Single cell type - SP3 - The Human Protein Atlas

SP3

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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.	SP3
Gene descriptionⁱ Full gene name according to HGNC.	Sp3 transcription factor
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Transcription factors
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.	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.	Monocytes - Innate 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.	Cell type enhanced (Monocytes)
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.	0.34
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 (Monocytes)

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

SP3 is part of cluster 29 Monocytes - Innate immune response with confidenceⁱ 0.95
447 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.
MED13	Mediator complex subunit 13	0.6206	55
YTHDF3	YTH N6-methyladenosine RNA binding protein 3	0.6014	29
CHD1	Chromodomain helicase DNA binding protein 1	0.5943	29
WAC	WW domain containing adaptor with coiled-coil	0.5925	55
ZNF207	Zinc finger protein 207	0.5611	15
TET2	Tet methylcytosine dioxygenase 2	0.5206	29
TENT4B	Terminal nucleotidyltransferase 4B	0.5160	78
CHSY1	Chondroitin sulfate synthase 1	0.5154	29
CSGALNACT2	Chondroitin sulfate N-acetylgalactosaminyltransferase 2	0.5050	29
UBXN7	UBX domain protein 7	0.4956	55
MAP3K2	Mitogen-activated protein kinase kinase kinase 2	0.4898	28
SRSF6	Serine and arginine rich splicing factor 6	0.4868	15
CYRIA	CYFIP related Rac1 interactor A	0.4867	29
WTAP	WT1 associated protein	0.4800	29
C9orf72	C9orf72-SMCR8 complex subunit	0.4796	29

IMMUNE CELLS

SP3 is part of cluster 4 Neutrophils - Degranulation with confidenceⁱ 1
86 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.
ZNF200	Zinc finger protein 200	0.9762	4
ORM2	Orosomucoid 2	0.9762	4
HSPA1A	Heat shock protein family A (Hsp70) member 1A	0.9762	4
FAM174A	Family with sequence similarity 174 member A	0.9762	4
RAB33B	RAB33B, member RAS oncogene family	0.9762	35
DHRS13	Dehydrogenase/reductase 13	0.9762	4
PDZK1IP1	PDZK1 interacting protein 1	0.9762	4
DOCK11	Dedicator of cytokinesis 11	0.9762	4
PARP16	Poly(ADP-ribose) polymerase family member 16	0.9762	35
GTDC1	Glycosyltransferase like domain containing 1	0.9762	35
RAB36	RAB36, member RAS oncogene family	0.9762	4
RSPH14	Radial spoke head 14 homolog	0.9762	4
SYNJ2	Synaptojanin 2	0.9762	4
TG	Thyroglobulin	0.9762	4
MMP9	Matrix metallopeptidase 9	0.9524	4

Adipocytes	41.1 nTPM
Adipose tissue	49.2 nTPM
Breast	32.9 nTPM

Alveolar cells type 1	33.2 nTPM
Lung	33.2 nTPM

Alveolar cells type 2	28.1 nTPM
Lung	28.1 nTPM

Astrocytes	42.4 nTPM
Brain	42.4 nTPM

B-cells	60.9 nTPM
Lymph node	88.9 nTPM
Salivary gland	74.5 nTPM
Kidney	72.8 nTPM
Adipose tissue	71.6 nTPM
Stomach	66.6 nTPM
Bone marrow	65.5 nTPM
Spleen	61.0 nTPM
Thymus	53.7 nTPM
Lung	52.3 nTPM
PBMC	49.3 nTPM
Liver	48.3 nTPM
Esophagus	47.2 nTPM
Skin	40.7 nTPM

Ciliated cells	29.6 nTPM
Bronchus	39.1 nTPM
Lung	28.9 nTPM
Endometrium	25.5 nTPM
Fallopian tube	24.7 nTPM

Club cells	35.6 nTPM
Prostate	37.6 nTPM
Bronchus	36.7 nTPM
Lung	32.6 nTPM

Dendritic cells	90.2 nTPM
Adipose tissue	94.1 nTPM
PBMC	86.3 nTPM

Endothelial cells	40.0 nTPM
Skin	75.7 nTPM
Heart muscle	53.2 nTPM
Esophagus	50.9 nTPM
Salivary gland	50.5 nTPM
Endometrium	47.8 nTPM
Skeletal muscle	45.2 nTPM
Tongue	43.4 nTPM
Prostate	42.7 nTPM
Fallopian tube	42.2 nTPM
Thymus	39.7 nTPM
Vascular	38.6 nTPM
Breast	35.2 nTPM
Testis	34.5 nTPM
Lung	33.9 nTPM
Ovary	27.9 nTPM
Liver	26.5 nTPM
Placenta	25.0 nTPM
Pancreas	7.8 nTPM

