Single cell type - N4BP3 - The Human Protein Atlas

N4BP3

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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.	N4BP3
Gene descriptionⁱ Full gene name according to HGNC.	NEDD4 binding protein 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.	1

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.	Extravillous trophoblasts - Unknown function (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 enriched (Extravillous trophoblasts)
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.	0.73
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.	Group enriched (plasmacytoid DC, memory B-cell, naive B-cell, naive CD8 T-cell)
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 enriched (Extravillous trophoblasts)

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: Group enriched (plasmacytoid DC, memory B-cell, naive B-cell, naive CD8 T-cell)
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

N4BP3 is part of cluster 4 Extravillous trophoblasts - Unknown function with confidenceⁱ 1
182 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.
GPR78	G protein-coupled receptor 78	0.7286	4
GPR32	G protein-coupled receptor 32	0.7262	4
GCM1	Glial cells missing transcription factor 1	0.7166	4
PGF	Placental growth factor	0.7092	4
BZW2	Basic leucine zipper and W2 domains 2	0.7020	4
HTRA4	HtrA serine peptidase 4	0.7002	4
DLX4	Distal-less homeobox 4	0.6932	4
NOTUM	Notum, palmitoleoyl-protein carboxylesterase	0.6904	4
C1QTNF6	C1q and TNF related 6	0.6856	4
CLDN19	Claudin 19	0.6788	4
DLX3	Distal-less homeobox 3	0.6764	4
CCNE1	Cyclin E1	0.6732	4
FANCE	FA complementation group E	0.6710	4
CSH1	Chorionic somatomammotropin hormone 1	0.6663	4
HMGB3	High mobility group box 3	0.6652	4

IMMUNE CELLS

N4BP3 is part of cluster 34 B-cells - Unknown function with confidenceⁱ 1
112 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.
PTK2	Protein tyrosine kinase 2	1.0000	34
ACSM1	Acyl-CoA synthetase medium chain family member 1	1.0000	34
DIPK1B	Divergent protein kinase domain 1B	1.0000	34
TCL1A	TCL1 family AKT coactivator A	1.0000	34
BCAS4	Breast carcinoma amplified sequence 4	0.9762	34
SLC2A5	Solute carrier family 2 member 5	0.9762	34
CD72	CD72 molecule	0.9762	34
NT5E	5'-nucleotidase ecto	0.9762	34
CHL1	Cell adhesion molecule L1 like	0.9762	34
PIK3C2B	Phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 beta	0.9762	34
HIP1R	Huntingtin interacting protein 1 related	0.9762	34
DBNDD1	Dysbindin domain containing 1	0.9762	34
CCN2	Cellular communication network factor 2	0.9762	34
ANGPTL1	Angiopoietin like 1	0.9762	34
CORO2B	Coronin 2B	0.9762	34

Adipocytes	7.6 nTPM
Adipose tissue	11.7 nTPM
Breast	3.6 nTPM

Alveolar cells type 1	0.6 nTPM
Lung	0.6 nTPM

Alveolar cells type 2	1.4 nTPM
Lung	1.4 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	13.5 nTPM
Esophagus	35.4 nTPM
Lymph node	21.5 nTPM
Liver	19.3 nTPM
Adipose tissue	16.9 nTPM
Lung	12.1 nTPM
Spleen	11.7 nTPM
Bone marrow	11.6 nTPM
Kidney	10.4 nTPM
Stomach	10.1 nTPM
Thymus	10.1 nTPM
Salivary gland	10.0 nTPM
PBMC	4.6 nTPM
Skin	1.7 nTPM

Ciliated cells	1.3 nTPM
Endometrium	2.4 nTPM
Fallopian tube	1.7 nTPM
Bronchus	0.9 nTPM
Lung	0.0 nTPM

Club cells	5.2 nTPM
Bronchus	6.7 nTPM
Prostate	5.8 nTPM
Lung	3.3 nTPM

Endothelial cells	12.2 nTPM
Pancreas	46.5 nTPM
Placenta	31.8 nTPM
Skeletal muscle	26.7 nTPM
Lung	21.8 nTPM
Tongue	14.9 nTPM
Breast	14.9 nTPM
Heart muscle	14.6 nTPM
Salivary gland	8.7 nTPM
Endometrium	7.5 nTPM
Ovary	7.5 nTPM
Fallopian tube	5.1 nTPM
Thymus	4.3 nTPM
Skin	4.2 nTPM
Vascular	3.8 nTPM
Testis	3.1 nTPM
Esophagus	3.0 nTPM
Prostate	1.9 nTPM
Liver	0.0 nTPM

