Single cell type - RAP1B - The Human Protein Atlas

RAP1B

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Cluster

Pathway

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.	RAP1B
Gene descriptionⁱ Full gene name according to HGNC.	RAP1B, member of RAS oncogene family
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Enzymes Plasma proteins RAS pathway related 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.	28

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.	Platelets - Hemostasis (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, NK-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.	0.32
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 (Leukocyte)
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.	Low immune cell specificity
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, NK-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 (Leukocyte)

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: Low immune cell specificity
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

RAP1B is part of cluster 57 Platelets - Hemostasis with confidenceⁱ 1
173 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.
NCOA4	Nuclear receptor coactivator 4	0.7288	57
GRAP2	GRB2 related adaptor protein 2	0.7198	57
PF4V1	Platelet factor 4 variant 1	0.7190	57
PTPN18	Protein tyrosine phosphatase non-receptor type 18	0.7089	57
TUBB1	Tubulin beta 1 class VI	0.7086	57
FERMT3	FERM domain containing kindlin 3	0.7053	57
LY6G6F	Lymphocyte antigen 6 family member G6F	0.7047	57
RUFY1	RUN and FYVE domain containing 1	0.7043	57
PF4	Platelet factor 4	0.7041	57
GP9	Glycoprotein IX platelet	0.7036	57
NT5C3A	5'-nucleotidase, cytosolic IIIA	0.7025	57
PPBP	Pro-platelet basic protein	0.7024	57
MMD	Monocyte to macrophage differentiation associated	0.7020	57
H2AC6	H2A clustered histone 6	0.7003	57
ITGA2B	Integrin subunit alpha 2b	0.6976	57

IMMUNE CELLS

RAP1B is part of cluster 28 Neutrophils - Unknown function with confidenceⁱ 0.81
118 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.
KCTD10	Potassium channel tetramerization domain containing 10	0.9524	33
NT5C2	5'-nucleotidase, cytosolic II	0.9286	28
ARFGAP3	ADP ribosylation factor GTPase activating protein 3	0.9048	37
HOXA1	Homeobox A1	0.9048	28
XAF1	XIAP associated factor 1	0.9048	28
ACBD5	Acyl-CoA binding domain containing 5	0.9048	28
WDR37	WD repeat domain 37	0.8810	15
SMAD2	SMAD family member 2	0.8810	33
PDXK	Pyridoxal kinase	0.8810	37
VPS26A	VPS26 retromer complex component A	0.8810	42
ETF1	Eukaryotic translation termination factor 1	0.8571	38
DTD1	D-aminoacyl-tRNA deacylase 1	0.8571	15
CHN2	Chimerin 2	0.8571	40
GPR65	G protein-coupled receptor 65	0.8571	5
GRAMD1A	GRAM domain containing 1A	0.8571	28

Adipocytes	190.2 nTPM
Adipose tissue	234.5 nTPM
Breast	145.9 nTPM

Alveolar cells type 1	66.7 nTPM
Lung	66.7 nTPM

Alveolar cells type 2	67.1 nTPM
Lung	67.1 nTPM

Astrocytes	39.0 nTPM
Brain	39.0 nTPM

B-cells	177.0 nTPM
Adipose tissue	365.0 nTPM
Skin	269.3 nTPM
PBMC	197.0 nTPM
Stomach	195.3 nTPM
Spleen	179.2 nTPM
Liver	159.4 nTPM
Bone marrow	158.0 nTPM
Salivary gland	157.1 nTPM
Thymus	155.7 nTPM
Lung	154.3 nTPM
Kidney	124.8 nTPM
Lymph node	109.6 nTPM
Esophagus	76.7 nTPM

Ciliated cells	87.0 nTPM
Bronchus	104.9 nTPM
Fallopian tube	100.2 nTPM
Endometrium	72.1 nTPM
Lung	70.9 nTPM

Club cells	104.4 nTPM
Bronchus	132.3 nTPM
Prostate	90.8 nTPM
Lung	90.2 nTPM

Dendritic cells	213.7 nTPM
Adipose tissue	279.9 nTPM
PBMC	147.5 nTPM

Endothelial cells	162.8 nTPM
Skin	336.2 nTPM
Fallopian tube	243.6 nTPM
Lung	218.6 nTPM
Pancreas	209.4 nTPM
Skeletal muscle	179.4 nTPM
Thymus	176.8 nTPM
Vascular	170.2 nTPM
Breast	162.6 nTPM
Salivary gland	159.3 nTPM
Esophagus	150.3 nTPM
Placenta	138.0 nTPM
Testis	129.7 nTPM
Prostate	128.0 nTPM
Endometrium	117.3 nTPM
Heart muscle	116.7 nTPM
Tongue	110.6 nTPM
Liver	94.5 nTPM
Ovary	90.2 nTPM

