Single cell type - PTPN6 - The Human Protein Atlas

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). Read more	Enzymes Metabolic proteins 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. Read more	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. Read more	B-cells - 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. Read more	Cell type enhanced (B-cells, Hofbauer cells, NK-cells, Macrophages, Kupffer cells, granulocytes, Langerhans cells)
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. Read more	Low immune cell specificity
Immune cell distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in all
Cell line specificityⁱ RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines. Read more	Cell line enhanced (HEL, HL-60, HMC-1, THP-1)
Cell line distributionⁱ RNA distribution category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into five different categories (detected in all, detected in many, detected in some, detected in single and not detected) according to their pattern of detected RNA expression across the panel of cell lines. Read more	Detected in many
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); a Human Protein Atlas antibody- or RNA based score (HPA evidence); and evidence based on PeptideAtlas (MS evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable. Read more	Evidence at protein level

SINGLE CELL TYPESⁱ A summary of 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 Group Expression Alphabetical RNA single cell type specificity: Cell type enhanced (B-cells, Hofbauer cells, NK-cells, Macrophages, Kupffer cells, granulocytes, Langerhans cells)

SINGLE CELL TISSUES OVERVIEWⁱ An overview of all tissues where single cell type expression has been analyzed. Each tissue name and corresponding UMAP plot is clickable and redirects to the selected tissue.
Adipose tissue Bone marrow Brain Breast Bronchus Colon Endometrium Esophagus Eye Heart muscle Kidney Liver Lung Lymph node Ovary Pancreas Placenta Prostate Rectum Skeletal muscle Skin Small intestine Spleen Stomach Testis

EXPRESSION CLUSTERING & CORRELATIONⁱ

PTPN6 is part of cluster 57 B-cells - Immune response with confidenceⁱ 1
204 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell type 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. Read more	Clusterⁱ ID of the expression cluster of the neighboring gene. Read more
SCIMP	SLP adaptor and CSK interacting membrane protein	0.8192	57
CSK	C-terminal Src kinase	0.8141	57
RCSD1	RCSD domain containing 1	0.8109	57
TLR6	Toll like receptor 6	0.8041	57
CR1	Complement C3b/C4b receptor 1 (Knops blood group)	0.8004	57
POU2F2	POU class 2 homeobox 2	0.7829	57
RGS19	Regulator of G protein signaling 19	0.7828	57
LAT2	Linker for activation of T cells family member 2	0.7788	57
CD37	CD37 molecule	0.7694	57
SIGLEC10	Sialic acid binding Ig like lectin 10	0.7603	57
CD72	CD72 molecule	0.7589	57
CD1D	CD1d molecule	0.7509	57
PIK3AP1	Phosphoinositide-3-kinase adaptor protein 1	0.7493	57
LYN	LYN proto-oncogene, Src family tyrosine kinase	0.7382	57
ARL11	ADP ribosylation factor like GTPase 11	0.7380	57

SINGLE CELL TISSUESⁱ Single cell RNA levels of annotated cell type clusters are shown separately for each analyzed tissue. For easier navigation across tissues, use the above Single cell tissue overview, where each tissue name and UMAP plot is clickable and redirects to the selected tissue, alternatively the grey browser on the left side of the window. Barchart shows nTPM levels in each annotated cluster of single cells. To the left, a UMAP plot illustrates the RNA expression profile. The tissue name and plots are clickable and redirect to a more detailed interactive page. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. Please note that the same cell type may be found in several clusters.
Cluster Expression Alphabetical Adipose tissue
Cluster Expression Alphabetical Bone marrow
Cluster Expression Alphabetical Brain
Cluster Expression Alphabetical Breast
Cluster Expression Alphabetical Bronchus
Cluster Expression Alphabetical Colon
Cluster Expression Alphabetical Endometrium
Cluster Expression Alphabetical Esophagus
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Lymph node
Cluster Expression Alphabetical Ovary
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skeletal muscle
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Spleen
Cluster Expression Alphabetical Stomach
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ

Organ

Expression

Alphabetical

Adipocytes	10.5 nTPM
Breast	18.1 nTPM
Adipose tissue	2.8 nTPM

Alveolar cells type 1	6.4 nTPM
Lung	6.4 nTPM

Alveolar cells type 2	13.8 nTPM
Lung	13.8 nTPM

Astrocytes	0.7 nTPM
Brain	0.7 nTPM

Basal keratinocytes	9.1 nTPM
Skin	9.1 nTPM

B-cells	214.6 nTPM
Bone marrow	412.8 nTPM
Lymph node	315.0 nTPM
PBMC	291.2 nTPM
Spleen	280.0 nTPM
Stomach	236.6 nTPM
Kidney	228.5 nTPM
Breast	145.8 nTPM
Liver	105.7 nTPM
Adipose tissue	73.1 nTPM
Colon	57.5 nTPM

