Single cell type - RAPGEF1 - The Human Protein Atlas

RAPGEF1

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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.	RAPGEF1
Gene descriptionⁱ Full gene name according to HGNC.	Rap guanine nucleotide exchange factor 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Plasma proteins
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.	Dendritic cells - Antigen presentation (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, Langerhans cells, Microglial 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.	0.43
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.	Cell type enhanced (Central nervous system macrophage)
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 (memory B-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 enhanced (Monocytes, Langerhans cells, Microglial 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: Cell type enhanced (Central nervous system macrophage)

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 (memory B-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

RAPGEF1 is part of cluster 28 Dendritic cells - Antigen presentation with confidenceⁱ 1
245 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.
EIF2AK4	Eukaryotic translation initiation factor 2 alpha kinase 4	0.6162	28
KLHL6	Kelch like family member 6	0.6134	28
ST8SIA4	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	0.5867	28
PTPN1	Protein tyrosine phosphatase non-receptor type 1	0.5545	28
EDEM1	ER degradation enhancing alpha-mannosidase like protein 1	0.5446	28
TAMALIN	Trafficking regulator and scaffold protein tamalin	0.5382	28
CFLAR	CASP8 and FADD like apoptosis regulator	0.5276	29
TAF5L	TATA-box binding protein associated factor 5 like	0.5240	28
HLA-DQA2	Major histocompatibility complex, class II, DQ alpha 2	0.5230	28
GNA12	G protein subunit alpha 12	0.5153	28
SERPINB9	Serpin family B member 9	0.5146	28
MAPK9	Mitogen-activated protein kinase 9	0.5135	28
HLA-DQB1	Major histocompatibility complex, class II, DQ beta 1	0.5085	28
HLA-DPA1	Major histocompatibility complex, class II, DP alpha 1	0.5042	28
FLT3	Fms related receptor tyrosine kinase 3	0.5015	28

IMMUNE CELLS

RAPGEF1 is part of cluster 32 Basophils - Transcription with confidenceⁱ 0.95
291 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.
ZSCAN12	Zinc finger and SCAN domain containing 12	1.0000	32
CSNK1G3	Casein kinase 1 gamma 3	1.0000	32
FBXW11	F-box and WD repeat domain containing 11	0.9762	32
CIPC	CLOCK interacting pacemaker	0.9762	32
ZNF3	Zinc finger protein 3	0.9762	32
BTAF1	B-TFIID TATA-box binding protein associated factor 1	0.9762	32
TJAP1	Tight junction associated protein 1	0.9524	32
SPCS2	Signal peptidase complex subunit 2	0.9524	32
ZNF547	Zinc finger protein 547	0.9524	32
FAIM	Fas apoptotic inhibitory molecule	0.9524	32
ZBTB39	Zinc finger and BTB domain containing 39	0.9524	32
UBA6	Ubiquitin like modifier activating enzyme 6	0.9524	32
NT5C	5', 3'-nucleotidase, cytosolic	0.9286	32
DYNC2LI1	Dynein cytoplasmic 2 light intermediate chain 1	0.9286	32
TCF7L1	Transcription factor 7 like 1	0.9286	32

Adipocytes	63.5 nTPM
Adipose tissue	66.6 nTPM
Breast	60.4 nTPM

Alveolar cells type 1	35.2 nTPM
Lung	35.2 nTPM

Alveolar cells type 2	14.0 nTPM
Lung	14.0 nTPM

Astrocytes	25.7 nTPM
Brain	25.7 nTPM

B-cells	42.4 nTPM
Adipose tissue	108.2 nTPM
Thymus	76.3 nTPM
Salivary gland	67.8 nTPM
Skin	66.1 nTPM
Esophagus	47.2 nTPM
Lung	32.2 nTPM
Stomach	31.6 nTPM
Spleen	27.2 nTPM
Lymph node	26.5 nTPM
PBMC	21.6 nTPM
Bone marrow	21.3 nTPM
Liver	14.5 nTPM
Kidney	10.4 nTPM

Ciliated cells	19.0 nTPM
Lung	28.9 nTPM
Fallopian tube	20.7 nTPM
Endometrium	14.6 nTPM
Bronchus	11.8 nTPM

Club cells	12.0 nTPM
Lung	21.1 nTPM
Bronchus	7.5 nTPM
Prostate	7.5 nTPM

Dendritic cells	73.9 nTPM
Adipose tissue	129.8 nTPM
PBMC	18.0 nTPM

Endothelial cells	43.1 nTPM
Skeletal muscle	96.0 nTPM
Lung	87.0 nTPM
Heart muscle	56.8 nTPM
Salivary gland	55.1 nTPM
Vascular	53.4 nTPM
Tongue	52.8 nTPM
Pancreas	49.1 nTPM
Thymus	47.8 nTPM
Fallopian tube	37.9 nTPM
Liver	37.8 nTPM
Prostate	35.4 nTPM
Placenta	31.2 nTPM
Skin	27.9 nTPM
Esophagus	26.7 nTPM
Endometrium	23.9 nTPM
Ovary	21.1 nTPM
Breast	19.3 nTPM
Testis	16.8 nTPM

