Single cell type - PRTG - The Human Protein Atlas

PRTG

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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.	PRTG
Gene descriptionⁱ Full gene name according to HGNC.	Protogenin
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.	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.	Photoreceptor cells - Visual perception (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, Rod photoreceptor cells, Oligodendrocyte precursor cells, Alveolar cells type 2)
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.	0.75
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 (Endothelial cell, Bergmann glia)
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 (Cone photoreceptor cells, Rod photoreceptor cells, Oligodendrocyte precursor cells, Alveolar cells type 2)

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 (Endothelial cell, Bergmann glia)

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

PRTG is part of cluster 66 Photoreceptor cells - Visual perception with confidenceⁱ 1
340 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.
MYO3B	Myosin IIIB	0.5448	66
GUCA1A	Guanylate cyclase activator 1A	0.5237	66
MPP4	MAGUK p55 scaffold protein 4	0.5226	66
CNGB3	Cyclic nucleotide gated channel subunit beta 3	0.5185	66
ENSG00000283536	Novel protein	0.5163	66
ABCG4	ATP binding cassette subfamily G member 4	0.5096	66
ENSG00000288593	Novel protein	0.5092	66
PCDHAC2	Protocadherin alpha subfamily C, 2	0.5091	50
EYS	Eyes shut homolog	0.5007	66
ZBTB8B	Zinc finger and BTB domain containing 8B	0.4967	76
RP1L1	RP1 like 1	0.4944	66
GRK7	G protein-coupled receptor kinase 7	0.4868	66
PSKH2	Protein serine kinase H2	0.4867	66
GJD2	Gap junction protein delta 2	0.4865	66
UBAP1L	Ubiquitin associated protein 1 like	0.4856	66

Adipocytes	3.5 nTPM
Breast	5.0 nTPM
Adipose tissue	2.0 nTPM

Alveolar cells type 1	2.7 nTPM
Lung	2.7 nTPM

Alveolar cells type 2	30.9 nTPM
Lung	30.9 nTPM

Astrocytes	16.7 nTPM
Brain	16.7 nTPM

B-cells	0.0 nTPM
Salivary gland	0.2 nTPM
Thymus	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
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM

Ciliated cells	1.2 nTPM
Endometrium	2.5 nTPM
Fallopian tube	1.3 nTPM
Lung	1.1 nTPM
Bronchus	0.0 nTPM

Club cells	0.4 nTPM
Lung	0.8 nTPM
Prostate	0.5 nTPM
Bronchus	0.0 nTPM

Endothelial cells	10.9 nTPM
Heart muscle	26.5 nTPM
Endometrium	21.4 nTPM
Placenta	19.3 nTPM
Ovary	19.0 nTPM
Prostate	18.8 nTPM
Esophagus	12.9 nTPM
Skeletal muscle	11.1 nTPM
Vascular	10.4 nTPM
Tongue	8.8 nTPM
Fallopian tube	8.8 nTPM
Testis	8.5 nTPM
Salivary gland	8.1 nTPM
Thymus	4.6 nTPM
Skin	4.5 nTPM
Breast	4.4 nTPM
Lung	3.6 nTPM
Pancreas	2.6 nTPM
Liver	2.5 nTPM

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

Fibroblasts	8.7 nTPM
Placenta	93.4 nTPM
Esophagus	7.1 nTPM
Fallopian tube	6.1 nTPM
Salivary gland	5.7 nTPM
Stomach	4.3 nTPM
Skeletal muscle	4.2 nTPM
Breast	3.7 nTPM
Adipose tissue	3.3 nTPM
Vascular	2.5 nTPM
Thymus	2.4 nTPM
Prostate	2.0 nTPM
Pancreas	1.4 nTPM
Liver	1.2 nTPM
Lung	1.2 nTPM
Skin	1.1 nTPM
Heart muscle	0.0 nTPM

Granulocytes	0.2 nTPM
Lung	0.5 nTPM
Tongue	0.0 nTPM
Fallopian tube	0.0 nTPM

Intestinal goblet cells	0.1 nTPM
Colon	0.2 nTPM
Rectum	0.1 nTPM
Small intestine	0.0 nTPM

Lymphatic endothelial cells	0.5 nTPM
Fallopian tube	1.1 nTPM
Ovary	0.0 nTPM

Macrophages	0.1 nTPM
Prostate	0.7 nTPM
Skeletal muscle	0.2 nTPM
Lung	0.2 nTPM
Thymus	0.2 nTPM
Vascular	0.2 nTPM
Breast	0.2 nTPM
Testis	0.0 nTPM
Kidney	0.0 nTPM
Endometrium	0.0 nTPM
Pancreas	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
Salivary gland	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

Bipolar cells	13.0 nTPM
Eye	13.0 nTPM

Collecting duct cells	13.6 nTPM
Kidney	13.6 nTPM

Cone photoreceptor cells	91.8 nTPM
Eye	91.8 nTPM

Cytotrophoblasts	20.2 nTPM
Placenta	20.2 nTPM

Plasma cells	0.2 nTPM
Stomach	0.8 nTPM
Fallopian tube	0.6 nTPM
Salivary gland	0.4 nTPM
Thymus	0.1 nTPM
Liver	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Schwann cells	0.2 nTPM
Vascular	0.5 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	0.2 nTPM
Salivary gland	0.5 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	2.7 nTPM
Placenta	6.4 nTPM
Adipose tissue	5.6 nTPM
Endometrium	4.7 nTPM
Tongue	4.2 nTPM
Breast	3.4 nTPM
Skeletal muscle	2.6 nTPM
Esophagus	2.4 nTPM
Prostate	2.4 nTPM
Liver	2.1 nTPM
Skin	2.0 nTPM
Ovary	2.0 nTPM
Salivary gland	1.4 nTPM
Fallopian tube	1.4 nTPM
Lung	1.2 nTPM
Vascular	1.1 nTPM
Thymus	0.9 nTPM

