Single cell type - VCAN - 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.	VCAN
Gene descriptionⁱ Full gene name according to HGNC.	Versican
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,Secreted
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	7

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	Monocytes & Neutrophils - 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	Cell type enhanced (Oligodendrocyte precursor cells, Granulosa cells, Endometrial stromal cells, monocytes, Macrophages, Kupffer cells)
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	Group enriched (classical monocyte, myeloid DC)
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	Cell line enhanced (AF22, HSkMC, hTERT-RPE1, RPTEC TERT1)
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 many
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
Extracellular locationⁱ A possible secretion of the protein was predicted based on N-terminal signal sequence (signal peptide) predictions and transmembrane region predictions, and subsequently annotated for its local or systemic secretion based on literature, function, and protein and RNA expression data. Read more	Protein predicted to be secreted

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 (Oligodendrocyte precursor cells, Granulosa cells, Endometrial stromal cells, monocytes, Macrophages, Kupffer cells)

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

VCAN is part of cluster 19 Monocytes & Neutrophils - Innate immune response with confidenceⁱ 1
175 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
RUFY4	RUN and FYVE domain containing 4	0.6396	40
OR52K2	Olfactory receptor family 52 subfamily K member 2	0.6175	19
IL17RA	Interleukin 17 receptor A	0.6148	19
SERPINE2	Serpin family E member 2	0.6026	40
FST	Follistatin	0.5944	40
GPBAR1	G protein-coupled bile acid receptor 1	0.5908	19
FCN1	Ficolin 1	0.5858	19
CLEC4D	C-type lectin domain family 4 member D	0.5844	19
CLEC12A	C-type lectin domain family 12 member A	0.5821	19
S100A12	S100 calcium binding protein A12	0.5777	19
NOTCH2	Notch receptor 2	0.5777	19
BST1	Bone marrow stromal cell antigen 1	0.5771	19
SNX18	Sorting nexin 18	0.5765	19
MYD88	MYD88 innate immune signal transduction adaptor	0.5703	19
NUP214	Nucleoporin 214	0.5623	19

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	23.4 nTPM
Adipose tissue	41.4 nTPM
Breast	5.4 nTPM

Alveolar cells type 1	19.2 nTPM
Lung	19.2 nTPM

Alveolar cells type 2	19.8 nTPM
Lung	19.8 nTPM

Astrocytes	128.9 nTPM
Brain	128.9 nTPM

B-cells	5.5 nTPM
Lymph node	19.8 nTPM
PBMC	12.9 nTPM
Liver	8.8 nTPM
Colon	6.4 nTPM
Breast	4.0 nTPM
Spleen	2.4 nTPM
Adipose tissue	0.5 nTPM
Stomach	0.5 nTPM
Kidney	0.0 nTPM
Bone marrow	0.0 nTPM

Dendritic cells	7.4 nTPM
PBMC	20.0 nTPM
Breast	1.1 nTPM
Adipose tissue	1.0 nTPM

Endothelial cells	29.9 nTPM
Endometrium	187.2 nTPM
Skin	48.1 nTPM
Heart muscle	38.7 nTPM
Lung	37.4 nTPM
Breast	34.4 nTPM
Liver	28.4 nTPM
Placenta	13.1 nTPM
Prostate	10.1 nTPM
Skeletal muscle	9.4 nTPM
Pancreas	7.7 nTPM
Ovary	1.8 nTPM
Esophagus	1.6 nTPM
Testis	0.3 nTPM
Eye	0.0 nTPM

Fibroblasts	348.1 nTPM
Placenta	896.5 nTPM
Heart muscle	636.5 nTPM
Skin	592.9 nTPM
Skeletal muscle	416.2 nTPM
Adipose tissue	350.7 nTPM
Breast	249.9 nTPM
Esophagus	196.5 nTPM
Lung	174.3 nTPM
Stomach	145.5 nTPM
Prostate	129.4 nTPM
Ovary	40.5 nTPM

Intestinal goblet cells	0.2 nTPM
Colon	0.7 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Macrophages	605.6 nTPM
Stomach	2886.2 nTPM
Spleen	1429.8 nTPM
Skeletal muscle	1122.4 nTPM
Bone marrow	989.6 nTPM
Lung	613.1 nTPM
Kidney	551.4 nTPM
Adipose tissue	494.9 nTPM
Testis	357.3 nTPM
Endometrium	232.7 nTPM
Esophagus	155.7 nTPM
Ovary	70.1 nTPM
PBMC	68.2 nTPM
Prostate	59.6 nTPM
Pancreas	35.7 nTPM
Breast	17.7 nTPM

Paneth cells	1.1 nTPM
Colon	3.3 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Plasma cells	2.5 nTPM
Adipose tissue	10.3 nTPM
Stomach	2.1 nTPM
Spleen	0.3 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

Respiratory ciliated cells	16.2 nTPM
Lung	27.7 nTPM
Bronchus	4.8 nTPM

Smooth muscle cells	80.6 nTPM
Pancreas	339.9 nTPM
Endometrium	259.5 nTPM
Ovary	85.9 nTPM
Bronchus	75.6 nTPM
Skin	39.5 nTPM
Adipose tissue	33.2 nTPM
Heart muscle	25.3 nTPM
Skeletal muscle	12.0 nTPM
Prostate	7.8 nTPM
Esophagus	6.2 nTPM
Breast	2.1 nTPM

T-cells	12.7 nTPM
Endometrium	82.9 nTPM
Lung	45.6 nTPM
Skin	42.3 nTPM
PBMC	21.9 nTPM
Skeletal muscle	9.7 nTPM
Prostate	4.7 nTPM
Liver	2.8 nTPM
Kidney	2.0 nTPM
Breast	1.1 nTPM
Colon	1.0 nTPM
Stomach	1.0 nTPM
Spleen	0.7 nTPM
Adipose tissue	0.6 nTPM
Bone marrow	0.2 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM

Basal keratinocytes	38.6 nTPM
Skin	38.6 nTPM

Basal prostatic cells	10.6 nTPM
Prostate	10.6 nTPM

Basal respiratory cells	14.9 nTPM
Bronchus	14.9 nTPM

Basal squamous epithelial cells	1.2 nTPM
Esophagus	1.2 nTPM

Undifferentiated cells	0.3 nTPM
Colon	0.9 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 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