Single cell type - TOP3A - The Human Protein Atlas

TOP3A

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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.	TOP3A
Gene descriptionⁱ Full gene name according to HGNC.	DNA topoisomerase III alpha
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Cancer-related genes Disease related genes Enzymes Human disease related genes 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.	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.	Non-specific - 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.	Low cell type specificity
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.	0.39
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: Low cell type specificity

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

TOP3A is part of cluster 55 Non-specific - Transcription with confidenceⁱ 1
709 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.
APAF1	Apoptotic peptidase activating factor 1	0.4946	28
CHAF1A	Chromatin assembly factor 1 subunit A	0.4820	52
NFATC2IP	Nuclear factor of activated T cells 2 interacting protein	0.4713	52
ANKRD52	Ankyrin repeat domain 52	0.4659	55
TRIM44	Tripartite motif containing 44	0.4657	55
THEMIS2	Thymocyte selection associated family member 2	0.4631	28
IQSEC3	IQ motif and Sec7 domain ArfGEF 3	0.4627	71
DMXL2	Dmx like 2	0.4516	29
KDM5A	Lysine demethylase 5A	0.4506	55
POLE	DNA polymerase epsilon, catalytic subunit	0.4453	79
MTMR9	Myotubularin related protein 9	0.4388	66
NOMO3	NODAL modulator 3	0.4357	55
SCFD1	Sec1 family domain containing 1	0.4281	55
IREB2	Iron responsive element binding protein 2	0.4258	55
TET2	Tet methylcytosine dioxygenase 2	0.4234	29

IMMUNE CELLS

TOP3A is part of cluster 7 Non-specific - Innate immune response with confidenceⁱ 1
237 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.
PSRC1	Proline and serine rich coiled-coil 1	1.0000	7
ATG7	Autophagy related 7	1.0000	7
NCF2	Neutrophil cytosolic factor 2	1.0000	7
BCKDK	Branched chain keto acid dehydrogenase kinase	1.0000	7
EDEM2	ER degradation enhancing alpha-mannosidase like protein 2	0.9762	7
TUBGCP3	Tubulin gamma complex associated protein 3	0.9762	7
SPATA20	Spermatogenesis associated 20	0.9762	7
GBGT1	Globoside alpha-1,3-N-acetylgalactosaminyltransferase 1 (FORS blood group)	0.9762	7
IL6R	Interleukin 6 receptor	0.9762	7
HGSNAT	Heparan-alpha-glucosaminide N-acetyltransferase	0.9762	7
SPINT1	Serine peptidase inhibitor, Kunitz type 1	0.9762	7
RBPJ	Recombination signal binding protein for immunoglobulin kappa J region	0.9762	7
OSCAR	Osteoclast associated Ig-like receptor	0.9762	7
TMEM11	Transmembrane protein 11	0.9762	7
HCLS1	Hematopoietic cell-specific Lyn substrate 1	0.9762	7

Adipocytes	5.2 nTPM
Adipose tissue	6.3 nTPM
Breast	4.1 nTPM

Alveolar cells type 1	9.5 nTPM
Lung	9.5 nTPM

Alveolar cells type 2	8.2 nTPM
Lung	8.2 nTPM

Astrocytes	6.2 nTPM
Brain	6.2 nTPM

B-cells	7.9 nTPM
Kidney	15.6 nTPM
Salivary gland	14.9 nTPM
Lung	13.4 nTPM
Thymus	10.4 nTPM
Adipose tissue	8.2 nTPM
Spleen	6.8 nTPM
Stomach	6.7 nTPM
Lymph node	6.6 nTPM
PBMC	6.2 nTPM
Esophagus	5.9 nTPM
Bone marrow	5.1 nTPM
Skin	3.4 nTPM
Liver	0.0 nTPM

Ciliated cells	6.5 nTPM
Lung	8.4 nTPM
Fallopian tube	6.3 nTPM
Bronchus	5.7 nTPM
Endometrium	5.5 nTPM

Club cells	5.7 nTPM
Lung	7.2 nTPM
Prostate	6.0 nTPM
Bronchus	4.0 nTPM

Dendritic cells	25.2 nTPM
Adipose tissue	32.5 nTPM
PBMC	18.0 nTPM

Endothelial cells	8.4 nTPM
Heart muscle	14.3 nTPM
Pancreas	12.9 nTPM
Salivary gland	10.3 nTPM
Vascular	10.1 nTPM
Endometrium	9.5 nTPM
Skeletal muscle	9.2 nTPM
Lung	9.1 nTPM
Fallopian tube	9.1 nTPM
Tongue	8.5 nTPM
Thymus	8.4 nTPM
Ovary	7.7 nTPM
Liver	7.6 nTPM
Testis	7.0 nTPM
Breast	7.0 nTPM
Prostate	6.7 nTPM
Placenta	5.1 nTPM
Skin	4.4 nTPM
Esophagus	3.9 nTPM

