Single cell type - PSPH - The Human Protein Atlas

PSPH

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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.	PSPH
Gene descriptionⁱ Full gene name according to HGNC.	Phosphoserine phosphatase
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Enzymes Human disease related genes Metabolic proteins Potential drug targets
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.	8

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.	Spermatids - Transcription (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 (Late spermatids, Early spermatids, Muller glia 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.	0.60
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.	Low cell type specificity
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 (Late spermatids, Early spermatids, Muller glia 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: Low cell type specificity

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

PSPH is part of cluster 13 Spermatids - Transcription with confidenceⁱ 1
116 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.
ENSG00000268533	Novel protein	0.8493	13
PRAMEF13	PRAME family member 13	0.8198	13
NPIPB2	Nuclear pore complex interacting protein family member B2	0.8158	13
ENSG00000261832	Novel protein	0.8061	13
FAM90A27P	Family with sequence similarity 90 member A27, pseudogene	0.8032	13
HSFY1	Heat shock transcription factor Y-linked 1	0.8029	13
NPIPB7	Nuclear pore complex interacting protein family member B7	0.8016	13
NPIPB6	Nuclear pore complex interacting protein family member B6	0.8003	13
SPANXN1	SPANX family member N1	0.7994	13
HSFY2	Heat shock transcription factor Y-linked 2	0.7976	13
FAM90A12P	Family with sequence similarity 90 member A12, pseudogene	0.7901	13
PCDHA2	Protocadherin alpha 2	0.7741	13
TP53TG3	TP53 target 3	0.7730	13
ENSG00000283952	Novel protein	0.7667	13
ZNF705D	Zinc finger protein 705D	0.7610	13

IMMUNE CELLS

PSPH is part of cluster 12 Non-specific - Mitochondrial translation with confidenceⁱ 0.99
566 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.
TAB1	TGF-beta activated kinase 1 (MAP3K7) binding protein 1	0.9048	12
MT-ND6	Mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 6	0.9048	12
TOMM22	Translocase of outer mitochondrial membrane 22	0.8810	12
HINFP	Histone H4 transcription factor	0.8810	7
GHDC	GH3 domain containing	0.8810	12
MT-ND5	Mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5	0.8571	30
CIITA	Class II major histocompatibility complex transactivator	0.8571	2
ING2	Inhibitor of growth family member 2	0.8571	12
POLE4	DNA polymerase epsilon 4, accessory subunit	0.8571	29
POU2F1	POU class 2 homeobox 1	0.8333	2
TMEM69	Transmembrane protein 69	0.8333	18
TVP23A	Trans-golgi network vesicle protein 23 homolog A	0.8333	2
TRAF3	TNF receptor associated factor 3	0.8333	12
ELOF1	Elongation factor 1	0.8333	12
ELP5	Elongator acetyltransferase complex subunit 5	0.8333	12

Adipocytes	1.6 nTPM
Breast	2.3 nTPM
Adipose tissue	1.0 nTPM

Alveolar cells type 1	3.6 nTPM
Lung	3.6 nTPM

Alveolar cells type 2	7.7 nTPM
Lung	7.7 nTPM

Astrocytes	10.8 nTPM
Brain	10.8 nTPM

B-cells	3.2 nTPM
Kidney	10.4 nTPM
Skin	6.8 nTPM
Esophagus	5.9 nTPM
PBMC	4.6 nTPM
Lung	4.0 nTPM
Thymus	3.2 nTPM
Adipose tissue	1.6 nTPM
Salivary gland	1.5 nTPM
Lymph node	1.2 nTPM
Spleen	1.0 nTPM
Bone marrow	0.7 nTPM
Stomach	0.4 nTPM
Liver	0.0 nTPM

Ciliated cells	27.5 nTPM
Endometrium	53.9 nTPM
Fallopian tube	23.5 nTPM
Lung	18.5 nTPM
Bronchus	14.1 nTPM

Club cells	6.4 nTPM
Bronchus	9.6 nTPM
Lung	6.0 nTPM
Prostate	3.7 nTPM

Endothelial cells	3.6 nTPM
Testis	6.7 nTPM
Liver	6.3 nTPM
Placenta	6.2 nTPM
Endometrium	4.8 nTPM
Tongue	4.7 nTPM
Breast	4.4 nTPM
Heart muscle	4.1 nTPM
Skin	3.9 nTPM
Prostate	3.4 nTPM
Ovary	3.4 nTPM
Vascular	3.3 nTPM
Thymus	3.0 nTPM
Esophagus	2.6 nTPM
Lung	2.6 nTPM
Salivary gland	2.4 nTPM
Fallopian tube	2.0 nTPM
Skeletal muscle	1.9 nTPM
Pancreas	0.0 nTPM

