Single cell type - VAMP4 - 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.	VAMP4
Gene descriptionⁱ Full gene name according to HGNC.	Vesicle associated membrane protein 4
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	Non-specific - Transcription (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

VAMP4 is part of cluster 59 Non-specific - Transcription with confidenceⁱ 1
354 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
CRBN	Cereblon	0.4626	66
RCHY1	Ring finger and CHY zinc finger domain containing 1	0.4539	39
SIRT3	Sirtuin 3	0.4457	59
PPP6C	Protein phosphatase 6 catalytic subunit	0.4316	59
TDRKH	Tudor and KH domain containing	0.4298	25
PPP3CC	Protein phosphatase 3 catalytic subunit gamma	0.4261	59
KLHL28	Kelch like family member 28	0.4209	31
LIN37	Lin-37 DREAM MuvB core complex component	0.4183	59
TRAF6	TNF receptor associated factor 6	0.4159	59
XRN1	5'-3' exoribonuclease 1	0.4094	59
RWDD3	RWD domain containing 3	0.4024	59
RASA3	RAS p21 protein activator 3	0.4000	63
NPAT	Nuclear protein, coactivator of histone transcription	0.3966	59
GTF2H1	General transcription factor IIH subunit 1	0.3964	66
ZNF287	Zinc finger protein 287	0.3949	66

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	22.3 nTPM
Adipose tissue	24.4 nTPM
Breast	20.3 nTPM

Alveolar cells type 1	22.4 nTPM
Lung	22.4 nTPM

Alveolar cells type 2	9.3 nTPM
Lung	9.3 nTPM

Astrocytes	18.3 nTPM
Brain	18.3 nTPM

B-cells	21.4 nTPM
Bone marrow	34.3 nTPM
Breast	29.4 nTPM
Spleen	28.7 nTPM
Stomach	28.6 nTPM
Adipose tissue	24.0 nTPM
Lymph node	22.7 nTPM
Colon	20.8 nTPM
Liver	12.2 nTPM
PBMC	8.5 nTPM
Kidney	4.8 nTPM

Dendritic cells	18.2 nTPM
Adipose tissue	22.9 nTPM
PBMC	16.0 nTPM
Breast	15.7 nTPM

Endothelial cells	20.3 nTPM
Heart muscle	40.4 nTPM
Testis	25.8 nTPM
Prostate	25.5 nTPM
Liver	21.1 nTPM
Eye	21.0 nTPM
Breast	20.8 nTPM
Esophagus	19.7 nTPM
Placenta	19.4 nTPM
Skeletal muscle	18.3 nTPM
Endometrium	18.2 nTPM
Ovary	17.5 nTPM
Skin	16.4 nTPM
Lung	12.5 nTPM
Pancreas	7.7 nTPM

Fibroblasts	20.4 nTPM
Adipose tissue	31.3 nTPM
Prostate	27.0 nTPM
Heart muscle	26.7 nTPM
Esophagus	25.8 nTPM
Stomach	25.3 nTPM
Placenta	20.4 nTPM
Skeletal muscle	19.5 nTPM
Breast	17.6 nTPM
Skin	16.8 nTPM
Ovary	9.8 nTPM
Lung	4.5 nTPM

Intestinal goblet cells	12.3 nTPM
Rectum	14.5 nTPM
Colon	11.4 nTPM
Small intestine	11.0 nTPM

Macrophages	20.1 nTPM
PBMC	40.9 nTPM
Spleen	34.2 nTPM
Bone marrow	31.2 nTPM
Ovary	27.6 nTPM
Stomach	26.4 nTPM
Kidney	21.1 nTPM
Lung	18.2 nTPM
Skeletal muscle	16.9 nTPM
Adipose tissue	16.4 nTPM
Prostate	16.0 nTPM
Esophagus	12.6 nTPM
Breast	12.5 nTPM
Endometrium	9.9 nTPM
Testis	9.8 nTPM
Pancreas	7.7 nTPM

Paneth cells	14.9 nTPM
Small intestine	18.8 nTPM
Rectum	15.9 nTPM
Colon	9.9 nTPM

Plasma cells	20.8 nTPM
Stomach	36.5 nTPM
Spleen	26.1 nTPM
Bone marrow	14.8 nTPM
Adipose tissue	14.2 nTPM
Esophagus	12.3 nTPM

Respiratory ciliated cells	11.4 nTPM
Bronchus	12.5 nTPM
Lung	10.2 nTPM

Smooth muscle cells	15.0 nTPM
Bronchus	22.4 nTPM
Esophagus	20.1 nTPM
Prostate	20.0 nTPM
Adipose tissue	17.0 nTPM
Pancreas	16.1 nTPM
Breast	15.9 nTPM
Heart muscle	14.2 nTPM
Skin	12.2 nTPM
Skeletal muscle	11.1 nTPM
Ovary	8.5 nTPM
Endometrium	7.9 nTPM

T-cells	23.1 nTPM
Bone marrow	40.3 nTPM
Stomach	34.3 nTPM
Adipose tissue	32.4 nTPM
Spleen	31.7 nTPM
Lymph node	29.1 nTPM
Liver	23.0 nTPM
Kidney	22.6 nTPM
Skeletal muscle	22.6 nTPM
Skin	21.2 nTPM
PBMC	20.3 nTPM
Lung	19.7 nTPM
Breast	19.6 nTPM
Ovary	17.8 nTPM
Colon	16.6 nTPM
Prostate	14.2 nTPM
Endometrium	13.7 nTPM
Esophagus	13.1 nTPM

Basal keratinocytes	15.4 nTPM
Skin	15.4 nTPM

Basal prostatic cells	13.8 nTPM
Prostate	13.8 nTPM

Basal respiratory cells	18.0 nTPM
Bronchus	18.0 nTPM

Cholangiocytes	10.0 nTPM
Liver	10.0 nTPM

Undifferentiated cells	7.4 nTPM
Rectum	10.9 nTPM
Small intestine	7.2 nTPM
Colon	4.0 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