Single cell type - PTPRT - The Human Protein Atlas

PTPRT

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Pathway

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.	PTPRT
Gene descriptionⁱ Full gene name according to HGNC.	Protein tyrosine phosphatase receptor type T
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Cancer-related genes Enzymes
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.	Membrane, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	10

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 - Synaptic 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.	Group enriched (Inhibitory neurons, Excitatory neurons, Oligodendrocyte precursor 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 (LAMP5-LHX6 and Chandelier)
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: Group enriched (Inhibitory neurons, Excitatory neurons, Oligodendrocyte precursor 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 (LAMP5-LHX6 and Chandelier)

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

PTPRT is part of cluster 65 Neurons - Synaptic function with confidenceⁱ 1
250 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.
MGAT4C	MGAT4 family member C	0.9685	65
GRIN2A	Glutamate ionotropic receptor NMDA type subunit 2A	0.9626	65
NYAP2	Neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	0.9503	65
ATP8A2	ATPase phospholipid transporting 8A2	0.9364	65
SGCZ	Sarcoglycan zeta	0.9286	65
PTCHD4	Patched domain containing 4	0.9194	65
MPPED1	Metallophosphoesterase domain containing 1	0.9138	65
CDK14	Cyclin dependent kinase 14	0.9055	65
UNC5D	Unc-5 netrin receptor D	0.9039	65
RAB3C	RAB3C, member RAS oncogene family	0.8995	65
SYN2	Synapsin II	0.8968	65
GRM5	Glutamate metabotropic receptor 5	0.8857	65
EXT1	Exostosin glycosyltransferase 1	0.8847	65
NXPH2	Neurexophilin 2	0.8847	65
PKNOX2	PBX/knotted 1 homeobox 2	0.8830	65

Adipocytes	0.6 nTPM
Adipose tissue	1.0 nTPM
Breast	0.1 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	0.1 nTPM
Lung	0.1 nTPM

Astrocytes	12.4 nTPM
Brain	12.4 nTPM

B-cells	0.1 nTPM
Bone marrow	0.7 nTPM
Spleen	0.4 nTPM
Salivary gland	0.1 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
Lymph node	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Thymus	0.0 nTPM

Ciliated cells	23.6 nTPM
Lung	74.2 nTPM
Fallopian tube	15.5 nTPM
Endometrium	4.0 nTPM
Bronchus	0.9 nTPM

Club cells	0.7 nTPM
Lung	1.6 nTPM
Prostate	0.4 nTPM
Bronchus	0.1 nTPM

Endothelial cells	0.4 nTPM
Prostate	2.7 nTPM
Liver	2.5 nTPM
Testis	0.9 nTPM
Fallopian tube	0.4 nTPM
Skeletal muscle	0.3 nTPM
Endometrium	0.2 nTPM
Salivary gland	0.2 nTPM
Tongue	0.1 nTPM
Vascular	0.1 nTPM
Heart muscle	0.0 nTPM
Placenta	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM
Thymus	0.0 nTPM
Breast	0.0 nTPM
Ovary	0.0 nTPM

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

Fibroblasts	2.1 nTPM
Liver	19.0 nTPM
Stomach	7.2 nTPM
Adipose tissue	2.3 nTPM
Thymus	1.3 nTPM
Vascular	0.9 nTPM
Salivary gland	0.8 nTPM
Skin	0.7 nTPM
Lung	0.6 nTPM
Skeletal muscle	0.3 nTPM
Fallopian tube	0.3 nTPM
Placenta	0.2 nTPM
Breast	0.1 nTPM
Heart muscle	0.0 nTPM
Pancreas	0.0 nTPM
Esophagus	0.0 nTPM
Prostate	0.0 nTPM

Granulocytes	0.0 nTPM
Lung	0.0 nTPM
Tongue	0.0 nTPM
Fallopian tube	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	0.0 nTPM
Fallopian tube	0.1 nTPM
Ovary	0.0 nTPM

Macrophages	0.1 nTPM
Prostate	1.0 nTPM
Salivary gland	0.1 nTPM
Vascular	0.1 nTPM
Breast	0.1 nTPM
Testis	0.0 nTPM
Kidney	0.0 nTPM
Endometrium	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	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
Lung	0.0 nTPM
Thymus	0.0 nTPM
Tongue	0.0 nTPM
Fallopian tube	0.0 nTPM

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

Basal prostatic cells	9.4 nTPM
Prostate	9.4 nTPM

Bipolar cells	32.9 nTPM
Eye	32.9 nTPM

Collecting duct cells	1.9 nTPM
Kidney	1.9 nTPM

Cone photoreceptor cells	1.7 nTPM
Eye	1.7 nTPM

Plasma cells	0.1 nTPM
Liver	0.5 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	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Vascular	0.0 nTPM

Serous glandular cells	4.5 nTPM
Tongue	8.8 nTPM
Salivary gland	0.1 nTPM

Smooth muscle cells	1.0 nTPM
Placenta	5.9 nTPM
Salivary gland	4.2 nTPM
Prostate	3.6 nTPM
Liver	1.3 nTPM
Fallopian tube	0.4 nTPM
Tongue	0.3 nTPM
Endometrium	0.2 nTPM
Adipose tissue	0.2 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM
Thymus	0.0 nTPM
Vascular	0.0 nTPM
Breast	0.0 nTPM
Ovary	0.0 nTPM

