Single cell type - VMA21 - 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.	VMA21
Gene descriptionⁱ Full gene name according to HGNC.	Vacuolar ATPase assembly factor VMA21
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	Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	2

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	Macrophages - Innate immune response (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

VMA21 is part of cluster 4 Macrophages - Innate immune response with confidenceⁱ 1
228 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
CEBPE	CCAAT enhancer binding protein epsilon	0.6336	4
IRF5	Interferon regulatory factor 5	0.6317	3
PPT1	Palmitoyl-protein thioesterase 1	0.6248	4
SPI1	Spi-1 proto-oncogene	0.6166	4
TYROBP	Transmembrane immune signaling adaptor TYROBP	0.6157	4
RHOG	Ras homolog family member G	0.6152	3
ARRB2	Arrestin beta 2	0.6136	4
TYMP	Thymidine phosphorylase	0.6109	3
TWF2	Twinfilin actin binding protein 2	0.6101	3
M6PR	Mannose-6-phosphate receptor, cation dependent	0.5989	4
LILRB4	Leukocyte immunoglobulin like receptor B4	0.5914	4
ADAP2	ArfGAP with dual PH domains 2	0.5825	4
CCR1	C-C motif chemokine receptor 1	0.5719	4
ARPC1B	Actin related protein 2/3 complex subunit 1B	0.5681	51
DBNL	Drebrin like	0.5634	3

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	38.5 nTPM
Breast	39.5 nTPM
Adipose tissue	37.5 nTPM

Alveolar cells type 1	22.4 nTPM
Lung	22.4 nTPM

Alveolar cells type 2	24.4 nTPM
Lung	24.4 nTPM

Astrocytes	9.1 nTPM
Brain	9.1 nTPM

B-cells	46.5 nTPM
Liver	84.9 nTPM
Colon	62.3 nTPM
Stomach	48.1 nTPM
Spleen	44.0 nTPM
Bone marrow	43.4 nTPM
PBMC	42.8 nTPM
Adipose tissue	40.1 nTPM
Lymph node	36.1 nTPM
Breast	34.7 nTPM
Kidney	28.5 nTPM

Dendritic cells	62.9 nTPM
PBMC	99.6 nTPM
Breast	46.3 nTPM
Adipose tissue	42.7 nTPM

Endothelial cells	34.6 nTPM
Pancreas	57.9 nTPM
Prostate	46.9 nTPM
Esophagus	42.9 nTPM
Testis	38.2 nTPM
Endometrium	37.2 nTPM
Ovary	37.2 nTPM
Placenta	34.7 nTPM
Liver	33.9 nTPM
Breast	33.9 nTPM
Skin	32.1 nTPM
Heart muscle	29.4 nTPM
Eye	27.5 nTPM
Skeletal muscle	26.6 nTPM
Lung	6.2 nTPM

Fibroblasts	28.0 nTPM
Prostate	55.1 nTPM
Lung	35.7 nTPM
Ovary	28.1 nTPM
Adipose tissue	27.7 nTPM
Placenta	26.6 nTPM
Skin	26.1 nTPM
Esophagus	25.6 nTPM
Breast	22.6 nTPM
Skeletal muscle	22.5 nTPM
Stomach	22.3 nTPM
Heart muscle	15.4 nTPM

Intestinal goblet cells	22.5 nTPM
Rectum	30.4 nTPM
Small intestine	21.3 nTPM
Colon	15.7 nTPM

Macrophages	89.8 nTPM
Prostate	136.5 nTPM
Ovary	134.1 nTPM
Stomach	108.4 nTPM
Testis	108.1 nTPM
Pancreas	107.2 nTPM
Kidney	99.1 nTPM
Adipose tissue	92.8 nTPM
Spleen	92.3 nTPM
Bone marrow	85.0 nTPM
Skeletal muscle	80.7 nTPM
Endometrium	76.5 nTPM
Esophagus	70.8 nTPM
Breast	66.9 nTPM
Lung	62.2 nTPM
PBMC	27.3 nTPM

Paneth cells	17.6 nTPM
Rectum	24.7 nTPM
Small intestine	15.0 nTPM
Colon	13.2 nTPM

Plasma cells	50.9 nTPM
Spleen	96.6 nTPM
Bone marrow	61.0 nTPM
Stomach	40.6 nTPM
Esophagus	30.7 nTPM
Adipose tissue	25.8 nTPM

Respiratory ciliated cells	28.6 nTPM
Bronchus	33.9 nTPM
Lung	23.3 nTPM

Smooth muscle cells	34.5 nTPM
Bronchus	105.6 nTPM
Pancreas	44.8 nTPM
Prostate	36.2 nTPM
Esophagus	32.5 nTPM
Skin	30.0 nTPM
Breast	26.5 nTPM
Ovary	26.1 nTPM
Adipose tissue	26.1 nTPM
Endometrium	20.3 nTPM
Skeletal muscle	19.2 nTPM
Heart muscle	12.3 nTPM

T-cells	41.6 nTPM
Colon	74.1 nTPM
PBMC	59.8 nTPM
Skin	53.9 nTPM
Stomach	52.6 nTPM
Spleen	47.3 nTPM
Lymph node	45.9 nTPM
Liver	43.6 nTPM
Ovary	42.2 nTPM
Bone marrow	40.0 nTPM
Adipose tissue	39.9 nTPM
Esophagus	39.3 nTPM
Breast	37.0 nTPM
Kidney	32.2 nTPM
Endometrium	30.7 nTPM
Skeletal muscle	28.6 nTPM
Lung	21.3 nTPM
Prostate	19.0 nTPM

Basal keratinocytes	44.9 nTPM
Skin	44.9 nTPM

Basal respiratory cells	35.3 nTPM
Bronchus	35.3 nTPM

Collecting duct cells	31.3 nTPM
Kidney	31.3 nTPM

Cone photoreceptor cells	18.8 nTPM
Eye	18.8 nTPM

Undifferentiated cells	21.8 nTPM
Rectum	27.2 nTPM
Small intestine	22.6 nTPM
Colon	15.6 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