Single cell type - VPS26A - 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.	VPS26A
Gene descriptionⁱ Full gene name according to HGNC.	VPS26, retromer complex component A
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Plasma proteins Transporters
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.	4

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	Syncytiotrophoblasts - Pregnancy hormone signaling (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 (Syncytiotrophoblasts)
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: Cell type enhanced (Syncytiotrophoblasts)

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

VPS26A is part of cluster 18 Syncytiotrophoblasts - Pregnancy hormone signaling with confidenceⁱ 1
186 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
APMAP	Adipocyte plasma membrane associated protein	0.5731	18
OLR1	Oxidized low density lipoprotein receptor 1	0.5722	47
TREX2	Three prime repair exonuclease 2	0.5665	47
GABARAPL1	GABA type A receptor associated protein like 1	0.5579	18
H2BC4	H2B clustered histone 4	0.5456	18
DNAJC8	DnaJ heat shock protein family (Hsp40) member C8	0.5332	39
CCNDBP1	Cyclin D1 binding protein 1	0.5303	18
C11orf58	Chromosome 11 open reading frame 58	0.5275	39
SIAH1	Siah E3 ubiquitin protein ligase 1	0.5200	18
NFYB	Nuclear transcription factor Y subunit beta	0.5098	18
H2AW	H2A.W histone	0.5081	24
SLC2A1	Solute carrier family 2 member 1	0.5037	18
BTG3	BTG anti-proliferation factor 3	0.5014	18
AEBP2	AE binding protein 2	0.4957	47
CSF3R	Colony stimulating factor 3 receptor	0.4944	18

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	49.0 nTPM
Breast	51.4 nTPM
Adipose tissue	46.6 nTPM

Alveolar cells type 1	73.7 nTPM
Lung	73.7 nTPM

Alveolar cells type 2	56.6 nTPM
Lung	56.6 nTPM

Astrocytes	21.5 nTPM
Brain	21.5 nTPM

B-cells	40.6 nTPM
Stomach	70.3 nTPM
Adipose tissue	65.6 nTPM
Spleen	47.1 nTPM
Lymph node	45.8 nTPM
Breast	36.0 nTPM
Colon	33.5 nTPM
Liver	28.7 nTPM
Kidney	28.5 nTPM
Bone marrow	26.2 nTPM
PBMC	24.3 nTPM

Dendritic cells	59.2 nTPM
Adipose tissue	98.7 nTPM
Breast	71.0 nTPM
PBMC	8.0 nTPM

Endothelial cells	52.7 nTPM
Heart muscle	72.4 nTPM
Skin	69.9 nTPM
Prostate	65.0 nTPM
Esophagus	61.4 nTPM
Lung	53.0 nTPM
Placenta	52.3 nTPM
Breast	51.1 nTPM
Endometrium	47.9 nTPM
Pancreas	46.4 nTPM
Eye	45.3 nTPM
Testis	45.3 nTPM
Skeletal muscle	44.7 nTPM
Ovary	42.5 nTPM
Liver	41.2 nTPM

Fibroblasts	57.4 nTPM
Heart muscle	103.5 nTPM
Skin	71.0 nTPM
Prostate	64.6 nTPM
Lung	60.3 nTPM
Placenta	57.4 nTPM
Adipose tissue	57.0 nTPM
Breast	52.0 nTPM
Skeletal muscle	47.7 nTPM
Esophagus	45.0 nTPM
Stomach	38.6 nTPM
Ovary	33.9 nTPM

Intestinal goblet cells	38.3 nTPM
Colon	43.6 nTPM
Rectum	35.8 nTPM
Small intestine	35.6 nTPM

Macrophages	66.0 nTPM
Lung	115.3 nTPM
Adipose tissue	112.1 nTPM
Pancreas	94.4 nTPM
Spleen	90.2 nTPM
Stomach	73.3 nTPM
Prostate	68.8 nTPM
Ovary	67.7 nTPM
Kidney	59.0 nTPM
Breast	56.9 nTPM
Testis	51.2 nTPM
Bone marrow	51.2 nTPM
Endometrium	50.9 nTPM
Skeletal muscle	50.1 nTPM
Esophagus	48.7 nTPM
PBMC	0.0 nTPM

Paneth cells	43.3 nTPM
Rectum	45.2 nTPM
Small intestine	45.0 nTPM
Colon	39.6 nTPM

Plasma cells	28.2 nTPM
Adipose tissue	51.6 nTPM
Stomach	33.7 nTPM
Bone marrow	28.0 nTPM
Spleen	21.4 nTPM
Esophagus	6.1 nTPM

Respiratory ciliated cells	45.5 nTPM
Lung	55.4 nTPM
Bronchus	35.6 nTPM

Smooth muscle cells	61.9 nTPM
Heart muscle	92.0 nTPM
Skin	87.2 nTPM
Prostate	81.0 nTPM
Breast	60.2 nTPM
Esophagus	57.4 nTPM
Ovary	57.2 nTPM
Pancreas	56.2 nTPM
Skeletal muscle	52.7 nTPM
Adipose tissue	49.3 nTPM
Bronchus	45.2 nTPM
Endometrium	42.5 nTPM

T-cells	59.5 nTPM
Adipose tissue	94.3 nTPM
Ovary	91.2 nTPM
Skin	82.0 nTPM
Lung	71.4 nTPM
Liver	65.0 nTPM
Bone marrow	62.6 nTPM
Prostate	61.6 nTPM
Stomach	61.4 nTPM
Breast	57.8 nTPM
Kidney	56.9 nTPM
Skeletal muscle	56.7 nTPM
Spleen	53.2 nTPM
Endometrium	50.2 nTPM
Lymph node	48.5 nTPM
Colon	35.1 nTPM
Esophagus	32.8 nTPM
PBMC	30.8 nTPM

Basal keratinocytes	120.7 nTPM
Skin	120.7 nTPM

Basal prostatic cells	83.4 nTPM
Prostate	83.4 nTPM

Basal respiratory cells	79.6 nTPM
Bronchus	79.6 nTPM

Cholangiocytes	40.0 nTPM
Liver	40.0 nTPM

Undifferentiated cells	44.4 nTPM
Colon	58.9 nTPM
Rectum	37.9 nTPM
Small intestine	36.5 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