T-cells	0.2 nTPM
Endometrium	1.7 nTPM
Prostate	0.8 nTPM
Lung	0.3 nTPM
Breast	0.2 nTPM
Stomach	0.1 nTPM
Fallopian tube	0.1 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
Liver	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
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM
Tongue	0.0 nTPM
Vascular	0.0 nTPM

Undifferentiated cells	0.3 nTPM
Rectum	0.8 nTPM
Colon	0.1 nTPM
Small intestine	0.0 nTPM

Amygdala excitatory	2.1 nTPM
Thalamus	6.8 nTPM
Basal ganglia	3.2 nTPM
Hypothalamus	0.8 nTPM
Amygdala	0.5 nTPM
Cerebral cortex	0.5 nTPM
Hippocampus	0.5 nTPM

Astrocyte	85.6 nTPM
Hypothalamus	123.7 nTPM
Pons	102.2 nTPM
Thalamus	100.7 nTPM
Midbrain	99.4 nTPM
Medulla oblongata	90.9 nTPM
Cerebellum	89.9 nTPM
Spinal cord	84.6 nTPM
Amygdala	80.4 nTPM
Basal ganglia	75.7 nTPM
Hippocampus	62.9 nTPM
Cerebral cortex	30.8 nTPM

Bergmann glia	195.3 nTPM
Medulla oblongata	215.2 nTPM
Cerebellum	199.6 nTPM
Pons	171.2 nTPM

Central nervous system macrophage	1.0 nTPM
Hypothalamus	1.5 nTPM
Cerebellum	1.2 nTPM
Spinal cord	1.2 nTPM
Midbrain	1.1 nTPM
Amygdala	1.0 nTPM
Basal ganglia	1.0 nTPM
Hippocampus	1.0 nTPM
Pons	1.0 nTPM
Thalamus	0.9 nTPM
Cerebral cortex	0.8 nTPM
Medulla oblongata	0.8 nTPM

Cerebellar inhibitory	1.1 nTPM
Spinal cord	2.7 nTPM
Cerebellum	1.0 nTPM
Pons	0.9 nTPM
Medulla oblongata	0.6 nTPM
Midbrain	0.3 nTPM

Cge interneuron	12.5 nTPM
Hypothalamus	15.7 nTPM
Amygdala	14.9 nTPM
Basal ganglia	14.6 nTPM
Cerebral cortex	13.8 nTPM
Hippocampus	13.4 nTPM
Midbrain	8.3 nTPM
Thalamus	6.7 nTPM

Choroid plexus epithelial cell	49.7 nTPM
Medulla oblongata	57.5 nTPM
Basal ganglia	55.8 nTPM
Hippocampus	49.9 nTPM
Thalamus	35.6 nTPM

Committed oligodendrocyte precursor	55.3 nTPM
Cerebellum	106.2 nTPM
Cerebral cortex	72.8 nTPM
Hippocampus	70.1 nTPM
Pons	58.4 nTPM
Basal ganglia	56.9 nTPM
Midbrain	56.3 nTPM
Amygdala	50.2 nTPM
Spinal cord	47.8 nTPM
Medulla oblongata	41.3 nTPM
Hypothalamus	34.8 nTPM
Thalamus	13.7 nTPM

Deep-layer corticothalamic and 6b	0.5 nTPM
Basal ganglia	1.0 nTPM
Amygdala	0.5 nTPM
Cerebral cortex	0.5 nTPM
Hippocampus	0.5 nTPM
Hypothalamus	0.4 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	0.5 nTPM
Amygdala	0.6 nTPM
Basal ganglia	0.6 nTPM
Hypothalamus	0.6 nTPM
Cerebral cortex	0.5 nTPM
Hippocampus	0.5 nTPM

Deep-layer near-projecting	0.7 nTPM
Basal ganglia	1.1 nTPM
Hypothalamus	1.1 nTPM
Hippocampus	0.7 nTPM
Cerebral cortex	0.4 nTPM
Amygdala	0.2 nTPM

Eccentric medium spiny neuron	0.8 nTPM
Hippocampus	1.2 nTPM
Amygdala	0.9 nTPM
Cerebral cortex	0.8 nTPM
Hypothalamus	0.6 nTPM
Basal ganglia	0.5 nTPM
Thalamus	0.5 nTPM

Endothelial cell	282.9 nTPM
Spinal cord	340.0 nTPM
Hippocampus	308.1 nTPM
Cerebral cortex	295.4 nTPM
Amygdala	294.0 nTPM
Thalamus	293.1 nTPM
Midbrain	287.3 nTPM
Pons	287.1 nTPM
Basal ganglia	266.6 nTPM
Hypothalamus	263.0 nTPM
Cerebellum	261.7 nTPM
Medulla oblongata	215.4 nTPM

Ependymal cell	26.5 nTPM
Hypothalamus	33.9 nTPM
Basal ganglia	32.4 nTPM
Amygdala	30.1 nTPM
Pons	28.3 nTPM
Spinal cord	26.8 nTPM
Midbrain	26.0 nTPM
Thalamus	22.3 nTPM
Hippocampus	20.1 nTPM
Medulla oblongata	18.2 nTPM