Single cell type - VCL - 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.	VCL
Gene descriptionⁱ Full gene name according to HGNC.	Vinculin
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Human disease related genes Plasma 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.	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	Endometrium - 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	Cell type enhanced (Cardiomyocytes)
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	Cell line enhanced (BJ hTERT+, hTERT-RPE1)
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 (Cardiomyocytes)

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

VCL is part of cluster 44 Endometrium - Transcription with confidenceⁱ 1
491 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
SLMAP	Sarcolemma associated protein	0.6709	54
RBPMS2	RNA binding protein, mRNA processing factor 2	0.6108	54
UBXN2A	UBX domain protein 2A	0.5529	51
NEXN	Nexilin F-actin binding protein	0.5426	54
MAP3K7CL	MAP3K7 C-terminal like	0.5404	51
MSANTD3	Myb/SANT DNA binding domain containing 3	0.5377	51
SPOCD1	SPOC domain containing 1	0.5306	22
PITPNB	Phosphatidylinositol transfer protein beta	0.5278	22
IFNK	Interferon kappa	0.5146	44
FNTB	Farnesyltransferase, CAAX box, beta	0.5062	51
BX276092.9	Chromosome X open reading frame 49-like	0.5035	44
KRTAP4-9	Keratin associated protein 4-9	0.5016	44
AC025287.4	Novel protein similar to cytoplasmic polyadenylated homeobox like CPHXL	0.4988	44
LIMS1	LIM zinc finger domain containing 1	0.4964	51
ITGAV	Integrin subunit alpha V	0.4949	44

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	68.0 nTPM
Adipose tissue	76.8 nTPM
Breast	59.3 nTPM

Alveolar cells type 1	99.3 nTPM
Lung	99.3 nTPM

Alveolar cells type 2	39.7 nTPM
Lung	39.7 nTPM

Astrocytes	56.5 nTPM
Brain	56.5 nTPM

B-cells	13.4 nTPM
PBMC	21.4 nTPM
Colon	19.2 nTPM
Adipose tissue	15.6 nTPM
Breast	14.7 nTPM
Bone marrow	11.5 nTPM
Spleen	11.1 nTPM
Stomach	10.9 nTPM
Lymph node	10.1 nTPM
Liver	9.7 nTPM
Kidney	9.5 nTPM

Dendritic cells	46.7 nTPM
PBMC	71.8 nTPM
Adipose tissue	36.6 nTPM
Breast	31.7 nTPM

Endothelial cells	60.4 nTPM
Heart muscle	92.8 nTPM
Skeletal muscle	89.2 nTPM
Ovary	80.2 nTPM
Endometrium	75.3 nTPM
Lung	74.8 nTPM
Eye	71.2 nTPM
Placenta	59.7 nTPM
Skin	56.0 nTPM
Breast	46.1 nTPM
Prostate	45.9 nTPM
Liver	45.8 nTPM
Esophagus	44.3 nTPM
Pancreas	38.6 nTPM
Testis	25.5 nTPM

Fibroblasts	74.4 nTPM
Ovary	95.2 nTPM
Adipose tissue	90.8 nTPM
Stomach	87.6 nTPM
Placenta	87.0 nTPM
Heart muscle	86.2 nTPM
Prostate	78.9 nTPM
Skin	71.8 nTPM
Lung	64.8 nTPM
Skeletal muscle	62.6 nTPM
Breast	50.8 nTPM
Esophagus	42.3 nTPM

Intestinal goblet cells	44.5 nTPM
Colon	78.7 nTPM
Rectum	35.1 nTPM
Small intestine	19.8 nTPM

Macrophages	77.9 nTPM
PBMC	709.3 nTPM
Stomach	76.2 nTPM
Adipose tissue	60.6 nTPM
Skeletal muscle	42.0 nTPM
Endometrium	41.0 nTPM
Testis	32.0 nTPM
Bone marrow	31.2 nTPM
Lung	30.1 nTPM
Spleen	30.0 nTPM
Kidney	29.5 nTPM
Prostate	27.5 nTPM
Esophagus	23.6 nTPM
Ovary	15.3 nTPM
Breast	15.2 nTPM
Pancreas	5.1 nTPM

Paneth cells	48.3 nTPM
Colon	102.1 nTPM
Rectum	35.2 nTPM
Small intestine	7.5 nTPM

Plasma cells	8.0 nTPM
Adipose tissue	26.4 nTPM
Stomach	5.5 nTPM
Spleen	4.8 nTPM
Bone marrow	3.3 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	37.7 nTPM
Bronchus	44.8 nTPM
Lung	30.6 nTPM

Smooth muscle cells	179.9 nTPM
Heart muscle	357.8 nTPM
Ovary	288.8 nTPM
Adipose tissue	253.6 nTPM
Skeletal muscle	236.9 nTPM
Endometrium	176.9 nTPM
Esophagus	158.1 nTPM
Breast	142.2 nTPM
Skin	134.3 nTPM
Prostate	115.4 nTPM
Pancreas	75.7 nTPM
Bronchus	39.6 nTPM

T-cells	18.3 nTPM
Skeletal muscle	36.3 nTPM
Lung	34.9 nTPM
PBMC	31.2 nTPM
Endometrium	26.6 nTPM
Skin	26.2 nTPM
Bone marrow	23.8 nTPM
Prostate	23.6 nTPM
Kidney	21.2 nTPM
Adipose tissue	18.7 nTPM
Spleen	16.0 nTPM
Liver	15.9 nTPM
Breast	9.5 nTPM
Colon	6.6 nTPM
Esophagus	6.6 nTPM
Lymph node	6.1 nTPM
Ovary	4.5 nTPM
Stomach	3.6 nTPM

Basal keratinocytes	114.7 nTPM
Skin	114.7 nTPM

Basal prostatic cells	161.4 nTPM
Prostate	161.4 nTPM

Basal respiratory cells	68.4 nTPM
Bronchus	68.4 nTPM

Basal squamous epithelial cells	30.7 nTPM
Esophagus	30.7 nTPM

Undifferentiated cells	48.7 nTPM
Colon	81.5 nTPM
Rectum	42.6 nTPM
Small intestine	21.9 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