T-cells	0.2 nTPM
Prostate	1.9 nTPM
Colon	1.0 nTPM
Lung	0.3 nTPM
Fallopian tube	0.2 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
Endometrium	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	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
Tongue	0.0 nTPM
Vascular	0.0 nTPM
Breast	0.0 nTPM

Undifferentiated cells	0.4 nTPM
Small intestine	1.3 nTPM
Colon	0.0 nTPM
Rectum	0.0 nTPM

Amygdala excitatory	583.2 nTPM
Cerebral cortex	1238.9 nTPM
Hippocampus	1200.4 nTPM
Basal ganglia	350.6 nTPM
Thalamus	290.8 nTPM
Hypothalamus	245.0 nTPM
Amygdala	173.4 nTPM

Astrocyte	110.7 nTPM
Cerebellum	357.7 nTPM
Medulla oblongata	271.8 nTPM
Pons	236.8 nTPM
Midbrain	115.1 nTPM
Hypothalamus	63.8 nTPM
Basal ganglia	49.4 nTPM
Spinal cord	43.4 nTPM
Thalamus	40.2 nTPM
Cerebral cortex	16.7 nTPM
Hippocampus	11.6 nTPM
Amygdala	11.4 nTPM

Bergmann glia	14.7 nTPM
Medulla oblongata	21.3 nTPM
Pons	12.9 nTPM
Cerebellum	9.8 nTPM

Central nervous system macrophage	8.5 nTPM
Cerebral cortex	20.6 nTPM
Hypothalamus	11.0 nTPM
Amygdala	9.8 nTPM
Medulla oblongata	9.2 nTPM
Pons	7.7 nTPM
Hippocampus	6.6 nTPM
Thalamus	6.4 nTPM
Cerebellum	5.9 nTPM
Basal ganglia	5.6 nTPM
Spinal cord	5.6 nTPM
Midbrain	5.5 nTPM

Cerebellar inhibitory	701.3 nTPM
Pons	759.1 nTPM
Midbrain	728.2 nTPM
Cerebellum	707.9 nTPM
Medulla oblongata	703.4 nTPM
Spinal cord	607.7 nTPM

Cge interneuron	838.1 nTPM
Thalamus	1376.0 nTPM
Midbrain	964.4 nTPM
Amygdala	865.0 nTPM
Hypothalamus	802.3 nTPM
Hippocampus	643.4 nTPM
Basal ganglia	640.4 nTPM
Cerebral cortex	575.2 nTPM

Choroid plexus epithelial cell	5.2 nTPM
Hippocampus	8.3 nTPM
Medulla oblongata	6.8 nTPM
Basal ganglia	3.0 nTPM
Thalamus	2.7 nTPM

Committed oligodendrocyte precursor	102.2 nTPM
Amygdala	150.0 nTPM
Midbrain	147.8 nTPM
Cerebral cortex	145.7 nTPM
Medulla oblongata	113.6 nTPM
Hypothalamus	107.9 nTPM
Basal ganglia	102.9 nTPM
Pons	93.8 nTPM
Cerebellum	93.5 nTPM
Hippocampus	88.0 nTPM
Thalamus	47.5 nTPM
Spinal cord	33.1 nTPM

Deep-layer corticothalamic and 6b	792.8 nTPM
Hypothalamus	1279.4 nTPM
Amygdala	1249.3 nTPM
Basal ganglia	746.6 nTPM
Midbrain	605.7 nTPM
Cerebral cortex	516.2 nTPM
Hippocampus	359.8 nTPM

Deep-layer intratelencephalic	1118.4 nTPM
Hypothalamus	2005.9 nTPM
Amygdala	1092.5 nTPM
Basal ganglia	1023.5 nTPM
Cerebral cortex	927.9 nTPM
Hippocampus	542.2 nTPM

Deep-layer near-projecting	981.8 nTPM
Hypothalamus	1622.4 nTPM
Amygdala	986.6 nTPM
Cerebral cortex	909.9 nTPM
Basal ganglia	899.5 nTPM
Hippocampus	490.5 nTPM

Eccentric medium spiny neuron	684.1 nTPM
Basal ganglia	785.4 nTPM
Thalamus	718.7 nTPM
Hippocampus	718.3 nTPM
Hypothalamus	688.9 nTPM
Cerebral cortex	672.1 nTPM
Amygdala	521.0 nTPM

Endothelial cell	6.3 nTPM
Hypothalamus	14.9 nTPM
Cerebral cortex	11.5 nTPM
Hippocampus	10.9 nTPM
Cerebellum	8.5 nTPM
Basal ganglia	4.7 nTPM
Amygdala	4.5 nTPM
Spinal cord	3.5 nTPM
Medulla oblongata	3.1 nTPM
Midbrain	2.8 nTPM
Thalamus	2.8 nTPM
Pons	2.5 nTPM

Ependymal cell	18.5 nTPM
Medulla oblongata	39.7 nTPM
Midbrain	32.4 nTPM
Hypothalamus	24.1 nTPM
Pons	21.6 nTPM
Basal ganglia	13.4 nTPM
Amygdala	10.2 nTPM
Spinal cord	9.6 nTPM
Thalamus	8.1 nTPM
Hippocampus	7.6 nTPM