Enteroendocrine cells	3.1 nTPM
Rectum	6.7 nTPM
Colon	2.7 nTPM
Small intestine	0.0 nTPM

Fibroblasts	1.1 nTPM
Esophagus	4.2 nTPM
Skeletal muscle	2.1 nTPM
Placenta	1.4 nTPM
Stomach	1.4 nTPM
Breast	1.2 nTPM
Pancreas	1.1 nTPM
Fallopian tube	1.1 nTPM
Prostate	0.7 nTPM
Salivary gland	0.7 nTPM
Lung	0.6 nTPM
Skin	0.5 nTPM
Adipose tissue	0.5 nTPM
Thymus	0.5 nTPM
Heart muscle	0.3 nTPM
Vascular	0.3 nTPM
Liver	0.0 nTPM

Granulocytes	5.1 nTPM
Fallopian tube	14.8 nTPM
Lung	0.5 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	2.5 nTPM
Colon	5.4 nTPM
Rectum	2.0 nTPM
Small intestine	0.1 nTPM

Lymphatic endothelial cells	10.0 nTPM
Fallopian tube	14.4 nTPM
Ovary	5.5 nTPM

Macrophages	1.1 nTPM
Pancreas	4.1 nTPM
Endometrium	3.7 nTPM
Tongue	2.8 nTPM
Skin	2.2 nTPM
Breast	1.6 nTPM
Adipose tissue	1.5 nTPM
Fallopian tube	1.2 nTPM
Prostate	1.0 nTPM
Kidney	0.9 nTPM
Skeletal muscle	0.8 nTPM
Salivary gland	0.8 nTPM
Thymus	0.6 nTPM
Vascular	0.2 nTPM
Lung	0.1 nTPM
Testis	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	16.4 nTPM
Colon	39.8 nTPM
Rectum	5.8 nTPM
Small intestine	3.5 nTPM

Basal respiratory cells	6.2 nTPM
Bronchus	6.2 nTPM

Basal squamous epithelial cells	4.9 nTPM
Esophagus	4.9 nTPM

Bipolar cells	31.3 nTPM
Eye	31.3 nTPM

Cone photoreceptor cells	18.7 nTPM
Eye	18.7 nTPM

Plasma cells	6.0 nTPM
Fallopian tube	11.3 nTPM
Esophagus	10.4 nTPM
Stomach	6.3 nTPM
Salivary gland	5.8 nTPM
Liver	5.5 nTPM
Spleen	4.1 nTPM
Thymus	3.1 nTPM
Bone marrow	1.5 nTPM

Schwann cells	2.0 nTPM
Adipose tissue	5.5 nTPM
Vascular	0.5 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	7.5 nTPM
Salivary gland	10.6 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	1.3 nTPM
Skeletal muscle	6.1 nTPM
Salivary gland	6.0 nTPM
Tongue	2.7 nTPM
Prostate	1.2 nTPM
Fallopian tube	1.1 nTPM
Liver	0.8 nTPM
Placenta	0.6 nTPM
Thymus	0.5 nTPM
Breast	0.5 nTPM
Skin	0.3 nTPM
Endometrium	0.2 nTPM
Vascular	0.2 nTPM
Ovary	0.2 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM

Suprabasal keratinocytes	20.7 nTPM
Tongue	33.6 nTPM
Skin	7.7 nTPM

T-cells	3.0 nTPM
Skin	8.1 nTPM
Endometrium	7.4 nTPM
Esophagus	7.3 nTPM
Adipose tissue	4.7 nTPM
Skeletal muscle	4.2 nTPM
Colon	3.9 nTPM
Salivary gland	3.6 nTPM
Tongue	3.2 nTPM
Breast	3.2 nTPM
PBMC	3.1 nTPM
Fallopian tube	2.7 nTPM
Vascular	2.0 nTPM
Lymph node	1.8 nTPM
Spleen	1.5 nTPM
Stomach	1.3 nTPM
Lung	1.3 nTPM
Bone marrow	1.2 nTPM
Thymus	1.0 nTPM
Kidney	0.9 nTPM
Prostate	0.9 nTPM
Liver	0.6 nTPM