Enteroendocrine cells	15.8 nTPM
Small intestine	24.0 nTPM
Rectum	15.1 nTPM
Colon	8.3 nTPM

Fibroblasts	13.5 nTPM
Liver	23.7 nTPM
Salivary gland	23.1 nTPM
Adipose tissue	19.8 nTPM
Skeletal muscle	19.1 nTPM
Vascular	16.6 nTPM
Lung	15.5 nTPM
Thymus	15.5 nTPM
Stomach	14.4 nTPM
Heart muscle	11.5 nTPM
Skin	11.1 nTPM
Breast	9.4 nTPM
Fallopian tube	8.2 nTPM
Placenta	8.0 nTPM
Prostate	7.9 nTPM
Pancreas	6.9 nTPM
Esophagus	5.4 nTPM

Granulocytes	15.9 nTPM
Lung	19.7 nTPM
Tongue	14.6 nTPM
Fallopian tube	13.6 nTPM

Intestinal goblet cells	12.9 nTPM
Small intestine	16.9 nTPM
Rectum	12.4 nTPM
Colon	9.3 nTPM

Lymphatic endothelial cells	23.2 nTPM
Ovary	27.3 nTPM
Fallopian tube	19.1 nTPM

Macrophages	62.5 nTPM
Adipose tissue	157.3 nTPM
Fallopian tube	105.6 nTPM
Lung	95.9 nTPM
Tongue	83.7 nTPM
Skeletal muscle	77.0 nTPM
Salivary gland	75.4 nTPM
Endometrium	69.5 nTPM
Prostate	62.4 nTPM
Thymus	60.1 nTPM
Pancreas	59.6 nTPM
Vascular	56.6 nTPM
Skin	54.6 nTPM
Esophagus	45.0 nTPM
Breast	44.4 nTPM
Stomach	36.0 nTPM
Spleen	32.1 nTPM
Bone marrow	29.4 nTPM
Kidney	27.4 nTPM
Testis	15.5 nTPM

Basal prostatic cells	15.0 nTPM
Prostate	15.0 nTPM

Basal respiratory cells	11.3 nTPM
Bronchus	11.3 nTPM

Basal squamous epithelial cells	4.9 nTPM
Esophagus	4.9 nTPM

Bipolar cells	17.1 nTPM
Eye	17.1 nTPM

Paneth cells	16.1 nTPM
Colon	21.7 nTPM
Small intestine	13.8 nTPM
Rectum	12.9 nTPM

Plasma cells	79.0 nTPM
Fallopian tube	146.0 nTPM
Stomach	127.7 nTPM
Esophagus	114.4 nTPM
Salivary gland	112.4 nTPM
Thymus	52.8 nTPM
Spleen	44.5 nTPM
Liver	20.5 nTPM
Bone marrow	13.6 nTPM

Schwann cells	49.2 nTPM
Adipose tissue	133.9 nTPM
Vascular	13.6 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	23.9 nTPM
Tongue	26.5 nTPM
Salivary gland	21.3 nTPM

Smooth muscle cells	15.2 nTPM
Skeletal muscle	26.0 nTPM
Lung	24.7 nTPM
Salivary gland	24.3 nTPM
Vascular	22.8 nTPM
Tongue	18.6 nTPM
Liver	16.1 nTPM
Prostate	15.8 nTPM
Thymus	15.2 nTPM
Breast	15.2 nTPM
Fallopian tube	13.0 nTPM
Adipose tissue	10.5 nTPM
Endometrium	9.2 nTPM
Esophagus	8.4 nTPM
Ovary	8.3 nTPM
Skin	7.8 nTPM
Placenta	6.8 nTPM

T-cells	33.9 nTPM
Adipose tissue	72.0 nTPM
Vascular	57.5 nTPM
Fallopian tube	56.0 nTPM
Tongue	55.9 nTPM
Skeletal muscle	54.1 nTPM
Thymus	43.0 nTPM
Lung	41.2 nTPM
Breast	40.6 nTPM
Endometrium	39.3 nTPM
Prostate	33.1 nTPM
Salivary gland	32.4 nTPM
Stomach	24.6 nTPM
Liver	23.0 nTPM
Spleen	21.9 nTPM
Skin	20.7 nTPM
Colon	20.5 nTPM
Bone marrow	19.3 nTPM
Lymph node	18.5 nTPM
PBMC	14.8 nTPM
Esophagus	12.2 nTPM
Kidney	10.6 nTPM

