Single cell type - RAB5B - 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.	RAB5B
Gene descriptionⁱ Full gene name according to HGNC.	RAB5B, member RAS oncogene family
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	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. Read more	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	7

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	Epithelial cell types - Mixed 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. Read more	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. 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: Low cell type specificity

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

RAB5B is part of cluster 22 Epithelial cell types - Mixed function with confidenceⁱ 1
298 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
TMEM127	Transmembrane protein 127	0.5210	53
TRAFD1	TRAF-type zinc finger domain containing 1	0.5075	3
MAL2	Mal, T cell differentiation protein 2	0.4997	22
FAM83H	Family with sequence similarity 83 member H	0.4966	61
FBXO46	F-box protein 46	0.4859	28
UBQLN4	Ubiquilin 4	0.4800	53
CTNND1	Catenin delta 1	0.4726	61
CDKN2B	Cyclin dependent kinase inhibitor 2B	0.4685	53
DSC2	Desmocollin 2	0.4676	61
FAM83G	Family with sequence similarity 83 member G	0.4631	61
SMIM14	Small integral membrane protein 14	0.4626	2
FOXN1	Forkhead box N1	0.4617	61
JUP	Junction plakoglobin	0.4605	22
RNF103	Ring finger protein 103	0.4605	35
PEX11B	Peroxisomal biogenesis factor 11 beta	0.4592	47

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	24.4 nTPM
Adipose tissue	28.8 nTPM
Breast	20.0 nTPM

Alveolar cells type 1	57.7 nTPM
Lung	57.7 nTPM

Alveolar cells type 2	37.1 nTPM
Lung	37.1 nTPM

Astrocytes	13.1 nTPM
Brain	13.1 nTPM

B-cells	26.7 nTPM
Bone marrow	44.2 nTPM
Spleen	33.6 nTPM
Lymph node	29.3 nTPM
Liver	29.2 nTPM
Colon	28.7 nTPM
PBMC	27.1 nTPM
Stomach	26.8 nTPM
Adipose tissue	19.5 nTPM
Breast	14.7 nTPM
Kidney	14.3 nTPM

Dendritic cells	29.1 nTPM
PBMC	47.8 nTPM
Adipose tissue	24.4 nTPM
Breast	14.9 nTPM

Endothelial cells	30.8 nTPM
Liver	55.9 nTPM
Placenta	42.6 nTPM
Esophagus	41.8 nTPM
Breast	40.7 nTPM
Skin	35.1 nTPM
Prostate	35.0 nTPM
Testis	31.4 nTPM
Heart muscle	26.5 nTPM
Ovary	25.0 nTPM
Skeletal muscle	24.3 nTPM
Eye	24.2 nTPM
Endometrium	24.1 nTPM
Pancreas	15.5 nTPM
Lung	9.3 nTPM

Fibroblasts	33.1 nTPM
Esophagus	60.4 nTPM
Skin	39.9 nTPM
Adipose tissue	38.1 nTPM
Stomach	37.1 nTPM
Prostate	33.3 nTPM
Skeletal muscle	31.8 nTPM
Breast	29.7 nTPM
Heart muscle	26.7 nTPM
Placenta	26.0 nTPM
Lung	21.2 nTPM
Ovary	20.1 nTPM

Intestinal goblet cells	51.1 nTPM
Rectum	70.8 nTPM
Colon	45.8 nTPM
Small intestine	36.7 nTPM

Macrophages	25.4 nTPM
Spleen	47.7 nTPM
Esophagus	36.2 nTPM
Bone marrow	35.0 nTPM
Prostate	28.7 nTPM
Ovary	28.1 nTPM
Kidney	27.2 nTPM
Testis	26.1 nTPM
Adipose tissue	25.5 nTPM
Skeletal muscle	24.5 nTPM
Pancreas	20.4 nTPM
Endometrium	18.5 nTPM
Stomach	17.6 nTPM
Lung	16.4 nTPM
Breast	15.7 nTPM
PBMC	13.6 nTPM

Paneth cells	44.4 nTPM
Rectum	58.1 nTPM
Small intestine	48.8 nTPM
Colon	26.4 nTPM

Plasma cells	27.1 nTPM
Esophagus	30.7 nTPM
Bone marrow	29.7 nTPM
Stomach	28.4 nTPM
Spleen	28.0 nTPM
Adipose tissue	18.8 nTPM

Respiratory ciliated cells	23.9 nTPM
Bronchus	37.5 nTPM
Lung	10.2 nTPM

Smooth muscle cells	33.2 nTPM
Esophagus	66.7 nTPM
Adipose tissue	44.8 nTPM
Skeletal muscle	42.6 nTPM
Skin	36.6 nTPM
Prostate	33.4 nTPM
Breast	27.5 nTPM
Ovary	27.4 nTPM
Pancreas	25.0 nTPM
Heart muscle	23.2 nTPM
Endometrium	20.8 nTPM
Bronchus	16.9 nTPM

T-cells	25.0 nTPM
Esophagus	52.4 nTPM
Bone marrow	37.8 nTPM
Colon	34.7 nTPM
Lymph node	31.0 nTPM
PBMC	29.8 nTPM
Spleen	29.0 nTPM
Stomach	27.9 nTPM
Kidney	25.3 nTPM
Liver	24.5 nTPM
Skin	22.6 nTPM
Skeletal muscle	22.4 nTPM
Adipose tissue	20.2 nTPM
Breast	16.5 nTPM
Prostate	14.2 nTPM
Lung	13.6 nTPM
Endometrium	12.8 nTPM
Ovary	11.1 nTPM

Basal keratinocytes	51.7 nTPM
Skin	51.7 nTPM

Basal respiratory cells	34.0 nTPM
Bronchus	34.0 nTPM

Basal squamous epithelial cells	35.3 nTPM
Esophagus	35.3 nTPM

Cholangiocytes	55.8 nTPM
Liver	55.8 nTPM

Undifferentiated cells	42.7 nTPM
Rectum	53.8 nTPM
Colon	39.8 nTPM
Small intestine	34.6 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