Single cell type - APBB3 - The Human Protein Atlas

APBB3

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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.	APBB3
Gene descriptionⁱ Full gene name according to HGNC.	Amyloid beta precursor protein binding family B member 3
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.	6

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.	Spermatocytes - 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, Late 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.	0.49
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.	Immune cell enhanced (basophil)
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, Late 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: Immune cell enhanced (basophil)
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

APBB3 is part of cluster 31 Spermatocytes - Spermatogenesis with confidenceⁱ 1
240 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.
PAN2	Poly(A) specific ribonuclease subunit PAN2	0.4872	55
TUBE1	Tubulin epsilon 1	0.4470	31
C3orf62	Chromosome 3 open reading frame 62	0.4337	31
MLLT10	MLLT10 histone lysine methyltransferase DOT1L cofactor	0.4150	31
TEX14	Testis expressed 14, intercellular bridge forming factor	0.4085	31
DNHD1	Dynein heavy chain domain 1	0.4038	47
CCDC154	Coiled-coil domain containing 154	0.3968	18
CETN3	Centrin 3	0.3949	31
ZNF546	Zinc finger protein 546	0.3928	31
FAM228B	Family with sequence similarity 228 member B	0.3881	6
WDR97	WD repeat domain 97	0.3866	26
DBF4B	DBF4 zinc finger B	0.3848	71
USP32	Ubiquitin specific peptidase 32	0.3807	31
SLC27A1	Solute carrier family 27 member 1	0.3802	47
NCKAP5L	NCK associated protein 5 like	0.3768	80

IMMUNE CELLS

APBB3 is part of cluster 2 Dendritic cells - Unknown function with confidenceⁱ 0.71
342 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.
PDPK1	3-phosphoinositide dependent protein kinase 1	1.0000	2
SERPING1	Serpin family G member 1	0.9762	2
TRIM3	Tripartite motif containing 3	0.9762	2
ZSWIM6	Zinc finger SWIM-type containing 6	0.9762	2
KIAA0753	KIAA0753	0.9524	2
HPD	4-hydroxyphenylpyruvate dioxygenase	0.9524	2
TRIM5	Tripartite motif containing 5	0.9524	2
MLLT1	MLLT1 super elongation complex subunit	0.9524	2
SIPA1L2	Signal induced proliferation associated 1 like 2	0.9524	2
ARID3A	AT-rich interaction domain 3A	0.9524	2
ZMIZ1	Zinc finger MIZ-type containing 1	0.9524	2
KLF16	KLF transcription factor 16	0.9286	2
FEM1A	Fem-1 homolog A	0.9286	13
ATXN7L3	Ataxin 7 like 3	0.9286	2
ELMOD2	ELMO domain containing 2	0.9286	2

Adipocytes	8.2 nTPM
Breast	9.1 nTPM
Adipose tissue	7.3 nTPM

Alveolar cells type 1	3.1 nTPM
Lung	3.1 nTPM

Alveolar cells type 2	3.9 nTPM
Lung	3.9 nTPM

Astrocytes	24.5 nTPM
Brain	24.5 nTPM

B-cells	6.2 nTPM
Bone marrow	12.0 nTPM
Esophagus	11.8 nTPM
Thymus	9.7 nTPM
Lymph node	8.9 nTPM
PBMC	7.7 nTPM
Stomach	7.6 nTPM
Spleen	6.3 nTPM
Liver	4.8 nTPM
Salivary gland	4.8 nTPM
Lung	4.0 nTPM
Adipose tissue	3.3 nTPM
Kidney	0.0 nTPM
Skin	0.0 nTPM

Ciliated cells	6.0 nTPM
Bronchus	12.8 nTPM
Fallopian tube	4.2 nTPM
Endometrium	3.7 nTPM
Lung	3.1 nTPM

Club cells	7.2 nTPM
Bronchus	14.0 nTPM
Prostate	4.3 nTPM
Lung	3.1 nTPM

Endothelial cells	5.5 nTPM
Ovary	9.9 nTPM
Liver	8.8 nTPM
Esophagus	8.7 nTPM
Skin	7.5 nTPM
Testis	6.7 nTPM
Thymus	6.4 nTPM
Placenta	6.2 nTPM
Breast	6.2 nTPM
Heart muscle	5.6 nTPM
Skeletal muscle	4.8 nTPM
Prostate	4.8 nTPM
Tongue	4.6 nTPM
Vascular	4.3 nTPM
Salivary gland	4.2 nTPM
Fallopian tube	3.7 nTPM
Endometrium	3.6 nTPM
Lung	2.7 nTPM
Pancreas	0.0 nTPM

