
Amygdala	1.9 nTPM
Midbrain	1.8 nTPM
Thalamus	1.8 nTPM
Basal ganglia	1.5 nTPM
Cerebral cortex	1.5 nTPM
Pons	1.5 nTPM
Medulla oblongata	1.4 nTPM
Spinal cord	1.1 nTPM
Hypothalamus	1.0 nTPM

Bergmann glia	0.4 nTPM
Cerebellum	1.1 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	27.4 nTPM
Midbrain	32.7 nTPM
Cerebellum	31.6 nTPM
Pons	30.7 nTPM
Cerebral cortex	30.3 nTPM
Hippocampus	30.3 nTPM
Spinal cord	30.3 nTPM
Basal ganglia	25.3 nTPM
Medulla oblongata	25.3 nTPM
Thalamus	23.4 nTPM
Amygdala	21.3 nTPM
Hypothalamus	19.8 nTPM

Cerebellar inhibitory	1.2 nTPM
Cerebellum	1.9 nTPM
Medulla oblongata	1.7 nTPM
Pons	1.7 nTPM
Midbrain	0.6 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	1.3 nTPM
Hypothalamus	2.0 nTPM
Amygdala	1.3 nTPM
Cerebral cortex	1.2 nTPM
Thalamus	1.2 nTPM
Midbrain	1.1 nTPM
Hippocampus	1.0 nTPM
Basal ganglia	0.9 nTPM

Choroid plexus epithelial cell	12.4 nTPM
Basal ganglia	16.0 nTPM
Thalamus	13.7 nTPM
Hippocampus	11.1 nTPM
Medulla oblongata	8.7 nTPM

Committed oligodendrocyte precursor	1.3 nTPM
Medulla oblongata	5.2 nTPM
Basal ganglia	3.8 nTPM
Amygdala	1.7 nTPM
Thalamus	1.4 nTPM
Hippocampus	1.0 nTPM
Hypothalamus	0.7 nTPM
Cerebellum	0.0 nTPM
Cerebral cortex	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM

Deep-layer corticothalamic and 6b	1.0 nTPM
Hypothalamus	1.9 nTPM
Basal ganglia	1.2 nTPM
Cerebral cortex	1.2 nTPM
Hippocampus	1.1 nTPM
Amygdala	0.8 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	1.3 nTPM
Hypothalamus	2.2 nTPM
Cerebral cortex	1.3 nTPM
Amygdala	1.0 nTPM
Hippocampus	1.0 nTPM
Basal ganglia	0.9 nTPM

Deep-layer near-projecting	1.3 nTPM
Hypothalamus	2.4 nTPM
Cerebral cortex	1.4 nTPM
Basal ganglia	1.2 nTPM
Hippocampus	1.0 nTPM
Amygdala	0.7 nTPM

Eccentric medium spiny neuron	1.3 nTPM
Thalamus	1.8 nTPM
Amygdala	1.6 nTPM
Hypothalamus	1.4 nTPM
Basal ganglia	1.3 nTPM
Cerebral cortex	1.2 nTPM
Hippocampus	0.4 nTPM

Endothelial cell	5.4 nTPM
Basal ganglia	8.4 nTPM
Amygdala	6.7 nTPM
Cerebellum	6.2 nTPM
Hippocampus	5.8 nTPM
Midbrain	5.7 nTPM
Thalamus	5.6 nTPM
Medulla oblongata	5.1 nTPM
Hypothalamus	5.0 nTPM
Cerebral cortex	4.5 nTPM
Pons	4.4 nTPM
Spinal cord	1.7 nTPM