Single cell type - APOBEC3A - The Human Protein Atlas

APOBEC3A

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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.	APOBEC3A
Gene descriptionⁱ Full gene name according to HGNC.	Apolipoprotein B mRNA editing enzyme catalytic subunit 3A
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.	3

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, Hofbauer cells, Suprabasal keratinocytes, Basal keratinocytes, Serous glandular cells, Macrophages, Squamous epithelial 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.	0.83
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.	Group enriched (Leukocyte, Hippocampal CA4)
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.	Immune cell enhanced (intermediate monocyte)
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, Hofbauer cells, Suprabasal keratinocytes, Basal keratinocytes, Serous glandular cells, Macrophages, Squamous epithelial 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: Group enriched (Leukocyte, Hippocampal CA4)

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: Immune cell enhanced (intermediate monocyte)
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

APOBEC3A 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.
LIPN	Lipase family member N	0.8148	29
CD300E	CD300e molecule	0.8011	29
MEFV	MEFV innate immuity regulator, pyrin	0.7671	29
LILRA5	Leukocyte immunoglobulin like receptor A5	0.7632	29
LILRB2	Leukocyte immunoglobulin like receptor B2	0.7533	29
ACOD1	Aconitate decarboxylase 1	0.7413	29
FCN1	Ficolin 1	0.7412	29
CD300LB	CD300 molecule like family member b	0.7258	29
FCAR	Fc alpha receptor	0.7237	29
VSTM1	V-set and transmembrane domain containing 1	0.7207	29
TMEM170B	Transmembrane protein 170B	0.7201	29
BCL2A1	BCL2 related protein A1	0.7173	29
C19orf38	Chromosome 19 open reading frame 38	0.7171	29
MTF1	Metal regulatory transcription factor 1	0.7009	29
C5AR1	Complement C5a receptor 1	0.6961	29

IMMUNE CELLS

APOBEC3A is part of cluster 40 Monocytes - Innate immune response with confidenceⁱ 0.99
228 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.
KNSTRN	Kinetochore localized astrin (SPAG5) binding protein	1.0000	40
KCNMA1	Potassium calcium-activated channel subfamily M alpha 1	1.0000	40
SLC5A10	Solute carrier family 5 member 10	1.0000	40
MERTK	MER proto-oncogene, tyrosine kinase	1.0000	40
UTRN	Utrophin	1.0000	40
CLEC4F	C-type lectin domain family 4 member F	1.0000	40
CDH13	Cadherin 13	1.0000	40
CTSL	Cathepsin L	1.0000	40
SFTPD	Surfactant protein D	1.0000	40
CDKN1C	Cyclin dependent kinase inhibitor 1C	1.0000	40
MSR1	Macrophage scavenger receptor 1	1.0000	40
AVPR2	Arginine vasopressin receptor 2	1.0000	40
RRAS	RAS related	1.0000	40
NR4A1	Nuclear receptor subfamily 4 group A member 1	1.0000	40
SASH1	SAM and SH3 domain containing 1	1.0000	40

Adipocytes	0.5 nTPM
Breast	0.9 nTPM
Adipose tissue	0.0 nTPM

Alveolar cells type 1	0.4 nTPM
Lung	0.4 nTPM

Alveolar cells type 2	0.5 nTPM
Lung	0.5 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	4.1 nTPM
Skin	45.7 nTPM
Adipose tissue	7.4 nTPM
Lymph node	0.1 nTPM
Salivary gland	0.1 nTPM
Thymus	0.1 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM

Ciliated cells	2.1 nTPM
Bronchus	5.6 nTPM
Fallopian tube	1.6 nTPM
Lung	0.7 nTPM
Endometrium	0.4 nTPM