Enteroendocrine cells	7.3 nTPM
Small intestine	10.3 nTPM
Colon	8.3 nTPM
Rectum	3.4 nTPM

Fibroblasts	6.8 nTPM
Pancreas	28.2 nTPM
Placenta	12.6 nTPM
Liver	8.3 nTPM
Heart muscle	7.3 nTPM
Prostate	7.3 nTPM
Lung	6.1 nTPM
Thymus	5.6 nTPM
Skeletal muscle	5.3 nTPM
Stomach	4.3 nTPM
Vascular	4.0 nTPM
Skin	3.8 nTPM
Esophagus	3.7 nTPM
Adipose tissue	3.5 nTPM
Salivary gland	3.1 nTPM
Breast	3.0 nTPM
Fallopian tube	3.0 nTPM

Granulocytes	0.9 nTPM
Lung	1.5 nTPM
Fallopian tube	1.0 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	4.0 nTPM
Colon	7.1 nTPM
Rectum	3.2 nTPM
Small intestine	1.7 nTPM

Lymphatic endothelial cells	1.1 nTPM
Fallopian tube	2.2 nTPM
Ovary	0.0 nTPM

Macrophages	3.3 nTPM
Kidney	8.0 nTPM
Lung	5.6 nTPM
Endometrium	5.5 nTPM
Prostate	4.8 nTPM
Thymus	4.5 nTPM
Breast	4.0 nTPM
Vascular	3.7 nTPM
Skeletal muscle	3.6 nTPM
Tongue	3.1 nTPM
Salivary gland	2.9 nTPM
Stomach	2.6 nTPM
Testis	2.5 nTPM
Fallopian tube	2.5 nTPM
Pancreas	2.1 nTPM
Spleen	2.0 nTPM
Adipose tissue	1.7 nTPM
Esophagus	1.3 nTPM
Skin	1.1 nTPM
Bone marrow	1.0 nTPM

Paneth cells	4.3 nTPM
Rectum	5.8 nTPM
Colon	3.6 nTPM
Small intestine	3.5 nTPM

Basal respiratory cells	16.8 nTPM
Bronchus	16.8 nTPM

Cholangiocytes	11.4 nTPM
Liver	11.4 nTPM

Cytotrophoblasts	13.4 nTPM
Placenta	13.4 nTPM

Distal tubular cells	12.3 nTPM
Kidney	12.3 nTPM

Plasma cells	11.0 nTPM
Liver	17.0 nTPM
Thymus	16.6 nTPM
Spleen	15.9 nTPM
Bone marrow	13.6 nTPM
Esophagus	10.4 nTPM
Stomach	6.3 nTPM
Salivary gland	4.9 nTPM
Fallopian tube	3.5 nTPM

Schwann cells	5.5 nTPM
Esophagus	12.0 nTPM
Vascular	4.2 nTPM
Adipose tissue	0.4 nTPM

Serous glandular cells	3.6 nTPM
Tongue	4.4 nTPM
Salivary gland	2.7 nTPM

Smooth muscle cells	3.1 nTPM
Endometrium	5.2 nTPM
Skin	4.1 nTPM
Placenta	3.9 nTPM
Adipose tissue	3.6 nTPM
Esophagus	3.6 nTPM
Fallopian tube	3.4 nTPM
Tongue	3.3 nTPM
Thymus	3.2 nTPM
Vascular	3.1 nTPM
Ovary	3.0 nTPM
Skeletal muscle	2.8 nTPM
Salivary gland	2.6 nTPM
Breast	2.6 nTPM
Lung	2.4 nTPM
Liver	2.1 nTPM
Prostate	1.2 nTPM

Suprabasal keratinocytes	10.4 nTPM
Tongue	16.4 nTPM
Skin	4.3 nTPM

T-cells	2.2 nTPM
Kidney	6.2 nTPM
Liver	4.4 nTPM
PBMC	3.7 nTPM
Endometrium	3.3 nTPM
Skin	2.5 nTPM
Prostate	2.5 nTPM
Esophagus	2.4 nTPM
Skeletal muscle	2.3 nTPM
Lymph node	2.3 nTPM
Thymus	2.3 nTPM
Breast	1.9 nTPM
Spleen	1.6 nTPM
Vascular	1.6 nTPM
Stomach	1.5 nTPM
Tongue	1.4 nTPM
Fallopian tube	1.4 nTPM
Lung	1.3 nTPM
Adipose tissue	1.1 nTPM
Salivary gland	1.1 nTPM
Bone marrow	0.8 nTPM
Colon	0.0 nTPM