Enteroendocrine cells	123.7 nTPM
Rectum	139.2 nTPM
Colon	128.9 nTPM
Small intestine	103.0 nTPM

Erythroid cells	133.5 nTPM
Bone marrow	148.2 nTPM
Liver	118.9 nTPM

Fibroblasts	149.0 nTPM
Adipose tissue	231.7 nTPM
Pancreas	220.4 nTPM
Skin	216.2 nTPM
Liver	200.4 nTPM
Skeletal muscle	194.7 nTPM
Fallopian tube	174.7 nTPM
Stomach	152.8 nTPM
Placenta	137.7 nTPM
Vascular	125.4 nTPM
Esophagus	120.8 nTPM
Salivary gland	112.1 nTPM
Breast	111.5 nTPM
Thymus	110.7 nTPM
Lung	100.4 nTPM
Prostate	91.1 nTPM
Heart muscle	84.1 nTPM

Granulocytes	157.6 nTPM
Fallopian tube	233.5 nTPM
Tongue	121.3 nTPM
Lung	118.0 nTPM

Intestinal goblet cells	85.0 nTPM
Colon	112.7 nTPM
Small intestine	74.6 nTPM
Rectum	67.7 nTPM

Lymphatic endothelial cells	161.4 nTPM
Fallopian tube	230.0 nTPM
Ovary	92.7 nTPM

Basal keratinocytes	188.4 nTPM
Skin	287.0 nTPM
Tongue	89.9 nTPM

Basal prostatic cells	78.9 nTPM
Prostate	78.9 nTPM

Basal respiratory cells	144.2 nTPM
Bronchus	144.2 nTPM

Basal squamous epithelial cells	74.2 nTPM
Esophagus	74.2 nTPM

Macrophages	249.8 nTPM
Adipose tissue	495.6 nTPM
Stomach	406.4 nTPM
Fallopian tube	382.6 nTPM
Spleen	353.9 nTPM
Kidney	297.4 nTPM
Lung	284.0 nTPM
Bone marrow	283.8 nTPM
Vascular	262.0 nTPM
Skeletal muscle	253.0 nTPM
Skin	235.1 nTPM
Testis	203.3 nTPM
Thymus	202.4 nTPM
Endometrium	191.3 nTPM
Pancreas	168.6 nTPM
Tongue	158.4 nTPM
Breast	147.1 nTPM
Esophagus	143.9 nTPM
Prostate	141.1 nTPM
Salivary gland	137.2 nTPM

Paneth cells	136.1 nTPM
Colon	199.0 nTPM
Small intestine	110.5 nTPM
Rectum	98.8 nTPM

Plasma cells	203.1 nTPM
Stomach	342.2 nTPM
Fallopian tube	321.6 nTPM
Thymus	195.0 nTPM
Salivary gland	180.0 nTPM
Spleen	179.9 nTPM
Bone marrow	155.5 nTPM
Esophagus	129.9 nTPM
Liver	120.7 nTPM

Schwann cells	158.2 nTPM
Adipose tissue	304.5 nTPM
Vascular	86.2 nTPM
Esophagus	83.9 nTPM

Serous glandular cells	66.3 nTPM
Salivary gland	75.2 nTPM
Tongue	57.4 nTPM

Smooth muscle cells	133.3 nTPM
Skin	247.7 nTPM
Adipose tissue	173.5 nTPM
Placenta	169.7 nTPM
Fallopian tube	169.7 nTPM
Skeletal muscle	139.4 nTPM
Esophagus	128.5 nTPM
Vascular	126.4 nTPM
Breast	124.6 nTPM
Prostate	122.9 nTPM
Endometrium	120.7 nTPM
Liver	118.4 nTPM
Thymus	112.9 nTPM
Ovary	99.5 nTPM
Lung	97.6 nTPM
Tongue	92.8 nTPM
Salivary gland	88.5 nTPM