Undifferentiated cells	8.4 nTPM
Rectum	10.7 nTPM
Small intestine	8.9 nTPM
Colon	5.5 nTPM

Amygdala excitatory	89.7 nTPM
Hypothalamus	140.0 nTPM
Amygdala	87.7 nTPM
Basal ganglia	82.5 nTPM
Cerebral cortex	77.9 nTPM
Hippocampus	75.4 nTPM
Thalamus	74.9 nTPM

Astrocyte	82.2 nTPM
Hypothalamus	97.1 nTPM
Amygdala	93.6 nTPM
Cerebellum	91.3 nTPM
Spinal cord	90.5 nTPM
Midbrain	80.9 nTPM
Thalamus	79.1 nTPM
Medulla oblongata	78.7 nTPM
Pons	77.5 nTPM
Hippocampus	73.8 nTPM
Basal ganglia	72.3 nTPM
Cerebral cortex	69.6 nTPM

Bergmann glia	74.4 nTPM
Pons	92.1 nTPM
Cerebellum	86.5 nTPM
Medulla oblongata	44.8 nTPM

Central nervous system macrophage	699.4 nTPM
Hypothalamus	860.8 nTPM
Spinal cord	847.5 nTPM
Amygdala	801.6 nTPM
Hippocampus	712.1 nTPM
Pons	693.2 nTPM
Midbrain	692.7 nTPM
Thalamus	651.2 nTPM
Cerebral cortex	627.0 nTPM
Medulla oblongata	622.4 nTPM
Cerebellum	594.9 nTPM
Basal ganglia	590.3 nTPM

Cerebellar inhibitory	67.0 nTPM
Spinal cord	79.7 nTPM
Cerebellum	66.2 nTPM
Pons	65.8 nTPM
Medulla oblongata	65.4 nTPM
Midbrain	58.2 nTPM

Cge interneuron	88.5 nTPM
Hypothalamus	127.4 nTPM
Amygdala	90.4 nTPM
Cerebral cortex	86.9 nTPM
Hippocampus	84.6 nTPM
Basal ganglia	79.9 nTPM
Thalamus	76.0 nTPM
Midbrain	74.1 nTPM

Choroid plexus epithelial cell	230.1 nTPM
Basal ganglia	426.9 nTPM
Medulla oblongata	171.1 nTPM
Hippocampus	163.6 nTPM
Thalamus	158.9 nTPM

Committed oligodendrocyte precursor	480.6 nTPM
Hippocampus	1013.3 nTPM
Cerebral cortex	701.1 nTPM
Cerebellum	632.6 nTPM
Spinal cord	573.9 nTPM
Midbrain	484.7 nTPM
Amygdala	479.3 nTPM
Basal ganglia	428.2 nTPM
Pons	376.3 nTPM
Hypothalamus	240.3 nTPM
Medulla oblongata	229.8 nTPM
Thalamus	127.2 nTPM

Deep-layer corticothalamic and 6b	104.7 nTPM
Hypothalamus	156.2 nTPM
Amygdala	113.7 nTPM
Cerebral cortex	102.8 nTPM
Hippocampus	95.3 nTPM
Basal ganglia	88.9 nTPM
Midbrain	71.0 nTPM

Deep-layer intratelencephalic	94.8 nTPM
Hypothalamus	143.1 nTPM
Amygdala	86.9 nTPM
Cerebral cortex	84.0 nTPM
Hippocampus	81.0 nTPM
Basal ganglia	78.8 nTPM

Deep-layer near-projecting	83.4 nTPM
Hypothalamus	128.6 nTPM
Amygdala	84.0 nTPM
Cerebral cortex	76.3 nTPM
Basal ganglia	72.0 nTPM
Hippocampus	55.9 nTPM

Eccentric medium spiny neuron	136.4 nTPM
Hypothalamus	154.6 nTPM
Basal ganglia	147.1 nTPM
Cerebral cortex	141.1 nTPM
Thalamus	138.8 nTPM
Amygdala	123.1 nTPM
Hippocampus	113.6 nTPM

Endothelial cell	553.5 nTPM
Basal ganglia	881.8 nTPM
Hypothalamus	807.7 nTPM
Amygdala	625.9 nTPM
Pons	559.9 nTPM
Cerebral cortex	512.7 nTPM
Hippocampus	507.5 nTPM
Cerebellum	470.0 nTPM
Midbrain	448.0 nTPM
Thalamus	441.7 nTPM
Spinal cord	433.2 nTPM
Medulla oblongata	400.0 nTPM