Single cell type - SETD3 - The Human Protein Atlas

SETD3

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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.	SETD3
Gene descriptionⁱ Full gene name according to HGNC.	SET domain containing 3, actin histidine methyltransferase
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	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.	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.	Spermatogonia - Spermatogenesis (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 (Early spermatids)
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.	0.37
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 (Early spermatids)

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

SETD3 is part of cluster 67 Spermatogonia - Spermatogenesis with confidenceⁱ 1
123 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.
OOEP	Oocyte expressed protein	0.4961	67
STRA8	Stimulated by retinoic acid 8	0.4866	67
PYROXD1	Pyridine nucleotide-disulphide oxidoreductase domain 1	0.4582	45
TSPYL6	TSPY like 6	0.4455	67
MTIF3	Mitochondrial translational initiation factor 3	0.4430	39
C16orf87	Chromosome 16 open reading frame 87	0.4405	56
DCAF4L1	DDB1 and CUL4 associated factor 4 like 1	0.4305	67
CEP63	Centrosomal protein 63	0.4296	70
SPRYD7	SPRY domain containing 7	0.4234	70
PAGE5	PAGE family member 5	0.4232	67
LIPT2	Lipoyl(octanoyl) transferase 2	0.4216	70
PAGE2B	PAGE family member 2B	0.4169	67
SOHLH1	Spermatogenesis and oogenesis specific basic helix-loop-helix 1	0.4108	67
HYLS1	HYLS1 centriolar and ciliogenesis associated	0.4021	31
SURF1	SURF1 cytochrome c oxidase assembly factor	0.3998	39

IMMUNE CELLS

SETD3 is part of cluster 38 Monocytes & Neutrophils - Degranulation with confidenceⁱ 1
501 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.
ETF1	Eukaryotic translation termination factor 1	1.0000	38
ADCY7	Adenylate cyclase 7	0.9524	10
SLC39A9	Solute carrier family 39 member 9	0.9286	38
TUBB4B	Tubulin beta 4B class IVb	0.9286	38
ATG13	Autophagy related 13	0.9286	38
FCER1G	Fc epsilon receptor Ig	0.9286	10
ECPAS	Ecm29 proteasome adaptor and scaffold	0.9286	10
HAVCR2	Hepatitis A virus cellular receptor 2	0.9286	38
CHN2	Chimerin 2	0.9286	40
SERAC1	Serine active site containing 1	0.9048	38
ACBD5	Acyl-CoA binding domain containing 5	0.9048	28
STK3	Serine/threonine kinase 3	0.9048	38
IFNAR2	Interferon alpha and beta receptor subunit 2	0.9048	10
MYD88	MYD88 innate immune signal transduction adaptor	0.9048	38
AGFG1	ArfGAP with FG repeats 1	0.9048	10

Adipocytes	28.9 nTPM
Adipose tissue	31.6 nTPM
Breast	26.2 nTPM

Alveolar cells type 1	54.3 nTPM
Lung	54.3 nTPM

Alveolar cells type 2	59.0 nTPM
Lung	59.0 nTPM

Astrocytes	40.9 nTPM
Brain	40.9 nTPM

B-cells	16.9 nTPM
Salivary gland	22.1 nTPM
PBMC	21.6 nTPM
Thymus	21.4 nTPM
Stomach	20.2 nTPM
Spleen	20.1 nTPM
Lymph node	19.8 nTPM
Liver	19.3 nTPM
Esophagus	17.7 nTPM
Lung	16.1 nTPM
Adipose tissue	15.6 nTPM
Bone marrow	13.9 nTPM
Skin	6.8 nTPM
Kidney	5.2 nTPM

Ciliated cells	29.9 nTPM
Fallopian tube	54.1 nTPM
Endometrium	29.2 nTPM
Lung	21.2 nTPM
Bronchus	15.3 nTPM

Club cells	21.2 nTPM
Prostate	26.2 nTPM
Lung	21.9 nTPM
Bronchus	15.4 nTPM

Dendritic cells	30.4 nTPM
Adipose tissue	35.7 nTPM
PBMC	25.2 nTPM

Endothelial cells	29.2 nTPM
Fallopian tube	46.4 nTPM
Lung	43.5 nTPM
Salivary gland	34.9 nTPM
Vascular	34.0 nTPM
Thymus	33.4 nTPM
Heart muscle	32.8 nTPM
Esophagus	31.1 nTPM
Breast	29.9 nTPM
Endometrium	28.2 nTPM
Liver	26.5 nTPM
Skeletal muscle	26.1 nTPM
Tongue	25.9 nTPM
Testis	25.6 nTPM
Prostate	24.9 nTPM
Placenta	23.8 nTPM
Pancreas	23.3 nTPM
Skin	20.1 nTPM
Ovary	14.5 nTPM

