Single cell type - CDH1 - 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.	CDH1
Gene descriptionⁱ Full gene name according to HGNC.	Cadherin 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes CD markers 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	Membrane
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	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 (Distal enterocytes, Glandular and luminal cells, Pancreatic endocrine 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 (plasmacytoid DC, 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 some
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 (BEWO, CACO-2, CAPAN-2, HaCaT, hTCEpi, MCF7, OE19, RT4, T-47d)
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 (Distal enterocytes, Glandular and luminal cells, Pancreatic endocrine 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

CDH1 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
OCLN	Occludin	0.7109	22
SCNN1A	Sodium channel epithelial 1 subunit alpha	0.6900	44
KIAA1522	KIAA1522	0.6730	53
DSG2	Desmoglein 2	0.6573	53
ILDR1	Immunoglobulin like domain containing receptor 1	0.6489	53
SLC22A5	Solute carrier family 22 member 5	0.6338	53
MAL2	Mal, T cell differentiation protein 2	0.6325	22
ERBB3	Erb-b2 receptor tyrosine kinase 3	0.6170	53
TFCP2L1	Transcription factor CP2 like 1	0.6149	44
F2RL1	F2R like trypsin receptor 1	0.6138	53
SLC26A2	Solute carrier family 26 member 2	0.6033	53
MARVELD2	MARVEL domain containing 2	0.6031	22
RBM47	RNA binding motif protein 47	0.5875	53
ARHGAP8	Rho GTPase activating protein 8	0.5803	22
TRPM6	Transient receptor potential cation channel subfamily M member 6	0.5773	53

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	0.6 nTPM
Breast	1.1 nTPM
Adipose tissue	0.0 nTPM

Alveolar cells type 1	131.4 nTPM
Lung	131.4 nTPM

Alveolar cells type 2	69.8 nTPM
Lung	69.8 nTPM

Astrocytes	0.7 nTPM
Brain	0.7 nTPM

B-cells	1.4 nTPM
Colon	6.4 nTPM
PBMC	2.8 nTPM
Stomach	1.8 nTPM
Liver	1.3 nTPM
Breast	1.3 nTPM
Adipose tissue	0.5 nTPM
Kidney	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Dendritic cells	2.5 nTPM
PBMC	4.0 nTPM
Breast	3.3 nTPM
Adipose tissue	0.2 nTPM

Endothelial cells	4.4 nTPM
Prostate	14.1 nTPM
Breast	13.6 nTPM
Pancreas	11.6 nTPM
Endometrium	9.8 nTPM
Skin	6.6 nTPM
Placenta	4.0 nTPM
Heart muscle	1.0 nTPM
Esophagus	1.0 nTPM
Skeletal muscle	0.2 nTPM
Eye	0.0 nTPM
Liver	0.0 nTPM
Lung	0.0 nTPM
Testis	0.0 nTPM
Ovary	0.0 nTPM

Enteroendocrine cells	86.7 nTPM
Colon	103.1 nTPM
Rectum	70.4 nTPM

Fibroblasts	3.4 nTPM
Prostate	9.9 nTPM
Placenta	9.6 nTPM
Lung	7.8 nTPM
Skin	3.9 nTPM
Breast	3.9 nTPM
Stomach	1.5 nTPM
Esophagus	0.6 nTPM
Heart muscle	0.1 nTPM
Ovary	0.1 nTPM
Skeletal muscle	0.0 nTPM
Adipose tissue	0.0 nTPM

Intestinal goblet cells	208.3 nTPM
Rectum	236.5 nTPM
Colon	205.9 nTPM
Small intestine	182.6 nTPM

Macrophages	3.2 nTPM
Endometrium	21.9 nTPM
Prostate	8.1 nTPM
Lung	6.7 nTPM
Pancreas	5.1 nTPM
Breast	3.2 nTPM
Kidney	0.8 nTPM
Testis	0.6 nTPM
Skeletal muscle	0.6 nTPM
Adipose tissue	0.4 nTPM
Ovary	0.2 nTPM
PBMC	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	204.6 nTPM
Colon	345.9 nTPM
Rectum	177.8 nTPM
Small intestine	90.1 nTPM

Plasma cells	2.2 nTPM
Adipose tissue	7.8 nTPM
Spleen	2.3 nTPM
Stomach	1.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

Respiratory ciliated cells	118.2 nTPM
Bronchus	156.2 nTPM
Lung	80.2 nTPM

Smooth muscle cells	7.1 nTPM
Bronchus	30.9 nTPM
Prostate	17.5 nTPM
Endometrium	11.6 nTPM
Pancreas	7.3 nTPM
Skin	4.9 nTPM
Breast	3.2 nTPM
Esophagus	1.5 nTPM
Heart muscle	1.4 nTPM
Ovary	0.3 nTPM
Skeletal muscle	0.0 nTPM
Adipose tissue	0.0 nTPM

Basal keratinocytes	94.1 nTPM
Skin	94.1 nTPM

Basal prostatic cells	130.3 nTPM
Prostate	130.3 nTPM

Basal respiratory cells	73.8 nTPM
Bronchus	73.8 nTPM

Cholangiocytes	128.7 nTPM
Liver	128.7 nTPM

T-cells	2.7 nTPM
Endometrium	25.3 nTPM
Lung	7.6 nTPM
Colon	6.6 nTPM
Breast	2.3 nTPM
Skin	1.9 nTPM
Stomach	1.2 nTPM
Bone marrow	0.3 nTPM
Spleen	0.3 nTPM
Liver	0.2 nTPM
PBMC	0.2 nTPM
Adipose tissue	0.2 nTPM
Kidney	0.0 nTPM
Prostate	0.0 nTPM
Skeletal muscle	0.0 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM

Undifferentiated cells	154.8 nTPM
Colon	171.4 nTPM
Rectum	169.9 nTPM
Small intestine	123.2 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