Single cell type - CDH3 - 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.	CDH3
Gene descriptionⁱ Full gene name according to HGNC.	Cadherin 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Human disease related genes
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.	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	Respiratory epithelial cells - Mucosal defense (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 (Basal respiratory cells, Pancreatic endocrine cells, Granulosa cells, Basal squamous epithelial cells, Basal prostatic cells, Basal keratinocytes, Melanocytes)
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, HaCaT, HBEC3-KT, hTCEpi, hTERT-HME1, 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 some
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 (Basal respiratory cells, Pancreatic endocrine cells, Granulosa cells, Basal squamous epithelial cells, Basal prostatic cells, Basal keratinocytes, Melanocytes)

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

CDH3 is part of cluster 26 Respiratory epithelial cells - Mucosal defense with confidenceⁱ 1
293 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
IGFL1	IGF like family member 1	0.7542	26
MMP10	Matrix metallopeptidase 10	0.7427	26
LHX5	LIM homeobox 5	0.7297	26
KRTAP19-3	Keratin associated protein 19-3	0.7294	26
MMP13	Matrix metallopeptidase 13	0.7291	26
SLC38A5	Solute carrier family 38 member 5	0.6935	26
MRGPRX4	MAS related GPR family member X4	0.6824	26
AMTN	Amelotin	0.6812	26
MRGPRX3	MAS related GPR family member X3	0.6787	26
LOXL4	Lysyl oxidase like 4	0.6723	26
DHCR7	7-dehydrocholesterol reductase	0.6511	15
PPP1R13L	Protein phosphatase 1 regulatory subunit 13 like	0.6403	40
PORCN	Porcupine O-acyltransferase	0.6294	26
S100A7	S100 calcium binding protein A7	0.6265	26
TRAPPC4	Trafficking protein particle complex 4	0.6216	40

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	0.2 nTPM
Breast	0.3 nTPM
Adipose tissue	0.0 nTPM

Alveolar cells type 1	16.0 nTPM
Lung	16.0 nTPM

Alveolar cells type 2	4.6 nTPM
Lung	4.6 nTPM

Astrocytes	0.7 nTPM
Brain	0.7 nTPM

B-cells	0.0 nTPM
Colon	0.0 nTPM
Kidney	0.0 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
Breast	0.0 nTPM

Dendritic cells	0.5 nTPM
Breast	1.1 nTPM
Adipose tissue	0.4 nTPM
PBMC	0.0 nTPM

Endothelial cells	1.3 nTPM
Prostate	7.4 nTPM
Skin	3.0 nTPM
Breast	1.9 nTPM
Testis	1.4 nTPM
Placenta	1.1 nTPM
Esophagus	1.0 nTPM
Skeletal muscle	0.9 nTPM
Heart muscle	0.5 nTPM
Endometrium	0.5 nTPM
Ovary	0.1 nTPM
Eye	0.0 nTPM
Liver	0.0 nTPM
Lung	0.0 nTPM
Pancreas	0.0 nTPM

Fibroblasts	3.7 nTPM
Lung	22.4 nTPM
Ovary	5.3 nTPM
Prostate	3.8 nTPM
Placenta	3.5 nTPM
Skin	3.3 nTPM
Breast	1.0 nTPM
Esophagus	0.6 nTPM
Heart muscle	0.5 nTPM
Skeletal muscle	0.5 nTPM
Adipose tissue	0.1 nTPM
Stomach	0.0 nTPM

Intestinal goblet cells	1.5 nTPM
Colon	2.2 nTPM
Rectum	1.4 nTPM
Small intestine	1.1 nTPM

Macrophages	0.7 nTPM
Lung	3.4 nTPM
Prostate	3.4 nTPM
Ovary	1.6 nTPM
Skeletal muscle	1.0 nTPM
Breast	0.4 nTPM
Adipose tissue	0.1 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Endometrium	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	0.1 nTPM
Rectum	0.2 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Plasma cells	1.2 nTPM
Esophagus	6.1 nTPM
Adipose tissue	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Respiratory ciliated cells	12.6 nTPM
Bronchus	20.9 nTPM
Lung	4.4 nTPM

Smooth muscle cells	5.9 nTPM
Bronchus	26.4 nTPM
Ovary	21.3 nTPM
Prostate	7.2 nTPM
Skin	2.8 nTPM
Pancreas	2.2 nTPM
Esophagus	1.5 nTPM
Skeletal muscle	1.4 nTPM
Endometrium	1.0 nTPM
Heart muscle	0.3 nTPM
Adipose tissue	0.2 nTPM
Breast	0.2 nTPM

T-cells	1.2 nTPM
Esophagus	6.6 nTPM
Prostate	4.7 nTPM
Skin	2.3 nTPM
Skeletal muscle	2.3 nTPM
Lung	1.5 nTPM
Colon	1.4 nTPM
Endometrium	0.8 nTPM
Breast	0.6 nTPM
PBMC	0.1 nTPM
Adipose tissue	0.1 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
Ovary	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Collecting duct cells	14.7 nTPM
Kidney	14.7 nTPM

Cone photoreceptor cells	2.1 nTPM
Eye	2.1 nTPM

Cytotrophoblasts	23.4 nTPM
Placenta	23.4 nTPM

Endometrial stromal cells	8.2 nTPM
Endometrium	8.2 nTPM

Undifferentiated cells	1.5 nTPM
Colon	3.1 nTPM
Rectum	1.1 nTPM
Small intestine	0.2 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