Single cell type - RABGEF1 - The Human Protein Atlas

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.	RABGEF1
Gene descriptionⁱ Full gene name according to HGNC.	RAB guanine nucleotide exchange factor 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Transporters
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. Read more	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	4

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. Read more	Oligodendrocytes - Myelin sheath organization (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. Read more	Cell type enhanced (Oligodendrocytes, Inhibitory neurons, Excitatory neurons, Oligodendrocyte precursor cells, Astrocytes)
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. Read more	Low immune cell specificity
Immune cell distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in all
Cell line specificityⁱ RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines. Read more	Low cell line specificity
Cell line distributionⁱ RNA distribution category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into five different categories (detected in all, detected in many, detected in some, detected in single and not detected) according to their pattern of detected RNA expression across the panel of cell lines. Read more	Detected in all
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); a Human Protein Atlas antibody- or RNA based score (HPA evidence); and evidence based on PeptideAtlas (MS evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable. Read more	Evidence at protein level

SINGLE CELL TYPESⁱ A summary of 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 Group Expression Alphabetical RNA single cell type specificity: Cell type enhanced (Oligodendrocytes, Inhibitory neurons, Excitatory neurons, Oligodendrocyte precursor cells, Astrocytes)

SINGLE CELL TISSUES OVERVIEWⁱ An overview of all tissues where single cell type expression has been analyzed. Each tissue name and corresponding UMAP plot is clickable and redirects to the selected tissue.
Adipose tissue Bone marrow Brain Breast Bronchus Colon Endometrium Esophagus Eye Heart muscle Kidney Liver Lung Lymph node Ovary Pancreas Placenta Prostate Rectum Skeletal muscle Skin Small intestine Spleen Stomach Testis

EXPRESSION CLUSTERING & CORRELATIONⁱ

RABGEF1 is part of cluster 42 Oligodendrocytes - Myelin sheath organization with confidenceⁱ 1
385 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell type 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. Read more	Clusterⁱ ID of the expression cluster of the neighboring gene. Read more
AUTS2	Activator of transcription and developmental regulator AUTS2	0.6927	8
RSC1A1	Regulator of solute carriers 1	0.6795	42
REPS2	RALBP1 associated Eps domain containing 2	0.6760	42
DIP2C	Disco interacting protein 2 homolog C	0.6738	42
SAMD12	Sterile alpha motif domain containing 12	0.6555	42
IL1RAPL1	Interleukin 1 receptor accessory protein like 1	0.6437	8
GRID1	Glutamate ionotropic receptor delta type subunit 1	0.6426	42
ENOX1	Ecto-NOX disulfide-thiol exchanger 1	0.6419	42
SIK3	SIK family kinase 3	0.6313	42
ZNF782	Zinc finger protein 782	0.6214	42
ANKIB1	Ankyrin repeat and IBR domain containing 1	0.6203	42
PPM1H	Protein phosphatase, Mg2+/Mn2+ dependent 1H	0.6184	42
DOCK3	Dedicator of cytokinesis 3	0.6177	8
DTNB	Dystrobrevin beta	0.6155	42
MTMR7	Myotubularin related protein 7	0.6155	8

SINGLE CELL TISSUESⁱ Single cell RNA levels of annotated cell type clusters are shown separately for each analyzed tissue. For easier navigation across tissues, use the above Single cell tissue overview, where each tissue name and UMAP plot is clickable and redirects to the selected tissue, alternatively the grey browser on the left side of the window. Barchart shows nTPM levels in each annotated cluster of single cells. To the left, a UMAP plot illustrates the RNA expression profile. The tissue name and plots are clickable and redirect to a more detailed interactive page. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. Please note that the same cell type may be found in several clusters.
Cluster Expression Alphabetical Adipose tissue
Cluster Expression Alphabetical Bone marrow
Cluster Expression Alphabetical Brain
Cluster Expression Alphabetical Breast
Cluster Expression Alphabetical Bronchus
Cluster Expression Alphabetical Colon
Cluster Expression Alphabetical Endometrium
Cluster Expression Alphabetical Esophagus
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Lymph node
Cluster Expression Alphabetical Ovary
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skeletal muscle
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Spleen
Cluster Expression Alphabetical Stomach
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ

Organ

Expression

Alphabetical

Adipocytes	7.3 nTPM
Adipose tissue	9.9 nTPM
Breast	4.7 nTPM

Alveolar cells type 1	12.8 nTPM
Lung	12.8 nTPM

Alveolar cells type 2	12.8 nTPM
Lung	12.8 nTPM

B-cells	11.5 nTPM
Stomach	25.9 nTPM
Adipose tissue	18.0 nTPM
Spleen	18.0 nTPM
Lymph node	12.6 nTPM
Bone marrow	9.8 nTPM
PBMC	7.1 nTPM
Breast	6.6 nTPM
Colon	6.4 nTPM
Liver	5.5 nTPM
Kidney	4.8 nTPM

