Single cell type - ARFGEF3 - The Human Protein Atlas

ARFGEF3

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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.	ARFGEF3
Gene descriptionⁱ Full gene name according to HGNC.	ARFGEF family 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.	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.	Serous glandular cells - Salivary secretion (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 (Oligodendrocytes, Prostatic glandular cells, Inhibitory neurons, Excitatory neurons, Oligodendrocyte precursor cells, Serous glandular 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.	0.63
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.	Not detected in immune cells
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 (Oligodendrocytes, Prostatic glandular cells, Inhibitory neurons, Excitatory neurons, Oligodendrocyte precursor cells, Serous glandular 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: 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: Not detected in immune cells
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

ARFGEF3 is part of cluster 75 Serous glandular cells - Salivary secretion with confidenceⁱ 1
145 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.
ELAPOR1	Endosome-lysosome associated apoptosis and autophagy regulator 1	0.7645	75
RASAL1	RAS protein activator like 1	0.6097	75
CHRM1	Cholinergic receptor muscarinic 1	0.6069	40
ADGRG2	Adhesion G protein-coupled receptor G2	0.6058	75
DTNB	Dystrobrevin beta	0.6010	69
NXPE2	Neurexophilin and PC-esterase domain family member 2	0.5989	75
FOLH1	Folate hydrolase 1	0.5974	40
ARHGEF38	Rho guanine nucleotide exchange factor 38	0.5892	40
LMAN1L	Lectin, mannose binding 1 like	0.5876	75
LMX1B	LIM homeobox transcription factor 1 beta	0.5866	75
AZGP1	Alpha-2-glycoprotein 1, zinc-binding	0.5729	75
ZG16B	Zymogen granule protein 16B	0.5715	75
TMED3	Transmembrane p24 trafficking protein 3	0.5712	75
SMR3B	Submaxillary gland androgen regulated protein 3B	0.5708	75
OR5G3	Olfactory receptor family 5 subfamily G member 3 (gene/pseudogene)	0.5694	75

Adipocytes	9.9 nTPM
Adipose tissue	11.9 nTPM
Breast	7.9 nTPM

Alveolar cells type 1	15.1 nTPM
Lung	15.1 nTPM

Alveolar cells type 2	94.4 nTPM
Lung	94.4 nTPM

Astrocytes	32.5 nTPM
Brain	32.5 nTPM

B-cells	1.1 nTPM
Salivary gland	6.9 nTPM
Lung	4.0 nTPM
Skin	1.7 nTPM
Adipose tissue	1.6 nTPM
Thymus	0.3 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Ciliated cells	47.8 nTPM
Lung	96.9 nTPM
Bronchus	58.8 nTPM
Fallopian tube	26.8 nTPM
Endometrium	8.8 nTPM

Club cells	63.6 nTPM
Prostate	79.0 nTPM
Lung	77.5 nTPM
Bronchus	34.2 nTPM

Endothelial cells	13.1 nTPM
Lung	32.4 nTPM
Salivary gland	30.3 nTPM
Heart muscle	23.6 nTPM
Skeletal muscle	20.3 nTPM
Prostate	17.9 nTPM
Fallopian tube	16.4 nTPM
Endometrium	16.2 nTPM
Esophagus	14.6 nTPM
Thymus	14.6 nTPM
Vascular	13.2 nTPM
Tongue	11.9 nTPM
Skin	8.0 nTPM
Placenta	7.4 nTPM
Testis	5.5 nTPM
Ovary	2.3 nTPM
Breast	1.8 nTPM
Liver	0.0 nTPM
Pancreas	0.0 nTPM

Enteroendocrine cells	101.8 nTPM
Small intestine	144.2 nTPM
Rectum	144.2 nTPM
Colon	16.9 nTPM

Fibroblasts	2.6 nTPM
Skin	12.3 nTPM
Salivary gland	5.6 nTPM
Lung	4.4 nTPM
Liver	3.6 nTPM
Prostate	3.3 nTPM
Stomach	2.9 nTPM
Heart muscle	1.8 nTPM
Pancreas	1.8 nTPM
Breast	1.1 nTPM
Placenta	1.0 nTPM
Esophagus	0.9 nTPM
Vascular	0.9 nTPM
Thymus	0.6 nTPM
Fallopian tube	0.6 nTPM
Skeletal muscle	0.4 nTPM
Adipose tissue	0.0 nTPM