Enteroendocrine cells	28.7 nTPM
Colon	35.3 nTPM
Rectum	26.8 nTPM
Small intestine	24.0 nTPM

Fibroblasts	48.0 nTPM
Skin	73.5 nTPM
Placenta	61.5 nTPM
Salivary gland	60.1 nTPM
Esophagus	58.5 nTPM
Fallopian tube	55.9 nTPM
Adipose tissue	51.2 nTPM
Breast	50.0 nTPM
Liver	49.8 nTPM
Prostate	48.8 nTPM
Heart muscle	46.8 nTPM
Skeletal muscle	43.5 nTPM
Vascular	43.1 nTPM
Stomach	37.5 nTPM
Thymus	36.0 nTPM
Lung	34.2 nTPM
Pancreas	18.4 nTPM

Granulocytes	40.7 nTPM
Fallopian tube	46.7 nTPM
Lung	41.3 nTPM
Tongue	34.0 nTPM

Intestinal goblet cells	38.4 nTPM
Small intestine	47.7 nTPM
Rectum	40.8 nTPM
Colon	26.6 nTPM

Lymphatic endothelial cells	23.2 nTPM
Fallopian tube	40.9 nTPM
Ovary	5.5 nTPM

Macrophages	69.4 nTPM
Skeletal muscle	138.9 nTPM
Stomach	115.7 nTPM
Fallopian tube	108.5 nTPM
Adipose tissue	105.1 nTPM
Spleen	95.2 nTPM
Skin	88.0 nTPM
Bone marrow	80.1 nTPM
Esophagus	78.3 nTPM
Tongue	60.4 nTPM
Prostate	55.9 nTPM
Salivary gland	55.1 nTPM
Vascular	53.6 nTPM
Kidney	46.9 nTPM
Thymus	45.5 nTPM
Testis	45.3 nTPM
Endometrium	41.8 nTPM
Lung	41.4 nTPM
Breast	39.0 nTPM
Pancreas	24.7 nTPM

Basal prostatic cells	44.8 nTPM
Prostate	44.8 nTPM

Basal squamous epithelial cells	58.1 nTPM
Esophagus	58.1 nTPM

Cholangiocytes	13.4 nTPM
Liver	13.4 nTPM

Collecting duct cells	23.3 nTPM
Kidney	23.3 nTPM

Paneth cells	17.9 nTPM
Rectum	32.5 nTPM
Colon	10.9 nTPM
Small intestine	10.4 nTPM

Plasma cells	59.3 nTPM
Stomach	80.0 nTPM
Salivary gland	69.4 nTPM
Esophagus	62.4 nTPM
Thymus	60.3 nTPM
Spleen	55.8 nTPM
Fallopian tube	52.4 nTPM
Liver	50.6 nTPM
Bone marrow	43.8 nTPM

Schwann cells	29.8 nTPM
Adipose tissue	47.6 nTPM
Vascular	29.8 nTPM
Esophagus	12.0 nTPM

Serous glandular cells	34.1 nTPM
Tongue	35.4 nTPM
Salivary gland	32.9 nTPM

Smooth muscle cells	44.4 nTPM
Adipose tissue	68.1 nTPM
Esophagus	67.3 nTPM
Skin	64.5 nTPM
Prostate	48.0 nTPM
Endometrium	47.3 nTPM
Tongue	47.0 nTPM
Breast	44.2 nTPM
Skeletal muscle	42.4 nTPM
Salivary gland	40.8 nTPM
Placenta	38.7 nTPM
Vascular	38.5 nTPM
Thymus	34.7 nTPM
Fallopian tube	34.1 nTPM
Liver	33.1 nTPM
Ovary	31.9 nTPM
Lung	30.6 nTPM

Suprabasal keratinocytes	42.0 nTPM
Skin	59.2 nTPM
Tongue	24.8 nTPM

T-cells	61.0 nTPM
Adipose tissue	96.5 nTPM
Skeletal muscle	82.0 nTPM
Lymph node	76.1 nTPM
Fallopian tube	71.3 nTPM
Salivary gland	67.8 nTPM
Spleen	66.8 nTPM
Endometrium	65.8 nTPM
Breast	64.0 nTPM
Esophagus	63.3 nTPM
Stomach	62.4 nTPM
Bone marrow	61.4 nTPM
Skin	57.5 nTPM
Prostate	56.5 nTPM
Lung	53.6 nTPM
Thymus	53.3 nTPM
PBMC	52.7 nTPM
Colon	49.7 nTPM
Tongue	49.7 nTPM
Liver	45.3 nTPM
Vascular	43.4 nTPM
Kidney	42.6 nTPM