Basal keratinocytes	4.1 nTPM
Skin	4.1 nTPM

Dendritic cells	13.2 nTPM
Adipose tissue	28.7 nTPM
Breast	6.9 nTPM
PBMC	4.0 nTPM

Endothelial cells	5.7 nTPM
Testis	9.8 nTPM
Prostate	8.8 nTPM
Eye	8.1 nTPM
Pancreas	7.7 nTPM
Breast	7.5 nTPM
Endometrium	7.4 nTPM
Lung	6.2 nTPM
Esophagus	5.8 nTPM
Skeletal muscle	4.5 nTPM
Liver	3.7 nTPM
Ovary	3.2 nTPM
Heart muscle	2.4 nTPM
Skin	2.3 nTPM
Placenta	2.2 nTPM

Fibroblasts	14.6 nTPM
Stomach	38.6 nTPM
Lung	36.9 nTPM
Prostate	21.3 nTPM
Adipose tissue	16.6 nTPM
Skeletal muscle	11.5 nTPM
Breast	7.9 nTPM
Esophagus	7.1 nTPM
Placenta	6.8 nTPM
Skin	5.8 nTPM
Heart muscle	4.2 nTPM
Ovary	3.8 nTPM

Intestinal goblet cells	4.3 nTPM
Rectum	6.1 nTPM
Colon	5.8 nTPM
Small intestine	1.1 nTPM

Macrophages	19.9 nTPM
Adipose tissue	53.7 nTPM
Stomach	49.8 nTPM
Endometrium	37.9 nTPM
Skeletal muscle	34.2 nTPM
Spleen	32.1 nTPM
Lung	17.3 nTPM
PBMC	13.6 nTPM
Pancreas	12.8 nTPM
Prostate	11.5 nTPM
Breast	10.8 nTPM
Kidney	9.1 nTPM
Bone marrow	7.5 nTPM
Ovary	6.4 nTPM
Testis	2.3 nTPM
Esophagus	0.0 nTPM

Paneth cells	13.4 nTPM
Colon	19.7 nTPM
Small intestine	15.0 nTPM
Rectum	5.5 nTPM

Plasma cells	15.2 nTPM
Esophagus	18.4 nTPM
Stomach	17.4 nTPM
Adipose tissue	16.1 nTPM
Spleen	14.1 nTPM
Bone marrow	9.9 nTPM

Respiratory ciliated cells	11.9 nTPM
Lung	21.9 nTPM
Bronchus	2.0 nTPM

Smooth muscle cells	8.5 nTPM
Esophagus	14.0 nTPM
Adipose tissue	13.3 nTPM
Heart muscle	12.8 nTPM
Prostate	11.2 nTPM
Endometrium	9.4 nTPM
Pancreas	8.4 nTPM
Skeletal muscle	7.0 nTPM
Ovary	6.4 nTPM
Breast	6.0 nTPM
Skin	4.5 nTPM
Bronchus	1.0 nTPM

T-cells	9.5 nTPM
Adipose tissue	26.0 nTPM
Endometrium	22.5 nTPM
Lung	18.2 nTPM
Stomach	15.8 nTPM
Spleen	15.5 nTPM
Breast	11.6 nTPM
Lymph node	10.5 nTPM
Bone marrow	8.9 nTPM
Skeletal muscle	8.5 nTPM
Liver	8.2 nTPM
PBMC	6.6 nTPM
Colon	4.3 nTPM
Kidney	2.7 nTPM
Skin	2.3 nTPM
Prostate	0.0 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM

Astrocytes	91.4 nTPM
Brain	91.4 nTPM

Cone photoreceptor cells	16.7 nTPM
Eye	16.7 nTPM

Distal enterocytes	10.0 nTPM
Rectum	11.7 nTPM
Colon	8.3 nTPM

Distal tubular cells	11.7 nTPM
Kidney	11.7 nTPM

Undifferentiated cells	5.5 nTPM
Rectum	7.3 nTPM
Small intestine	5.8 nTPM
Colon	3.5 nTPM

Adipose tissue

Bone marrow

Brain

Breast

Bronchus

Colon

Endometrium

Esophagus

Eye

Heart muscle

Kidney

Liver

Lung

Lymph node

Ovary

Pancreas

Placenta

Prostate

Rectum

Skeletal muscle

Skin

Small intestine

Spleen

Stomach

Testis

PBMC