Undifferentiated cells	1.2 nTPM
Colon	1.8 nTPM
Rectum	1.3 nTPM
Small intestine	0.4 nTPM

Amygdala excitatory	2.4 nTPM
Hypothalamus	3.1 nTPM
Thalamus	2.7 nTPM
Cerebral cortex	2.5 nTPM
Basal ganglia	2.3 nTPM
Amygdala	2.0 nTPM
Hippocampus	2.0 nTPM

Astrocyte	0.3 nTPM
Thalamus	0.5 nTPM
Medulla oblongata	0.4 nTPM
Midbrain	0.4 nTPM
Pons	0.4 nTPM
Spinal cord	0.4 nTPM
Amygdala	0.2 nTPM
Basal ganglia	0.2 nTPM
Cerebral cortex	0.2 nTPM
Hippocampus	0.2 nTPM
Hypothalamus	0.2 nTPM
Cerebellum	0.1 nTPM

Bergmann glia	0.1 nTPM
Cerebellum	0.3 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	0.2 nTPM
Thalamus	0.7 nTPM
Hypothalamus	0.5 nTPM
Medulla oblongata	0.4 nTPM
Pons	0.4 nTPM
Midbrain	0.2 nTPM
Amygdala	0.1 nTPM
Basal ganglia	0.1 nTPM
Cerebral cortex	0.1 nTPM
Hippocampus	0.1 nTPM
Cerebellum	0.0 nTPM
Spinal cord	0.0 nTPM

Cerebellar inhibitory	5.5 nTPM
Midbrain	7.8 nTPM
Cerebellum	6.2 nTPM
Spinal cord	5.5 nTPM
Pons	4.2 nTPM
Medulla oblongata	3.7 nTPM

Cge interneuron	3.5 nTPM
Hippocampus	4.0 nTPM
Hypothalamus	4.0 nTPM
Cerebral cortex	3.8 nTPM
Basal ganglia	3.4 nTPM
Midbrain	3.4 nTPM
Amygdala	3.2 nTPM
Thalamus	2.7 nTPM

Choroid plexus epithelial cell	3.1 nTPM
Basal ganglia	3.8 nTPM
Medulla oblongata	3.1 nTPM
Hippocampus	2.8 nTPM
Thalamus	2.7 nTPM

Committed oligodendrocyte precursor	1.4 nTPM
Midbrain	3.4 nTPM
Medulla oblongata	2.6 nTPM
Cerebral cortex	2.5 nTPM
Basal ganglia	2.2 nTPM
Pons	1.8 nTPM
Hypothalamus	1.4 nTPM
Thalamus	1.4 nTPM
Hippocampus	0.3 nTPM
Amygdala	0.0 nTPM
Cerebellum	0.0 nTPM
Spinal cord	0.0 nTPM

Deep-layer corticothalamic and 6b	3.1 nTPM
Amygdala	4.0 nTPM
Hypothalamus	3.8 nTPM
Hippocampus	3.5 nTPM
Cerebral cortex	3.4 nTPM
Basal ganglia	3.0 nTPM
Midbrain	1.1 nTPM

Deep-layer intratelencephalic	2.9 nTPM
Amygdala	3.3 nTPM
Hypothalamus	3.3 nTPM
Cerebral cortex	3.0 nTPM
Hippocampus	2.5 nTPM
Basal ganglia	2.2 nTPM

Deep-layer near-projecting	3.3 nTPM
Hypothalamus	4.3 nTPM
Hippocampus	3.6 nTPM
Cerebral cortex	3.4 nTPM
Amygdala	2.9 nTPM
Basal ganglia	2.4 nTPM

Eccentric medium spiny neuron	3.4 nTPM
Hippocampus	4.1 nTPM
Cerebral cortex	3.9 nTPM
Hypothalamus	3.3 nTPM
Thalamus	3.1 nTPM
Amygdala	3.0 nTPM
Basal ganglia	2.9 nTPM

Endothelial cell	7.8 nTPM
Spinal cord	12.1 nTPM
Cerebellum	10.8 nTPM
Cerebral cortex	10.2 nTPM
Hypothalamus	8.7 nTPM
Hippocampus	8.0 nTPM
Thalamus	7.3 nTPM
Pons	6.9 nTPM
Basal ganglia	6.5 nTPM
Midbrain	5.7 nTPM
Amygdala	5.6 nTPM
Medulla oblongata	4.1 nTPM