Club cells	6.0 nTPM
Bronchus	10.6 nTPM
Prostate	6.5 nTPM
Lung	1.0 nTPM

Endothelial cells	3.4 nTPM
Tongue	50.8 nTPM
Liver	7.6 nTPM
Placenta	0.6 nTPM
Lung	0.6 nTPM
Skin	0.5 nTPM
Thymus	0.2 nTPM
Vascular	0.2 nTPM
Fallopian tube	0.2 nTPM
Endometrium	0.1 nTPM
Skeletal muscle	0.1 nTPM
Testis	0.0 nTPM
Heart muscle	0.0 nTPM
Pancreas	0.0 nTPM
Esophagus	0.0 nTPM
Prostate	0.0 nTPM
Salivary gland	0.0 nTPM
Breast	0.0 nTPM
Ovary	0.0 nTPM

Enteroendocrine cells	0.6 nTPM
Colon	1.8 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Fibroblasts	0.3 nTPM
Breast	0.8 nTPM
Skin	0.6 nTPM
Fallopian tube	0.6 nTPM
Skeletal muscle	0.4 nTPM
Thymus	0.4 nTPM
Vascular	0.4 nTPM
Lung	0.3 nTPM
Placenta	0.2 nTPM
Esophagus	0.2 nTPM
Salivary gland	0.2 nTPM
Adipose tissue	0.1 nTPM
Heart muscle	0.0 nTPM
Liver	0.0 nTPM
Pancreas	0.0 nTPM
Stomach	0.0 nTPM
Prostate	0.0 nTPM

Granulocytes	14.8 nTPM
Tongue	43.7 nTPM
Fallopian tube	0.8 nTPM
Lung	0.0 nTPM

Intestinal goblet cells	0.7 nTPM
Colon	1.2 nTPM
Small intestine	0.9 nTPM
Rectum	0.0 nTPM

Lymphatic endothelial cells	0.2 nTPM
Fallopian tube	0.4 nTPM
Ovary	0.0 nTPM

Macrophages	73.3 nTPM
Fallopian tube	423.1 nTPM
Stomach	326.7 nTPM
Skeletal muscle	198.9 nTPM
Kidney	100.0 nTPM
Adipose tissue	87.1 nTPM
Tongue	69.0 nTPM
Bone marrow	52.7 nTPM
Spleen	46.1 nTPM
Lung	32.0 nTPM
Esophagus	14.1 nTPM
Breast	12.4 nTPM
Endometrium	8.0 nTPM
Prostate	5.1 nTPM
Thymus	5.1 nTPM
Vascular	5.0 nTPM
Testis	4.3 nTPM
Salivary gland	3.2 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM

Paneth cells	3.6 nTPM
Colon	10.9 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Collecting duct cells	1.9 nTPM
Kidney	1.9 nTPM

Cone photoreceptor cells	1.7 nTPM
Eye	1.7 nTPM

Plasma cells	8.4 nTPM
Esophagus	46.8 nTPM
Fallopian tube	10.0 nTPM
Stomach	6.7 nTPM
Liver	2.0 nTPM
Salivary gland	0.9 nTPM
Spleen	0.5 nTPM
Thymus	0.3 nTPM
Bone marrow	0.0 nTPM

Schwann cells	11.8 nTPM
Adipose tissue	35.5 nTPM
Esophagus	0.0 nTPM
Vascular	0.0 nTPM

Serous glandular cells	81.6 nTPM
Tongue	159.1 nTPM
Salivary gland	4.2 nTPM

Smooth muscle cells	1.6 nTPM
Tongue	21.0 nTPM
Salivary gland	0.9 nTPM
Ovary	0.8 nTPM
Skin	0.6 nTPM
Skeletal muscle	0.5 nTPM
Placenta	0.3 nTPM
Adipose tissue	0.2 nTPM
Thymus	0.2 nTPM
Vascular	0.2 nTPM
Fallopian tube	0.1 nTPM
Liver	0.0 nTPM
Endometrium	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Breast	0.0 nTPM