Dendritic cells	77.7 nTPM
Breast	121.0 nTPM
PBMC	71.8 nTPM
Adipose tissue	40.3 nTPM

Endothelial cells	7.5 nTPM
Eye	30.7 nTPM
Pancreas	11.6 nTPM
Liver	10.1 nTPM
Skin	9.2 nTPM
Skeletal muscle	8.0 nTPM
Breast	8.0 nTPM
Esophagus	6.1 nTPM
Testis	4.4 nTPM
Heart muscle	3.9 nTPM
Ovary	3.7 nTPM
Placenta	3.4 nTPM
Prostate	3.3 nTPM
Endometrium	2.2 nTPM
Lung	0.0 nTPM

Fibroblasts	3.0 nTPM
Lung	6.7 nTPM
Placenta	6.4 nTPM
Stomach	4.4 nTPM
Skin	4.0 nTPM
Esophagus	3.7 nTPM
Breast	2.8 nTPM
Prostate	1.5 nTPM
Ovary	1.4 nTPM
Skeletal muscle	1.0 nTPM
Heart muscle	0.9 nTPM
Adipose tissue	0.2 nTPM

Intestinal goblet cells	13.2 nTPM
Colon	15.0 nTPM
Small intestine	12.9 nTPM
Rectum	11.6 nTPM

Macrophages	152.1 nTPM
Bone marrow	301.2 nTPM
Kidney	272.3 nTPM
Pancreas	262.9 nTPM
Spleen	211.5 nTPM
Stomach	175.8 nTPM
Testis	130.2 nTPM
Esophagus	125.9 nTPM
Lung	122.7 nTPM
Skeletal muscle	114.7 nTPM
Ovary	114.5 nTPM
Adipose tissue	112.3 nTPM
PBMC	109.1 nTPM
Breast	97.9 nTPM
Endometrium	66.0 nTPM
Prostate	65.4 nTPM

Paneth cells	16.9 nTPM
Rectum	19.8 nTPM
Colon	19.7 nTPM
Small intestine	11.3 nTPM

Plasma cells	53.5 nTPM
Bone marrow	80.7 nTPM
Stomach	78.4 nTPM
Spleen	56.6 nTPM
Esophagus	30.7 nTPM
Adipose tissue	21.3 nTPM

Respiratory ciliated cells	17.2 nTPM
Bronchus	21.3 nTPM
Lung	13.1 nTPM

Smooth muscle cells	4.0 nTPM
Skin	8.7 nTPM
Bronchus	8.5 nTPM
Breast	6.2 nTPM
Ovary	4.9 nTPM
Esophagus	4.6 nTPM
Skeletal muscle	3.9 nTPM
Heart muscle	2.8 nTPM
Endometrium	2.3 nTPM
Adipose tissue	1.6 nTPM
Pancreas	0.6 nTPM
Prostate	0.4 nTPM

Cholangiocytes	11.5 nTPM
Liver	11.5 nTPM

Collecting duct cells	5.5 nTPM
Kidney	5.5 nTPM

Cytotrophoblasts	25.6 nTPM
Placenta	25.6 nTPM

Distal enterocytes	16.0 nTPM
Colon	17.4 nTPM
Rectum	14.6 nTPM

T-cells	86.2 nTPM
Bone marrow	176.6 nTPM
Kidney	138.9 nTPM
Liver	137.1 nTPM
Stomach	132.7 nTPM
PBMC	113.2 nTPM
Spleen	112.0 nTPM
Lymph node	110.0 nTPM
Lung	103.3 nTPM
Ovary	86.7 nTPM
Esophagus	72.0 nTPM
Skin	70.4 nTPM
Breast	66.9 nTPM
Skeletal muscle	42.8 nTPM
Colon	35.1 nTPM
Endometrium	31.0 nTPM
Prostate	23.6 nTPM
Adipose tissue	13.2 nTPM

Undifferentiated cells	15.6 nTPM
Small intestine	17.0 nTPM
Rectum	16.5 nTPM
Colon	13.5 nTPM

Adipose tissue

Bone marrow

Brain

Breast

Bronchus

Colon

Endometrium

Esophagus

Eye

Heart muscle

Kidney

Liver

Lung

Lymph node

Ovary

Pancreas

Placenta

Prostate

Rectum

Skeletal muscle

Skin

Small intestine

Spleen

Stomach

Testis

PBMC