Undifferentiated cells	11.5 nTPM
Colon	17.4 nTPM
Small intestine	8.6 nTPM
Rectum	8.4 nTPM

Amygdala excitatory	14.8 nTPM
Hypothalamus	20.5 nTPM
Amygdala	17.9 nTPM
Cerebral cortex	15.8 nTPM
Hippocampus	15.0 nTPM
Basal ganglia	12.2 nTPM
Thalamus	7.3 nTPM

Astrocyte	22.1 nTPM
Cerebellum	27.6 nTPM
Spinal cord	24.2 nTPM
Midbrain	23.5 nTPM
Basal ganglia	22.2 nTPM
Hypothalamus	21.8 nTPM
Thalamus	21.6 nTPM
Amygdala	21.3 nTPM
Hippocampus	20.7 nTPM
Cerebral cortex	20.4 nTPM
Pons	20.1 nTPM
Medulla oblongata	19.4 nTPM

Bergmann glia	20.8 nTPM
Medulla oblongata	21.3 nTPM
Cerebellum	20.9 nTPM
Pons	20.1 nTPM

Central nervous system macrophage	10.9 nTPM
Amygdala	12.6 nTPM
Hypothalamus	12.5 nTPM
Hippocampus	11.7 nTPM
Thalamus	11.7 nTPM
Cerebral cortex	11.1 nTPM
Basal ganglia	10.8 nTPM
Midbrain	10.6 nTPM
Cerebellum	10.2 nTPM
Pons	9.9 nTPM
Medulla oblongata	9.8 nTPM
Spinal cord	9.4 nTPM

Cerebellar inhibitory	18.5 nTPM
Cerebellum	23.2 nTPM
Medulla oblongata	22.3 nTPM
Midbrain	19.6 nTPM
Pons	13.7 nTPM
Spinal cord	13.7 nTPM

Cge interneuron	12.2 nTPM
Hypothalamus	14.9 nTPM
Amygdala	12.8 nTPM
Cerebral cortex	12.7 nTPM
Hippocampus	12.4 nTPM
Thalamus	12.4 nTPM
Basal ganglia	11.8 nTPM
Midbrain	8.6 nTPM

Choroid plexus epithelial cell	28.0 nTPM
Thalamus	30.1 nTPM
Medulla oblongata	28.7 nTPM
Basal ganglia	28.2 nTPM
Hippocampus	25.0 nTPM

Committed oligodendrocyte precursor	16.8 nTPM
Amygdala	27.1 nTPM
Cerebellum	22.2 nTPM
Hypothalamus	21.8 nTPM
Thalamus	21.6 nTPM
Medulla oblongata	16.8 nTPM
Basal ganglia	14.8 nTPM
Cerebral cortex	14.6 nTPM
Pons	13.3 nTPM
Midbrain	12.6 nTPM
Hippocampus	12.2 nTPM
Spinal cord	7.4 nTPM

Deep-layer corticothalamic and 6b	16.2 nTPM
Hypothalamus	23.1 nTPM
Amygdala	16.5 nTPM
Cerebral cortex	16.5 nTPM
Basal ganglia	16.4 nTPM
Hippocampus	16.0 nTPM
Midbrain	8.9 nTPM

Deep-layer intratelencephalic	17.9 nTPM
Hypothalamus	21.2 nTPM
Basal ganglia	18.3 nTPM
Amygdala	16.8 nTPM
Cerebral cortex	16.8 nTPM
Hippocampus	16.2 nTPM

Deep-layer near-projecting	12.7 nTPM
Hypothalamus	17.8 nTPM
Cerebral cortex	13.9 nTPM
Amygdala	12.1 nTPM
Basal ganglia	11.6 nTPM
Hippocampus	8.1 nTPM

Eccentric medium spiny neuron	14.4 nTPM
Basal ganglia	16.3 nTPM
Hypothalamus	15.7 nTPM
Thalamus	15.7 nTPM
Amygdala	14.4 nTPM
Cerebral cortex	13.0 nTPM
Hippocampus	11.6 nTPM

Endothelial cell	11.2 nTPM
Amygdala	16.8 nTPM
Basal ganglia	15.8 nTPM
Cerebral cortex	14.7 nTPM
Midbrain	14.2 nTPM
Cerebellum	12.4 nTPM
Medulla oblongata	11.3 nTPM
Pons	11.2 nTPM
Hippocampus	8.3 nTPM
Thalamus	7.9 nTPM
Spinal cord	6.9 nTPM
Hypothalamus	3.7 nTPM