Enteroendocrine cells	31.9 nTPM
Small intestine	34.3 nTPM
Colon	31.2 nTPM
Rectum	30.2 nTPM

Fibroblasts	24.1 nTPM
Heart muscle	39.8 nTPM
Stomach	31.7 nTPM
Vascular	29.8 nTPM
Lung	29.5 nTPM
Fallopian tube	29.4 nTPM
Placenta	29.0 nTPM
Liver	24.9 nTPM
Thymus	21.7 nTPM
Pancreas	21.1 nTPM
Salivary gland	20.6 nTPM
Prostate	20.5 nTPM
Adipose tissue	18.9 nTPM
Esophagus	18.8 nTPM
Skeletal muscle	18.4 nTPM
Breast	16.3 nTPM
Skin	15.8 nTPM

Granulocytes	30.3 nTPM
Fallopian tube	37.9 nTPM
Lung	28.7 nTPM
Tongue	24.3 nTPM

Intestinal goblet cells	30.2 nTPM
Small intestine	36.3 nTPM
Colon	28.3 nTPM
Rectum	26.0 nTPM

Lymphatic endothelial cells	35.1 nTPM
Fallopian tube	64.7 nTPM
Ovary	5.5 nTPM

Macrophages	38.3 nTPM
Vascular	53.5 nTPM
Salivary gland	50.4 nTPM
Lung	50.0 nTPM
Adipose tissue	47.7 nTPM
Thymus	45.3 nTPM
Fallopian tube	42.6 nTPM
Prostate	39.3 nTPM
Pancreas	39.1 nTPM
Spleen	38.1 nTPM
Tongue	37.9 nTPM
Bone marrow	36.5 nTPM
Skeletal muscle	35.8 nTPM
Esophagus	34.7 nTPM
Skin	32.3 nTPM
Breast	31.5 nTPM
Endometrium	31.4 nTPM
Testis	29.1 nTPM
Kidney	26.6 nTPM
Stomach	25.7 nTPM

Basal prostatic cells	32.6 nTPM
Prostate	32.6 nTPM

Basal respiratory cells	13.4 nTPM
Bronchus	13.4 nTPM

Basal squamous epithelial cells	24.6 nTPM
Esophagus	24.6 nTPM

Bipolar cells	22.6 nTPM
Eye	22.6 nTPM

Paneth cells	22.4 nTPM
Rectum	28.4 nTPM
Small intestine	20.7 nTPM
Colon	18.1 nTPM

Plasma cells	26.6 nTPM
Fallopian tube	44.7 nTPM
Spleen	37.0 nTPM
Thymus	28.3 nTPM
Salivary gland	22.4 nTPM
Liver	21.5 nTPM
Esophagus	20.8 nTPM
Bone marrow	19.6 nTPM
Stomach	18.4 nTPM

Schwann cells	29.5 nTPM
Vascular	42.8 nTPM
Adipose tissue	33.6 nTPM
Esophagus	12.0 nTPM

Serous glandular cells	58.2 nTPM
Salivary gland	81.0 nTPM
Tongue	35.4 nTPM

Smooth muscle cells	28.3 nTPM
Salivary gland	51.0 nTPM
Vascular	48.3 nTPM
Prostate	39.5 nTPM
Fallopian tube	37.6 nTPM
Thymus	32.3 nTPM
Adipose tissue	28.7 nTPM
Liver	26.3 nTPM
Skeletal muscle	24.8 nTPM
Breast	24.4 nTPM
Tongue	22.2 nTPM
Skin	22.0 nTPM
Lung	21.2 nTPM
Esophagus	20.4 nTPM
Placenta	18.6 nTPM
Ovary	18.5 nTPM
Endometrium	17.3 nTPM

Suprabasal keratinocytes	31.9 nTPM
Tongue	32.7 nTPM
Skin	31.0 nTPM

T-cells	26.8 nTPM
Spleen	37.6 nTPM
Thymus	35.5 nTPM
Vascular	33.8 nTPM
Breast	32.6 nTPM
Lung	31.7 nTPM
Bone marrow	30.3 nTPM
Liver	29.9 nTPM
Tongue	29.5 nTPM
Prostate	27.9 nTPM
Fallopian tube	27.4 nTPM
Endometrium	27.0 nTPM
Esophagus	26.8 nTPM
Adipose tissue	26.0 nTPM
Salivary gland	24.2 nTPM
Skeletal muscle	23.4 nTPM
Lymph node	23.4 nTPM
Stomach	22.5 nTPM
PBMC	21.1 nTPM
Colon	17.5 nTPM
Skin	17.5 nTPM
Kidney	16.8 nTPM

