Single cell type - CHMP4B - 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.	CHMP4B
Gene descriptionⁱ Full gene name according to HGNC.	Charged multivesicular body protein 4B
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Human disease related genes
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.	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. Read more	Intestinal epithelial cells - Unknown 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 many
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

CHMP4B is part of cluster 53 Intestinal epithelial cells - Unknown function with confidenceⁱ 1
611 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
TNIP1	TNFAIP3 interacting protein 1	0.6824	53
TAX1BP3	Tax1 binding protein 3	0.6777	53
LRP10	LDL receptor related protein 10	0.6713	53
GNG12	G protein subunit gamma 12	0.6513	53
TMBIM1	Transmembrane BAX inhibitor motif containing 1	0.6503	53
PRSS3	Serine protease 3	0.6374	53
ACHE	Acetylcholinesterase (Cartwright blood group)	0.6345	53
RHOC	Ras homolog family member C	0.6337	16
CDKN2B	Cyclin dependent kinase inhibitor 2B	0.6194	53
CEACAM1	CEA cell adhesion molecule 1	0.6130	53
CRB3	Crumbs cell polarity complex component 3	0.6114	53
SQSTM1	Sequestosome 1	0.6090	22
MALL	Mal, T cell differentiation protein like	0.6085	53
CHMP2B	Charged multivesicular body protein 2B	0.6048	53
CLCA4	Chloride channel accessory 4	0.6041	53

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	66.0 nTPM
Adipose tissue	85.5 nTPM
Breast	46.5 nTPM

Alveolar cells type 1	60.9 nTPM
Lung	60.9 nTPM

Alveolar cells type 2	54.6 nTPM
Lung	54.6 nTPM

Astrocytes	17.9 nTPM
Brain	17.9 nTPM

B-cells	71.5 nTPM
Liver	118.8 nTPM
Breast	86.9 nTPM
Kidney	80.9 nTPM
Colon	70.3 nTPM
Spleen	69.6 nTPM
Lymph node	66.4 nTPM
Adipose tissue	62.1 nTPM
PBMC	57.1 nTPM
Bone marrow	56.4 nTPM
Stomach	46.4 nTPM

Basal squamous epithelial cells	113.3 nTPM
Esophagus	113.3 nTPM

Dendritic cells	77.9 nTPM
PBMC	99.6 nTPM
Adipose tissue	83.0 nTPM
Breast	51.0 nTPM

Endothelial cells	126.0 nTPM
Pancreas	343.6 nTPM
Prostate	320.9 nTPM
Skin	280.5 nTPM
Esophagus	128.7 nTPM
Breast	124.0 nTPM
Placenta	102.3 nTPM
Liver	96.3 nTPM
Testis	75.8 nTPM
Endometrium	65.5 nTPM
Lung	62.4 nTPM
Skeletal muscle	61.8 nTPM
Eye	35.6 nTPM
Heart muscle	34.4 nTPM
Ovary	32.6 nTPM

Enteroendocrine cells	127.4 nTPM
Rectum	155.3 nTPM
Colon	99.5 nTPM

Fibroblasts	130.1 nTPM
Prostate	365.3 nTPM
Skin	254.4 nTPM
Esophagus	159.6 nTPM
Stomach	118.8 nTPM
Placenta	108.7 nTPM
Adipose tissue	100.3 nTPM
Breast	90.6 nTPM
Lung	73.7 nTPM
Skeletal muscle	70.2 nTPM
Heart muscle	54.7 nTPM
Ovary	34.5 nTPM

Intestinal goblet cells	212.7 nTPM
Colon	226.5 nTPM
Rectum	220.5 nTPM
Small intestine	190.9 nTPM

Macrophages	140.2 nTPM
Pancreas	308.9 nTPM
Kidney	223.8 nTPM
Prostate	221.2 nTPM
Stomach	216.8 nTPM
Adipose tissue	196.2 nTPM
Endometrium	153.1 nTPM
Spleen	130.6 nTPM
Esophagus	127.4 nTPM
Bone marrow	114.9 nTPM
Testis	88.9 nTPM
Skeletal muscle	76.2 nTPM
Lung	75.0 nTPM
Breast	69.6 nTPM
PBMC	54.6 nTPM
Ovary	45.3 nTPM

Paneth cells	536.6 nTPM
Colon	1014.5 nTPM
Rectum	351.2 nTPM
Small intestine	244.0 nTPM

Plasma cells	139.0 nTPM
Esophagus	197.1 nTPM
Stomach	178.9 nTPM
Bone marrow	130.1 nTPM
Spleen	128.7 nTPM
Adipose tissue	60.0 nTPM

Respiratory ciliated cells	101.6 nTPM
Bronchus	124.6 nTPM
Lung	78.7 nTPM

Cholangiocytes	112.9 nTPM
Liver	112.9 nTPM

Collecting duct cells	110.3 nTPM
Kidney	110.3 nTPM

Cone photoreceptor cells	18.8 nTPM
Eye	18.8 nTPM

Cytotrophoblasts	197.7 nTPM
Placenta	197.7 nTPM

Smooth muscle cells	120.5 nTPM
Skin	235.8 nTPM
Prostate	207.2 nTPM
Bronchus	177.3 nTPM
Pancreas	163.5 nTPM
Esophagus	162.8 nTPM
Skeletal muscle	77.8 nTPM
Adipose tissue	76.5 nTPM
Breast	74.6 nTPM
Endometrium	63.7 nTPM
Heart muscle	46.7 nTPM
Ovary	39.7 nTPM

T-cells	62.9 nTPM
Skin	120.2 nTPM
Esophagus	98.3 nTPM
Prostate	94.7 nTPM
Kidney	78.0 nTPM
Adipose tissue	73.6 nTPM
Colon	71.3 nTPM
Liver	66.4 nTPM
Endometrium	66.0 nTPM
Stomach	53.8 nTPM
Spleen	52.9 nTPM
PBMC	49.9 nTPM
Breast	46.9 nTPM
Lung	45.6 nTPM
Lymph node	45.1 nTPM
Bone marrow	45.1 nTPM
Skeletal muscle	40.1 nTPM
Ovary	22.3 nTPM

Undifferentiated cells	227.4 nTPM
Colon	267.4 nTPM
Rectum	215.5 nTPM
Small intestine	199.5 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