Granulocytes	2.0 nTPM
Lung	5.0 nTPM
Fallopian tube	1.0 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	68.2 nTPM
Rectum	82.0 nTPM
Small intestine	65.9 nTPM
Colon	56.8 nTPM

Lymphatic endothelial cells	5.3 nTPM
Ovary	5.5 nTPM
Fallopian tube	5.1 nTPM

Macrophages	1.8 nTPM
Salivary gland	25.0 nTPM
Pancreas	2.1 nTPM
Prostate	1.9 nTPM
Thymus	1.6 nTPM
Endometrium	1.2 nTPM
Skeletal muscle	0.9 nTPM
Lung	0.7 nTPM
Breast	0.7 nTPM
Fallopian tube	0.4 nTPM
Vascular	0.3 nTPM
Adipose tissue	0.2 nTPM
Testis	0.0 nTPM
Kidney	0.0 nTPM
Skin	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Tongue	0.0 nTPM

Paneth cells	14.4 nTPM
Rectum	18.2 nTPM
Colon	18.1 nTPM
Small intestine	6.9 nTPM

Basal prostatic cells	11.4 nTPM
Prostate	11.4 nTPM

Basal respiratory cells	15.5 nTPM
Bronchus	15.5 nTPM

Basal squamous epithelial cells	7.3 nTPM
Esophagus	7.3 nTPM

Bipolar cells	14.3 nTPM
Eye	14.3 nTPM

Plasma cells	6.8 nTPM
Salivary gland	27.8 nTPM
Fallopian tube	20.6 nTPM
Liver	1.5 nTPM
Bone marrow	1.5 nTPM
Spleen	1.4 nTPM
Stomach	0.8 nTPM
Thymus	0.7 nTPM
Esophagus	0.0 nTPM

Schwann cells	1.5 nTPM
Vascular	4.2 nTPM
Adipose tissue	0.4 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	162.3 nTPM
Salivary gland	258.3 nTPM
Tongue	66.3 nTPM

Smooth muscle cells	7.5 nTPM
Salivary gland	92.6 nTPM
Liver	11.5 nTPM
Skeletal muscle	4.8 nTPM
Prostate	3.6 nTPM
Tongue	1.8 nTPM
Lung	1.2 nTPM
Skin	0.9 nTPM
Fallopian tube	0.9 nTPM
Breast	0.8 nTPM
Endometrium	0.6 nTPM
Placenta	0.4 nTPM
Adipose tissue	0.4 nTPM
Vascular	0.3 nTPM
Thymus	0.1 nTPM
Ovary	0.1 nTPM
Esophagus	0.0 nTPM

T-cells	0.8 nTPM
Salivary gland	7.5 nTPM
Prostate	2.2 nTPM
Colon	1.0 nTPM
Endometrium	1.0 nTPM
Stomach	0.8 nTPM
Lung	0.8 nTPM
Skin	0.7 nTPM
Liver	0.6 nTPM
Breast	0.6 nTPM
Skeletal muscle	0.4 nTPM
Tongue	0.4 nTPM
Vascular	0.4 nTPM
Fallopian tube	0.4 nTPM
PBMC	0.2 nTPM
Adipose tissue	0.1 nTPM
Thymus	0.1 nTPM
Kidney	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Undifferentiated cells	19.4 nTPM
Rectum	27.3 nTPM
Small intestine	17.1 nTPM
Colon	13.8 nTPM

Amygdala excitatory	371.3 nTPM
Amygdala	421.0 nTPM
Hippocampus	410.8 nTPM
Hypothalamus	408.6 nTPM
Cerebral cortex	387.9 nTPM
Basal ganglia	364.8 nTPM
Thalamus	234.6 nTPM

Astrocyte	46.9 nTPM
Amygdala	81.0 nTPM
Hypothalamus	78.1 nTPM
Cerebral cortex	71.6 nTPM
Hippocampus	57.8 nTPM
Thalamus	54.9 nTPM
Basal ganglia	52.9 nTPM
Midbrain	44.3 nTPM
Pons	25.8 nTPM
Spinal cord	23.2 nTPM
Cerebellum	13.2 nTPM
Medulla oblongata	13.1 nTPM