Suprabasal keratinocytes	121.2 nTPM
Tongue	236.3 nTPM
Skin	6.1 nTPM

T-cells	2.8 nTPM
Tongue	49.1 nTPM
PBMC	1.5 nTPM
Skin	1.4 nTPM
Lung	1.3 nTPM
Colon	1.0 nTPM
Fallopian tube	1.0 nTPM
Adipose tissue	0.4 nTPM
Prostate	0.4 nTPM
Vascular	0.4 nTPM
Breast	0.4 nTPM
Liver	0.3 nTPM
Spleen	0.3 nTPM
Endometrium	0.2 nTPM
Thymus	0.2 nTPM
Bone marrow	0.1 nTPM
Kidney	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Stomach	0.0 nTPM
Salivary gland	0.0 nTPM

Undifferentiated cells	0.9 nTPM
Colon	2.2 nTPM
Small intestine	0.3 nTPM
Rectum	0.1 nTPM

Amygdala excitatory	0.1 nTPM
Amygdala	0.2 nTPM
Cerebral cortex	0.2 nTPM
Hippocampus	0.2 nTPM
Basal ganglia	0.1 nTPM
Hypothalamus	0.1 nTPM
Thalamus	0.0 nTPM

Astrocyte	0.3 nTPM
Spinal cord	0.7 nTPM
Medulla oblongata	0.4 nTPM
Cerebral cortex	0.3 nTPM
Hippocampus	0.3 nTPM
Midbrain	0.3 nTPM
Pons	0.3 nTPM
Thalamus	0.3 nTPM
Amygdala	0.2 nTPM
Basal ganglia	0.2 nTPM
Cerebellum	0.2 nTPM
Hypothalamus	0.2 nTPM

Bergmann glia	0.1 nTPM
Cerebellum	0.2 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	0.1 nTPM
Medulla oblongata	0.3 nTPM
Spinal cord	0.3 nTPM
Cerebral cortex	0.2 nTPM
Hippocampus	0.2 nTPM
Basal ganglia	0.1 nTPM
Cerebellum	0.1 nTPM
Hypothalamus	0.1 nTPM
Pons	0.1 nTPM
Thalamus	0.1 nTPM
Amygdala	0.0 nTPM
Midbrain	0.0 nTPM

Cerebellar inhibitory	0.1 nTPM
Cerebellum	0.2 nTPM
Medulla oblongata	0.2 nTPM
Pons	0.2 nTPM
Midbrain	0.0 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	0.1 nTPM
Midbrain	0.2 nTPM
Amygdala	0.1 nTPM
Basal ganglia	0.1 nTPM
Cerebral cortex	0.1 nTPM
Hippocampus	0.1 nTPM
Hypothalamus	0.1 nTPM
Thalamus	0.0 nTPM

Choroid plexus epithelial cell	0.0 nTPM
Basal ganglia	0.2 nTPM
Hippocampus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	0.2 nTPM
Medulla oblongata	1.3 nTPM
Cerebral cortex	0.6 nTPM
Hippocampus	0.5 nTPM
Thalamus	0.2 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebellum	0.0 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM

Deep-layer corticothalamic and 6b	0.3 nTPM
Hippocampus	0.8 nTPM
Amygdala	0.2 nTPM
Basal ganglia	0.2 nTPM
Cerebral cortex	0.2 nTPM
Hypothalamus	0.1 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	0.2 nTPM
Hippocampus	0.4 nTPM
Amygdala	0.1 nTPM
Basal ganglia	0.1 nTPM
Cerebral cortex	0.1 nTPM
Hypothalamus	0.1 nTPM

Deep-layer near-projecting	0.1 nTPM
Basal ganglia	0.2 nTPM
Cerebral cortex	0.1 nTPM
Amygdala	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM

Eccentric medium spiny neuron	0.1 nTPM
Hippocampus	0.4 nTPM
Amygdala	0.1 nTPM
Basal ganglia	0.1 nTPM
Thalamus	0.1 nTPM
Cerebral cortex	0.0 nTPM
Hypothalamus	0.0 nTPM

Endothelial cell	0.1 nTPM
Cerebral cortex	0.6 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebellum	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM
Thalamus	0.0 nTPM