Enteroendocrine cells	7.4 nTPM
Small intestine	10.3 nTPM
Rectum	8.4 nTPM
Colon	3.7 nTPM

Fibroblasts	6.3 nTPM
Breast	12.8 nTPM
Stomach	11.5 nTPM
Esophagus	10.7 nTPM
Placenta	10.3 nTPM
Fallopian tube	7.7 nTPM
Thymus	6.9 nTPM
Adipose tissue	6.7 nTPM
Skeletal muscle	4.8 nTPM
Liver	4.7 nTPM
Skin	4.7 nTPM
Salivary gland	4.0 nTPM
Lung	3.8 nTPM
Vascular	3.6 nTPM
Prostate	3.3 nTPM
Pancreas	3.2 nTPM
Heart muscle	1.7 nTPM

Granulocytes	5.7 nTPM
Lung	9.6 nTPM
Tongue	4.9 nTPM
Fallopian tube	2.7 nTPM

Intestinal goblet cells	3.6 nTPM
Rectum	5.3 nTPM
Small intestine	3.7 nTPM
Colon	1.7 nTPM

Lymphatic endothelial cells	6.7 nTPM
Ovary	10.9 nTPM
Fallopian tube	2.4 nTPM

Macrophages	10.7 nTPM
Skin	25.6 nTPM
Breast	20.1 nTPM
Fallopian tube	18.5 nTPM
Esophagus	18.0 nTPM
Tongue	16.1 nTPM
Spleen	12.0 nTPM
Endometrium	11.1 nTPM
Skeletal muscle	10.5 nTPM
Stomach	10.3 nTPM
Thymus	9.3 nTPM
Adipose tissue	9.2 nTPM
Bone marrow	7.1 nTPM
Vascular	6.7 nTPM
Prostate	6.3 nTPM
Lung	5.7 nTPM
Testis	5.6 nTPM
Salivary gland	5.5 nTPM
Kidney	4.4 nTPM
Pancreas	2.1 nTPM

Paneth cells	5.3 nTPM
Small intestine	10.4 nTPM
Colon	3.6 nTPM
Rectum	1.9 nTPM

Bipolar cells	28.4 nTPM
Eye	28.4 nTPM

Cholangiocytes	13.4 nTPM
Liver	13.4 nTPM

Collecting duct cells	5.8 nTPM
Kidney	5.8 nTPM

Cone photoreceptor cells	25.5 nTPM
Eye	25.5 nTPM

Plasma cells	4.5 nTPM
Liver	7.5 nTPM
Thymus	6.1 nTPM
Stomach	5.9 nTPM
Salivary gland	4.9 nTPM
Bone marrow	4.5 nTPM
Fallopian tube	4.2 nTPM
Spleen	3.1 nTPM
Esophagus	0.0 nTPM

Schwann cells	5.7 nTPM
Esophagus	12.0 nTPM
Vascular	3.7 nTPM
Adipose tissue	1.6 nTPM

Serous glandular cells	8.9 nTPM
Tongue	13.3 nTPM
Salivary gland	4.5 nTPM

Smooth muscle cells	7.6 nTPM
Skin	14.7 nTPM
Breast	11.0 nTPM
Placenta	9.7 nTPM
Esophagus	9.6 nTPM
Adipose tissue	9.4 nTPM
Thymus	9.2 nTPM
Fallopian tube	8.8 nTPM
Ovary	8.8 nTPM
Liver	8.1 nTPM
Tongue	6.3 nTPM
Endometrium	6.2 nTPM
Skeletal muscle	5.0 nTPM
Lung	4.7 nTPM
Prostate	4.3 nTPM
Vascular	3.2 nTPM
Salivary gland	2.6 nTPM

T-cells	4.7 nTPM
Breast	10.5 nTPM
Lymph node	9.4 nTPM
Thymus	8.3 nTPM
Skin	6.7 nTPM
Bone marrow	6.6 nTPM
Spleen	5.3 nTPM
Endometrium	5.1 nTPM
Salivary gland	4.6 nTPM
Liver	4.5 nTPM
Kidney	4.4 nTPM
Lung	4.4 nTPM
Stomach	4.2 nTPM
Fallopian tube	4.1 nTPM
Prostate	4.0 nTPM
Tongue	3.4 nTPM
PBMC	3.3 nTPM
Skeletal muscle	3.0 nTPM
Adipose tissue	2.9 nTPM
Vascular	2.4 nTPM
Colon	1.0 nTPM
Esophagus	0.0 nTPM

Undifferentiated cells	2.9 nTPM
Rectum	3.5 nTPM
Small intestine	2.8 nTPM
Colon	2.3 nTPM