Enteroendocrine cells	2.8 nTPM
Colon	5.1 nTPM
Small intestine	3.4 nTPM
Rectum	0.0 nTPM

Fibroblasts	6.8 nTPM
Vascular	11.9 nTPM
Salivary gland	11.2 nTPM
Adipose tissue	9.7 nTPM
Skeletal muscle	9.0 nTPM
Stomach	8.6 nTPM
Thymus	8.4 nTPM
Fallopian tube	7.2 nTPM
Breast	6.7 nTPM
Pancreas	6.4 nTPM
Placenta	6.1 nTPM
Skin	5.1 nTPM
Liver	4.7 nTPM
Prostate	4.6 nTPM
Lung	4.4 nTPM
Esophagus	3.9 nTPM
Heart muscle	1.0 nTPM

Granulocytes	7.7 nTPM
Tongue	9.7 nTPM
Fallopian tube	8.3 nTPM
Lung	5.0 nTPM

Intestinal goblet cells	5.7 nTPM
Small intestine	7.9 nTPM
Colon	4.9 nTPM
Rectum	4.4 nTPM

Lymphatic endothelial cells	8.6 nTPM
Ovary	10.9 nTPM
Fallopian tube	6.3 nTPM

Macrophages	12.7 nTPM
Adipose tissue	21.1 nTPM
Fallopian tube	16.8 nTPM
Skeletal muscle	16.6 nTPM
Salivary gland	15.8 nTPM
Thymus	15.7 nTPM
Spleen	15.0 nTPM
Bone marrow	14.2 nTPM
Breast	13.8 nTPM
Kidney	13.3 nTPM
Tongue	13.1 nTPM
Vascular	13.1 nTPM
Stomach	12.9 nTPM
Lung	12.1 nTPM
Esophagus	10.3 nTPM
Endometrium	9.8 nTPM
Prostate	9.6 nTPM
Testis	8.1 nTPM
Skin	6.7 nTPM
Pancreas	4.1 nTPM

Bipolar cells	22.4 nTPM
Eye	22.4 nTPM

Cholangiocytes	3.8 nTPM
Liver	3.8 nTPM

Collecting duct cells	11.7 nTPM
Kidney	11.7 nTPM

Distal enterocytes	2.3 nTPM
Colon	2.4 nTPM
Rectum	2.1 nTPM

Paneth cells	5.4 nTPM
Colon	7.2 nTPM
Rectum	5.6 nTPM
Small intestine	3.5 nTPM

Plasma cells	10.5 nTPM
Thymus	17.2 nTPM
Bone marrow	15.1 nTPM
Spleen	13.5 nTPM
Salivary gland	11.2 nTPM
Liver	7.5 nTPM
Stomach	7.5 nTPM
Fallopian tube	7.1 nTPM
Esophagus	5.2 nTPM

Schwann cells	21.1 nTPM
Adipose tissue	36.3 nTPM
Vascular	15.1 nTPM
Esophagus	12.0 nTPM

Serous glandular cells	5.7 nTPM
Salivary gland	6.9 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	7.5 nTPM
Lung	12.9 nTPM
Endometrium	10.6 nTPM
Vascular	9.9 nTPM
Salivary gland	9.0 nTPM
Thymus	8.7 nTPM
Tongue	8.1 nTPM
Liver	7.2 nTPM
Ovary	7.2 nTPM
Skeletal muscle	7.1 nTPM
Fallopian tube	6.3 nTPM
Skin	6.2 nTPM
Placenta	5.7 nTPM
Prostate	5.5 nTPM
Breast	5.4 nTPM
Adipose tissue	4.9 nTPM
Esophagus	4.8 nTPM

T-cells	10.8 nTPM
Esophagus	19.5 nTPM
Tongue	16.3 nTPM
Salivary gland	14.3 nTPM
PBMC	13.6 nTPM
Adipose tissue	12.7 nTPM
Skeletal muscle	12.1 nTPM
Lung	11.7 nTPM
Vascular	11.7 nTPM
Prostate	11.1 nTPM
Fallopian tube	10.8 nTPM
Thymus	10.7 nTPM
Endometrium	10.6 nTPM
Colon	9.7 nTPM
Stomach	9.7 nTPM
Breast	9.4 nTPM
Bone marrow	8.7 nTPM
Lymph node	7.5 nTPM
Spleen	7.2 nTPM
Kidney	7.1 nTPM
Liver	6.2 nTPM
Skin	5.6 nTPM