Undifferentiated cells	27.6 nTPM
Colon	29.0 nTPM
Rectum	27.4 nTPM
Small intestine	26.4 nTPM

Amygdala excitatory	83.4 nTPM
Hypothalamus	102.0 nTPM
Amygdala	92.9 nTPM
Cerebral cortex	89.7 nTPM
Hippocampus	83.8 nTPM
Basal ganglia	68.7 nTPM
Thalamus	63.1 nTPM

Astrocyte	91.4 nTPM
Amygdala	155.2 nTPM
Hippocampus	109.9 nTPM
Cerebral cortex	101.9 nTPM
Basal ganglia	97.5 nTPM
Hypothalamus	89.6 nTPM
Spinal cord	83.7 nTPM
Thalamus	79.8 nTPM
Midbrain	77.2 nTPM
Pons	75.2 nTPM
Medulla oblongata	75.1 nTPM
Cerebellum	60.6 nTPM

Bergmann glia	61.1 nTPM
Cerebellum	68.3 nTPM
Pons	61.9 nTPM
Medulla oblongata	53.3 nTPM

Central nervous system macrophage	147.4 nTPM
Amygdala	199.3 nTPM
Hypothalamus	162.9 nTPM
Midbrain	153.6 nTPM
Hippocampus	152.0 nTPM
Thalamus	151.2 nTPM
Basal ganglia	149.3 nTPM
Cerebral cortex	146.0 nTPM
Cerebellum	139.8 nTPM
Pons	137.5 nTPM
Medulla oblongata	122.1 nTPM
Spinal cord	107.7 nTPM

Cerebellar inhibitory	79.8 nTPM
Spinal cord	101.7 nTPM
Medulla oblongata	83.0 nTPM
Cerebellum	75.2 nTPM
Midbrain	70.6 nTPM
Pons	68.3 nTPM

Cge interneuron	54.6 nTPM
Thalamus	64.8 nTPM
Hypothalamus	62.2 nTPM
Amygdala	56.0 nTPM
Cerebral cortex	50.6 nTPM
Midbrain	50.3 nTPM
Hippocampus	49.9 nTPM
Basal ganglia	48.6 nTPM

Choroid plexus epithelial cell	119.1 nTPM
Basal ganglia	171.6 nTPM
Medulla oblongata	111.9 nTPM
Hippocampus	97.1 nTPM
Thalamus	95.9 nTPM

Committed oligodendrocyte precursor	58.5 nTPM
Hypothalamus	77.8 nTPM
Spinal cord	69.9 nTPM
Amygdala	62.6 nTPM
Cerebellum	61.8 nTPM
Thalamus	61.5 nTPM
Medulla oblongata	60.7 nTPM
Cerebral cortex	58.3 nTPM
Hippocampus	55.6 nTPM
Midbrain	47.9 nTPM
Pons	45.2 nTPM
Basal ganglia	42.7 nTPM

Deep-layer corticothalamic and 6b	63.1 nTPM
Hippocampus	66.4 nTPM
Hypothalamus	66.0 nTPM
Amygdala	65.2 nTPM
Cerebral cortex	65.0 nTPM
Midbrain	64.3 nTPM
Basal ganglia	51.8 nTPM

Deep-layer intratelencephalic	73.7 nTPM
Hypothalamus	86.0 nTPM
Hippocampus	75.8 nTPM
Cerebral cortex	70.5 nTPM
Amygdala	70.0 nTPM
Basal ganglia	66.5 nTPM

Deep-layer near-projecting	60.7 nTPM
Hypothalamus	67.2 nTPM
Hippocampus	60.5 nTPM
Cerebral cortex	60.1 nTPM
Amygdala	60.0 nTPM
Basal ganglia	55.6 nTPM

Eccentric medium spiny neuron	76.4 nTPM
Amygdala	79.8 nTPM
Hypothalamus	78.1 nTPM
Cerebral cortex	76.1 nTPM
Thalamus	75.5 nTPM
Basal ganglia	75.3 nTPM
Hippocampus	73.8 nTPM