Single cell type - CLDN4 - 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.	CLDN4
Gene descriptionⁱ Full gene name according to HGNC.	Claudin 4
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes Disease related genes Human disease related genes Potential drug targets 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	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	Epithelial cell types - Mixed 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 (Urothelial cells, Basal prostatic cells, Glandular and luminal cells, Prostatic glandular cells, Paneth 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, BEWO, CAPAN-2, MCF7, OE19, PC-3, RT4, SK-BR-3)
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 (Urothelial cells, Basal prostatic cells, Glandular and luminal cells, Prostatic glandular cells, Paneth 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

CLDN4 is part of cluster 22 Epithelial cell types - Mixed function with confidenceⁱ 1
298 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
PADI3	Peptidyl arginine deiminase 3	0.8277	22
TMEM30B	Transmembrane protein 30B	0.8105	22
PLEKHN1	Pleckstrin homology domain containing N1	0.8032	22
ADGRF1	Adhesion G protein-coupled receptor F1	0.8030	22
RNF39	Ring finger protein 39	0.7949	22
ARTN	Artemin	0.7769	22
GJB4	Gap junction protein beta 4	0.7743	22
OCLN	Occludin	0.7715	22
C3orf52	Chromosome 3 open reading frame 52	0.7674	22
KRT17	Keratin 17	0.7630	22
TACSTD2	Tumor associated calcium signal transducer 2	0.7601	22
TRAF4	TNF receptor associated factor 4	0.7579	22
LRRC8A	Leucine rich repeat containing 8 VRAC subunit A	0.7543	22
RNASE7	Ribonuclease A family member 7	0.7533	22
GADD45A	Growth arrest and DNA damage inducible alpha	0.7502	22

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	5.1 nTPM
Breast	9.7 nTPM
Adipose tissue	0.5 nTPM

Alveolar cells type 1	275.7 nTPM
Lung	275.7 nTPM

Alveolar cells type 2	230.2 nTPM
Lung	230.2 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	12.2 nTPM
Colon	73.5 nTPM
Breast	44.1 nTPM
Kidney	4.8 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Dendritic cells	18.7 nTPM
Breast	56.2 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM

Distal enterocytes	1985.0 nTPM
Colon	2196.3 nTPM
Rectum	1773.6 nTPM

Endothelial cells	41.3 nTPM
Breast	263.6 nTPM
Prostate	172.9 nTPM
Endometrium	80.3 nTPM
Placenta	30.7 nTPM
Pancreas	15.5 nTPM
Lung	6.2 nTPM
Esophagus	4.2 nTPM
Skin	3.4 nTPM
Liver	0.9 nTPM
Heart muscle	0.6 nTPM
Skeletal muscle	0.3 nTPM
Eye	0.0 nTPM
Testis	0.0 nTPM
Ovary	0.0 nTPM

Enteroendocrine cells	675.5 nTPM
Colon	717.7 nTPM
Rectum	633.4 nTPM

Fibroblasts	27.0 nTPM
Prostate	127.9 nTPM
Placenta	73.2 nTPM
Breast	54.7 nTPM
Lung	27.9 nTPM
Esophagus	4.8 nTPM
Adipose tissue	3.8 nTPM
Skin	3.7 nTPM
Skeletal muscle	0.8 nTPM
Heart muscle	0.1 nTPM
Ovary	0.0 nTPM
Stomach	0.0 nTPM

Glandular and luminal cells	2298.8 nTPM
Endometrium	2298.8 nTPM

Intestinal goblet cells	1266.9 nTPM
Colon	1826.7 nTPM
Small intestine	1118.8 nTPM
Rectum	855.2 nTPM

Macrophages	29.3 nTPM
Prostate	213.2 nTPM
Endometrium	141.1 nTPM
Breast	27.2 nTPM
Pancreas	17.8 nTPM
PBMC	13.6 nTPM
Lung	12.4 nTPM
Esophagus	6.3 nTPM
Adipose tissue	2.9 nTPM
Kidney	2.3 nTPM
Skeletal muscle	1.9 nTPM
Ovary	0.1 nTPM
Testis	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	2081.0 nTPM
Colon	3534.2 nTPM
Small intestine	1666.9 nTPM
Rectum	1041.7 nTPM

Plasma cells	2.5 nTPM
Esophagus	12.3 nTPM
Adipose tissue	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Cholangiocytes	287.4 nTPM
Liver	287.4 nTPM

Collecting duct cells	218.8 nTPM
Kidney	218.8 nTPM

Cytotrophoblasts	771.7 nTPM
Placenta	771.7 nTPM

Endometrial ciliated cells	1201.7 nTPM
Endometrium	1201.7 nTPM

Respiratory ciliated cells	635.6 nTPM
Bronchus	918.4 nTPM
Lung	352.8 nTPM

Smooth muscle cells	68.2 nTPM
Bronchus	331.7 nTPM
Prostate	235.1 nTPM
Endometrium	97.7 nTPM
Pancreas	42.4 nTPM
Breast	33.2 nTPM
Esophagus	7.8 nTPM
Skin	1.8 nTPM
Heart muscle	0.4 nTPM
Ovary	0.3 nTPM
Skeletal muscle	0.0 nTPM
Adipose tissue	0.0 nTPM

T-cells	40.7 nTPM
Prostate	274.6 nTPM
Endometrium	196.7 nTPM
Colon	127.8 nTPM
Breast	73.1 nTPM
Lung	13.6 nTPM
Kidney	2.7 nTPM
Skin	1.9 nTPM
Liver	0.7 nTPM
PBMC	0.3 nTPM
Skeletal muscle	0.3 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	965.1 nTPM
Colon	1367.8 nTPM
Small intestine	868.7 nTPM
Rectum	658.8 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