Single cell type - EPCAM - 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.	EPCAM
Gene descriptionⁱ Full gene name according to HGNC.	Epithelial cell adhesion molecule
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes CD markers Disease related genes FDA approved drug targets 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,Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	3

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	Intestinal epithelial cells - Unknown function (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 (Proximal enterocytes, Paneth cells, Distal enterocytes, Undifferentiated cells, Intestinal goblet cells, Ductal 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	Not detected in immune cells
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	Not detected
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 (A-431, CACO-2, CAPAN-2, OE19, 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

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 (Proximal enterocytes, Paneth cells, Distal enterocytes, Undifferentiated cells, Intestinal goblet cells, Ductal 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

EPCAM is part of cluster 53 Intestinal epithelial cells - Unknown function with confidenceⁱ 1
611 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
CDX2	Caudal type homeobox 2	0.8801	53
LGALS4	Galectin 4	0.8737	53
B3GALT5	Beta-1,3-galactosyltransferase 5	0.8386	53
TSPAN8	Tetraspanin 8	0.8376	45
PRR15L	Proline rich 15 like	0.8024	45
PIGR	Polymeric immunoglobulin receptor	0.7661	53
ISX	Intestine specific homeobox	0.7612	53
DEFA6	Defensin alpha 6	0.7550	53
SMIM22	Small integral membrane protein 22	0.7536	53
NUTM2A	NUT family member 2A	0.7435	53
CA7	Carbonic anhydrase 7	0.7409	53
VSIG10	V-set and immunoglobulin domain containing 10	0.7256	53
DEFA5	Defensin alpha 5	0.7248	45
PHGR1	Proline, histidine and glycine rich 1	0.7050	45
MUC3A	Mucin 3A, cell surface associated	0.7026	45

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	3.7 nTPM
Breast	7.0 nTPM
Adipose tissue	0.5 nTPM

Alveolar cells type 1	310.9 nTPM
Lung	310.9 nTPM

Alveolar cells type 2	148.1 nTPM
Lung	148.1 nTPM

Astrocytes	1.3 nTPM
Brain	1.3 nTPM

B-cells	7.0 nTPM
Colon	49.5 nTPM
Kidney	14.3 nTPM
Liver	3.7 nTPM
PBMC	1.4 nTPM
Stomach	1.4 nTPM
Adipose tissue	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Breast	0.0 nTPM

Dendritic cells	2.3 nTPM
Breast	6.5 nTPM
Adipose tissue	0.4 nTPM
PBMC	0.0 nTPM

Distal enterocytes	2317.0 nTPM
Rectum	3061.8 nTPM
Colon	1572.2 nTPM

Endothelial cells	5.8 nTPM
Breast	22.9 nTPM
Prostate	16.4 nTPM
Endometrium	15.0 nTPM
Heart muscle	4.6 nTPM
Pancreas	3.9 nTPM
Testis	3.8 nTPM
Skeletal muscle	3.6 nTPM
Lung	3.1 nTPM
Eye	2.4 nTPM
Liver	1.8 nTPM
Skin	1.4 nTPM
Placenta	1.1 nTPM
Ovary	0.5 nTPM
Esophagus	0.5 nTPM

Enteroendocrine cells	498.1 nTPM
Rectum	502.4 nTPM
Colon	493.9 nTPM

Fibroblasts	6.3 nTPM
Ovary	17.8 nTPM
Prostate	17.7 nTPM
Placenta	12.9 nTPM
Lung	12.3 nTPM
Breast	5.7 nTPM
Heart muscle	1.5 nTPM
Skin	0.9 nTPM
Skeletal muscle	0.2 nTPM
Adipose tissue	0.1 nTPM
Esophagus	0.1 nTPM
Stomach	0.0 nTPM

Intestinal goblet cells	1378.2 nTPM
Rectum	1447.4 nTPM
Colon	1345.8 nTPM
Small intestine	1341.4 nTPM

Macrophages	5.6 nTPM
Endometrium	36.9 nTPM
Kidney	12.0 nTPM
Lung	10.1 nTPM
Breast	7.6 nTPM
Prostate	5.7 nTPM
Pancreas	5.1 nTPM
Testis	2.3 nTPM
Esophagus	1.6 nTPM
Skeletal muscle	1.3 nTPM
Adipose tissue	0.8 nTPM
Ovary	0.3 nTPM
PBMC	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	2437.0 nTPM
Small intestine	2481.6 nTPM
Colon	2434.1 nTPM
Rectum	2395.2 nTPM

Plasma cells	1.8 nTPM
Esophagus	6.1 nTPM
Adipose tissue	1.3 nTPM
Stomach	1.0 nTPM
Spleen	0.7 nTPM
Bone marrow	0.0 nTPM

Respiratory ciliated cells	219.0 nTPM
Bronchus	241.2 nTPM
Lung	196.8 nTPM

Basal keratinocytes	9.3 nTPM
Skin	9.3 nTPM

Basal prostatic cells	227.6 nTPM
Prostate	227.6 nTPM

Basal respiratory cells	127.4 nTPM
Bronchus	127.4 nTPM

Cholangiocytes	243.1 nTPM
Liver	243.1 nTPM

Smooth muscle cells	13.7 nTPM
Bronchus	60.6 nTPM
Pancreas	28.9 nTPM
Prostate	18.7 nTPM
Endometrium	18.5 nTPM
Ovary	15.0 nTPM
Breast	6.3 nTPM
Esophagus	1.5 nTPM
Skeletal muscle	0.7 nTPM
Skin	0.4 nTPM
Heart muscle	0.2 nTPM
Adipose tissue	0.2 nTPM

T-cells	9.4 nTPM
Endometrium	56.2 nTPM
Colon	52.7 nTPM
Kidney	17.8 nTPM
Prostate	14.2 nTPM
Breast	10.3 nTPM
Lung	6.1 nTPM
Skin	1.4 nTPM
Liver	0.4 nTPM
Skeletal muscle	0.3 nTPM
PBMC	0.0 nTPM
Ovary	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Undifferentiated cells	1607.7 nTPM
Small intestine	1909.8 nTPM
Rectum	1619.5 nTPM
Colon	1293.8 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