Undifferentiated cells	32.6 nTPM
Rectum	37.1 nTPM
Small intestine	31.8 nTPM
Colon	28.7 nTPM

Amygdala excitatory	72.8 nTPM
Amygdala	76.0 nTPM
Thalamus	75.3 nTPM
Hypothalamus	75.1 nTPM
Basal ganglia	73.2 nTPM
Cerebral cortex	69.2 nTPM
Hippocampus	67.8 nTPM

Astrocyte	75.2 nTPM
Amygdala	108.0 nTPM
Cerebral cortex	86.6 nTPM
Hippocampus	85.3 nTPM
Basal ganglia	82.9 nTPM
Hypothalamus	79.1 nTPM
Thalamus	72.1 nTPM
Midbrain	67.5 nTPM
Pons	66.3 nTPM
Medulla oblongata	63.0 nTPM
Cerebellum	61.7 nTPM
Spinal cord	54.6 nTPM

Bergmann glia	103.4 nTPM
Cerebellum	110.0 nTPM
Pons	102.1 nTPM
Medulla oblongata	98.0 nTPM

Central nervous system macrophage	217.8 nTPM
Amygdala	273.7 nTPM
Hypothalamus	243.3 nTPM
Basal ganglia	229.3 nTPM
Thalamus	213.7 nTPM
Hippocampus	212.5 nTPM
Spinal cord	212.3 nTPM
Midbrain	212.0 nTPM
Cerebellum	206.9 nTPM
Pons	203.2 nTPM
Cerebral cortex	198.9 nTPM
Medulla oblongata	190.3 nTPM

Cerebellar inhibitory	61.2 nTPM
Midbrain	65.3 nTPM
Cerebellum	64.6 nTPM
Spinal cord	60.5 nTPM
Pons	59.4 nTPM
Medulla oblongata	56.3 nTPM

Cge interneuron	69.1 nTPM
Amygdala	76.0 nTPM
Thalamus	75.7 nTPM
Hypothalamus	73.7 nTPM
Midbrain	68.0 nTPM
Basal ganglia	65.4 nTPM
Cerebral cortex	64.4 nTPM
Hippocampus	60.8 nTPM

Choroid plexus epithelial cell	85.8 nTPM
Basal ganglia	113.0 nTPM
Medulla oblongata	87.1 nTPM
Thalamus	74.0 nTPM
Hippocampus	69.3 nTPM

Committed oligodendrocyte precursor	83.7 nTPM
Spinal cord	106.7 nTPM
Cerebral cortex	101.3 nTPM
Cerebellum	87.2 nTPM
Amygdala	86.8 nTPM
Hypothalamus	82.6 nTPM
Pons	80.6 nTPM
Thalamus	76.3 nTPM
Basal ganglia	75.6 nTPM
Medulla oblongata	74.9 nTPM
Hippocampus	74.2 nTPM
Midbrain	73.9 nTPM

Deep-layer corticothalamic and 6b	67.6 nTPM
Amygdala	74.5 nTPM
Cerebral cortex	72.2 nTPM
Hypothalamus	69.3 nTPM
Basal ganglia	64.9 nTPM
Hippocampus	62.9 nTPM
Midbrain	62.1 nTPM

Deep-layer intratelencephalic	66.5 nTPM
Amygdala	70.5 nTPM
Hypothalamus	68.3 nTPM
Hippocampus	66.8 nTPM
Cerebral cortex	66.7 nTPM
Basal ganglia	60.3 nTPM

Deep-layer near-projecting	53.1 nTPM
Hypothalamus	58.4 nTPM
Amygdala	57.3 nTPM
Basal ganglia	54.4 nTPM
Cerebral cortex	53.7 nTPM
Hippocampus	41.6 nTPM

Eccentric medium spiny neuron	95.1 nTPM
Hippocampus	100.7 nTPM
Amygdala	99.5 nTPM
Thalamus	99.1 nTPM
Basal ganglia	92.5 nTPM
Hypothalamus	90.7 nTPM
Cerebral cortex	88.2 nTPM