Suprabasal keratinocytes	164.7 nTPM
Skin	260.1 nTPM
Tongue	69.4 nTPM

T-cells	285.2 nTPM
Adipose tissue	434.0 nTPM
Kidney	374.2 nTPM
Liver	362.6 nTPM
Fallopian tube	349.1 nTPM
Lung	339.5 nTPM
PBMC	324.0 nTPM
Spleen	317.5 nTPM
Bone marrow	298.6 nTPM
Skin	293.0 nTPM
Skeletal muscle	290.0 nTPM
Stomach	281.5 nTPM
Tongue	272.1 nTPM
Prostate	270.6 nTPM
Colon	269.1 nTPM
Thymus	252.9 nTPM
Breast	249.8 nTPM
Vascular	229.1 nTPM
Salivary gland	228.9 nTPM
Esophagus	187.4 nTPM
Lymph node	186.5 nTPM
Endometrium	179.9 nTPM

Undifferentiated cells	66.7 nTPM
Colon	79.5 nTPM
Small intestine	66.5 nTPM
Rectum	54.0 nTPM

Amygdala excitatory	58.8 nTPM
Amygdala	67.2 nTPM
Hypothalamus	64.6 nTPM
Thalamus	59.9 nTPM
Cerebral cortex	55.7 nTPM
Hippocampus	54.1 nTPM
Basal ganglia	51.5 nTPM

Astrocyte	76.7 nTPM
Spinal cord	104.8 nTPM
Amygdala	96.4 nTPM
Hypothalamus	95.8 nTPM
Basal ganglia	74.8 nTPM
Hippocampus	74.3 nTPM
Cerebral cortex	73.7 nTPM
Medulla oblongata	68.9 nTPM
Thalamus	66.3 nTPM
Pons	65.5 nTPM
Midbrain	65.2 nTPM
Cerebellum	58.4 nTPM

Bergmann glia	94.0 nTPM
Pons	107.9 nTPM
Cerebellum	97.5 nTPM
Medulla oblongata	76.7 nTPM

Central nervous system macrophage	251.4 nTPM
Amygdala	318.2 nTPM
Hypothalamus	283.6 nTPM
Spinal cord	256.1 nTPM
Basal ganglia	252.4 nTPM
Hippocampus	252.0 nTPM
Midbrain	248.4 nTPM
Pons	243.7 nTPM
Cerebellum	240.0 nTPM
Thalamus	235.6 nTPM
Cerebral cortex	218.0 nTPM
Medulla oblongata	217.1 nTPM

Cerebellar inhibitory	60.3 nTPM
Medulla oblongata	65.9 nTPM
Cerebellum	64.7 nTPM
Spinal cord	60.5 nTPM
Pons	55.4 nTPM
Midbrain	55.1 nTPM

Cge interneuron	48.6 nTPM
Hypothalamus	54.8 nTPM
Amygdala	53.2 nTPM
Thalamus	49.4 nTPM
Basal ganglia	46.7 nTPM
Cerebral cortex	46.3 nTPM
Midbrain	45.6 nTPM
Hippocampus	44.4 nTPM

Choroid plexus epithelial cell	134.6 nTPM
Basal ganglia	189.0 nTPM
Medulla oblongata	140.0 nTPM
Thalamus	120.6 nTPM
Hippocampus	88.7 nTPM

Committed oligodendrocyte precursor	62.8 nTPM
Cerebellum	74.5 nTPM
Hypothalamus	69.0 nTPM
Amygdala	67.7 nTPM
Thalamus	64.6 nTPM
Basal ganglia	62.4 nTPM
Hippocampus	62.3 nTPM
Medulla oblongata	62.0 nTPM
Midbrain	59.6 nTPM
Spinal cord	58.9 nTPM
Pons	56.7 nTPM
Cerebral cortex	53.2 nTPM

Deep-layer corticothalamic and 6b	59.0 nTPM
Amygdala	69.8 nTPM
Hypothalamus	63.6 nTPM
Basal ganglia	58.2 nTPM
Cerebral cortex	57.3 nTPM
Hippocampus	52.9 nTPM
Midbrain	52.1 nTPM

Deep-layer intratelencephalic	57.8 nTPM
Hippocampus	62.5 nTPM
Hypothalamus	59.8 nTPM
Amygdala	59.2 nTPM
Cerebral cortex	55.0 nTPM
Basal ganglia	52.4 nTPM

Deep-layer near-projecting	46.3 nTPM
Amygdala	56.6 nTPM
Hypothalamus	52.0 nTPM
Cerebral cortex	46.6 nTPM
Basal ganglia	44.1 nTPM
Hippocampus	32.2 nTPM