Undifferentiated cells	8.5 nTPM
Colon	9.0 nTPM
Rectum	8.5 nTPM
Small intestine	8.0 nTPM

Amygdala excitatory	37.1 nTPM
Hypothalamus	44.8 nTPM
Basal ganglia	38.1 nTPM
Hippocampus	37.0 nTPM
Amygdala	36.8 nTPM
Cerebral cortex	34.3 nTPM
Thalamus	31.8 nTPM

Astrocyte	19.8 nTPM
Spinal cord	22.3 nTPM
Amygdala	21.9 nTPM
Hippocampus	20.7 nTPM
Thalamus	20.6 nTPM
Hypothalamus	20.4 nTPM
Pons	19.8 nTPM
Midbrain	19.6 nTPM
Cerebellum	19.2 nTPM
Cerebral cortex	19.0 nTPM
Medulla oblongata	17.4 nTPM
Basal ganglia	17.3 nTPM

Bergmann glia	15.1 nTPM
Pons	20.1 nTPM
Cerebellum	18.7 nTPM
Medulla oblongata	6.4 nTPM

Central nervous system macrophage	24.2 nTPM
Amygdala	32.3 nTPM
Hypothalamus	27.4 nTPM
Thalamus	26.3 nTPM
Hippocampus	25.1 nTPM
Pons	24.3 nTPM
Midbrain	24.2 nTPM
Cerebellum	23.5 nTPM
Cerebral cortex	22.3 nTPM
Basal ganglia	21.4 nTPM
Medulla oblongata	20.8 nTPM
Spinal cord	18.8 nTPM

Cerebellar inhibitory	26.5 nTPM
Midbrain	31.1 nTPM
Medulla oblongata	30.8 nTPM
Cerebellum	30.4 nTPM
Pons	26.6 nTPM
Spinal cord	13.7 nTPM

Cge interneuron	32.5 nTPM
Hypothalamus	40.4 nTPM
Amygdala	34.5 nTPM
Cerebral cortex	31.9 nTPM
Hippocampus	31.9 nTPM
Basal ganglia	30.7 nTPM
Thalamus	29.9 nTPM
Midbrain	28.2 nTPM

Choroid plexus epithelial cell	20.7 nTPM
Basal ganglia	40.2 nTPM
Medulla oblongata	20.6 nTPM
Hippocampus	13.9 nTPM
Thalamus	8.2 nTPM

Committed oligodendrocyte precursor	24.2 nTPM
Hippocampus	29.2 nTPM
Amygdala	28.8 nTPM
Cerebral cortex	27.2 nTPM
Hypothalamus	25.9 nTPM
Spinal cord	25.8 nTPM
Basal ganglia	25.2 nTPM
Thalamus	23.6 nTPM
Pons	23.0 nTPM
Cerebellum	22.2 nTPM
Midbrain	21.8 nTPM
Medulla oblongata	12.9 nTPM

Deep-layer corticothalamic and 6b	37.6 nTPM
Hypothalamus	43.0 nTPM
Amygdala	39.8 nTPM
Hippocampus	38.7 nTPM
Basal ganglia	38.2 nTPM
Cerebral cortex	35.7 nTPM
Midbrain	30.0 nTPM

Deep-layer intratelencephalic	36.8 nTPM
Hypothalamus	44.0 nTPM
Basal ganglia	37.5 nTPM
Hippocampus	34.7 nTPM
Cerebral cortex	34.0 nTPM
Amygdala	33.7 nTPM

Deep-layer near-projecting	40.6 nTPM
Hypothalamus	48.8 nTPM
Amygdala	41.8 nTPM
Basal ganglia	41.1 nTPM
Cerebral cortex	37.0 nTPM
Hippocampus	34.5 nTPM

Eccentric medium spiny neuron	33.0 nTPM
Hippocampus	40.2 nTPM
Hypothalamus	34.8 nTPM
Basal ganglia	31.3 nTPM
Thalamus	30.9 nTPM
Amygdala	30.7 nTPM
Cerebral cortex	30.1 nTPM

Endothelial cell	19.6 nTPM
Hypothalamus	27.3 nTPM
Thalamus	25.4 nTPM
Basal ganglia	21.4 nTPM
Spinal cord	20.7 nTPM
Amygdala	19.0 nTPM
Midbrain	18.9 nTPM
Pons	18.1 nTPM
Medulla oblongata	17.4 nTPM
Cerebral cortex	16.6 nTPM
Cerebellum	15.5 nTPM
Hippocampus	15.1 nTPM