Bergmann glia	5.5 nTPM
Cerebellum	8.6 nTPM
Pons	5.8 nTPM
Medulla oblongata	2.1 nTPM

Central nervous system macrophage	9.7 nTPM
Cerebral cortex	13.5 nTPM
Hypothalamus	12.7 nTPM
Amygdala	12.3 nTPM
Hippocampus	11.7 nTPM
Thalamus	11.7 nTPM
Spinal cord	10.0 nTPM
Midbrain	9.0 nTPM
Cerebellum	8.0 nTPM
Pons	6.8 nTPM
Medulla oblongata	5.7 nTPM
Basal ganglia	4.8 nTPM

Cerebellar inhibitory	148.7 nTPM
Spinal cord	187.0 nTPM
Midbrain	149.6 nTPM
Cerebellum	147.6 nTPM
Medulla oblongata	133.1 nTPM
Pons	126.1 nTPM

Cge interneuron	261.1 nTPM
Hypothalamus	339.3 nTPM
Amygdala	297.3 nTPM
Cerebral cortex	271.8 nTPM
Basal ganglia	252.0 nTPM
Hippocampus	251.5 nTPM
Midbrain	217.6 nTPM
Thalamus	197.9 nTPM

Choroid plexus epithelial cell	67.8 nTPM
Basal ganglia	102.4 nTPM
Thalamus	98.7 nTPM
Hippocampus	36.1 nTPM
Medulla oblongata	34.0 nTPM

Committed oligodendrocyte precursor	343.0 nTPM
Hypothalamus	592.0 nTPM
Thalamus	539.4 nTPM
Amygdala	510.3 nTPM
Cerebral cortex	362.3 nTPM
Hippocampus	335.5 nTPM
Basal ganglia	313.7 nTPM
Cerebellum	260.0 nTPM
Midbrain	256.2 nTPM
Spinal cord	235.5 nTPM
Pons	213.4 nTPM
Medulla oblongata	154.9 nTPM

Deep-layer corticothalamic and 6b	324.2 nTPM
Hypothalamus	441.2 nTPM
Amygdala	349.4 nTPM
Cerebral cortex	312.2 nTPM
Basal ganglia	302.3 nTPM
Midbrain	288.4 nTPM
Hippocampus	251.7 nTPM

Deep-layer intratelencephalic	308.3 nTPM
Amygdala	375.1 nTPM
Hypothalamus	357.2 nTPM
Hippocampus	299.8 nTPM
Cerebral cortex	254.9 nTPM
Basal ganglia	254.7 nTPM

Deep-layer near-projecting	203.1 nTPM
Hypothalamus	285.5 nTPM
Amygdala	229.1 nTPM
Basal ganglia	195.6 nTPM
Cerebral cortex	168.9 nTPM
Hippocampus	136.6 nTPM

Eccentric medium spiny neuron	253.6 nTPM
Hypothalamus	286.6 nTPM
Amygdala	281.9 nTPM
Cerebral cortex	255.6 nTPM
Hippocampus	241.7 nTPM
Thalamus	236.5 nTPM
Basal ganglia	219.2 nTPM

Endothelial cell	166.6 nTPM
Amygdala	199.0 nTPM
Hippocampus	178.2 nTPM
Pons	174.1 nTPM
Midbrain	173.9 nTPM
Cerebral cortex	173.3 nTPM
Thalamus	172.3 nTPM
Cerebellum	171.9 nTPM
Spinal cord	157.1 nTPM
Basal ganglia	156.6 nTPM
Hypothalamus	155.1 nTPM
Medulla oblongata	121.0 nTPM

Ependymal cell	14.6 nTPM
Amygdala	22.8 nTPM
Hypothalamus	21.4 nTPM
Basal ganglia	18.4 nTPM
Thalamus	16.2 nTPM
Hippocampus	12.9 nTPM
Medulla oblongata	11.4 nTPM
Pons	11.4 nTPM
Spinal cord	9.6 nTPM
Midbrain	7.0 nTPM