Amygdala excitatory	13.0 nTPM
Hippocampus	14.7 nTPM
Thalamus	13.6 nTPM
Basal ganglia	13.2 nTPM
Amygdala	12.6 nTPM
Cerebral cortex	12.6 nTPM
Hypothalamus	11.2 nTPM

Astrocyte	36.0 nTPM
Spinal cord	58.5 nTPM
Pons	42.4 nTPM
Cerebellum	40.8 nTPM
Midbrain	40.8 nTPM
Cerebral cortex	38.0 nTPM
Hippocampus	37.9 nTPM
Thalamus	34.6 nTPM
Medulla oblongata	31.3 nTPM
Basal ganglia	29.4 nTPM
Amygdala	23.6 nTPM
Hypothalamus	18.9 nTPM

Bergmann glia	20.0 nTPM
Pons	24.5 nTPM
Medulla oblongata	19.2 nTPM
Cerebellum	16.3 nTPM

Central nervous system macrophage	15.9 nTPM
Spinal cord	38.9 nTPM
Cerebellum	16.4 nTPM
Hippocampus	16.3 nTPM
Pons	16.1 nTPM
Amygdala	14.9 nTPM
Cerebral cortex	14.8 nTPM
Midbrain	13.3 nTPM
Thalamus	12.3 nTPM
Hypothalamus	11.6 nTPM
Medulla oblongata	10.2 nTPM
Basal ganglia	10.1 nTPM

Cerebellar inhibitory	18.3 nTPM
Midbrain	19.6 nTPM
Pons	19.5 nTPM
Spinal cord	19.2 nTPM
Cerebellum	17.5 nTPM
Medulla oblongata	15.5 nTPM

Cge interneuron	14.7 nTPM
Midbrain	17.4 nTPM
Thalamus	15.9 nTPM
Cerebral cortex	15.4 nTPM
Hippocampus	14.8 nTPM
Amygdala	13.7 nTPM
Basal ganglia	13.6 nTPM
Hypothalamus	12.2 nTPM

Choroid plexus epithelial cell	14.9 nTPM
Thalamus	24.7 nTPM
Medulla oblongata	18.0 nTPM
Basal ganglia	14.2 nTPM
Hippocampus	2.8 nTPM

Committed oligodendrocyte precursor	16.7 nTPM
Cerebellum	20.6 nTPM
Thalamus	20.0 nTPM
Pons	18.6 nTPM
Cerebral cortex	17.7 nTPM
Basal ganglia	17.5 nTPM
Hippocampus	16.0 nTPM
Medulla oblongata	15.5 nTPM
Amygdala	15.2 nTPM
Midbrain	15.1 nTPM
Spinal cord	14.7 nTPM
Hypothalamus	13.0 nTPM

Deep-layer corticothalamic and 6b	13.7 nTPM
Midbrain	15.5 nTPM
Hippocampus	15.4 nTPM
Cerebral cortex	14.5 nTPM
Basal ganglia	13.8 nTPM
Amygdala	13.0 nTPM
Hypothalamus	10.2 nTPM

Deep-layer intratelencephalic	13.5 nTPM
Cerebral cortex	15.0 nTPM
Basal ganglia	14.1 nTPM
Hippocampus	13.2 nTPM
Amygdala	13.1 nTPM
Hypothalamus	11.9 nTPM

Deep-layer near-projecting	14.3 nTPM
Amygdala	17.1 nTPM
Cerebral cortex	16.6 nTPM
Hippocampus	13.3 nTPM
Basal ganglia	13.0 nTPM
Hypothalamus	11.6 nTPM

Eccentric medium spiny neuron	12.3 nTPM
Thalamus	13.4 nTPM
Hippocampus	12.4 nTPM
Hypothalamus	12.4 nTPM
Cerebral cortex	12.3 nTPM
Basal ganglia	11.6 nTPM
Amygdala	11.4 nTPM

Endothelial cell	9.1 nTPM
Hippocampus	13.5 nTPM
Cerebellum	11.6 nTPM
Spinal cord	10.4 nTPM
Amygdala	10.1 nTPM
Pons	8.7 nTPM
Midbrain	8.5 nTPM
Thalamus	8.5 nTPM
Cerebral cortex	8.3 nTPM
Medulla oblongata	8.2 nTPM
Basal ganglia	6.5 nTPM
Hypothalamus	6.2 nTPM

Ependymal cell	16.6 nTPM
Basal ganglia	23.5 nTPM
Hippocampus	20.4 nTPM
Spinal cord	19.2 nTPM
Amygdala	18.8 nTPM
Thalamus	17.0 nTPM
Midbrain	15.2 nTPM
Pons	13.7 nTPM
Medulla oblongata	13.4 nTPM
Hypothalamus	8.0 nTPM