Single cell type - CLCA4 - 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.	CLCA4
Gene descriptionⁱ Full gene name according to HGNC.	Chloride channel accessory 4
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	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.	1

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	Group enriched (Distal enterocytes, Paneth cells, Urothelial cells, Squamous epithelial 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 enriched (RT4)
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 single
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: Group enriched (Distal enterocytes, Paneth cells, Urothelial cells, Squamous epithelial 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

CLCA4 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
CEACAM7	CEA cell adhesion molecule 7	0.9505	53
AQP8	Aquaporin 8	0.9454	53
MIER3	MIER family member 3	0.9363	53
MYO15B	Myosin XVB	0.9355	53
TRIM31	Tripartite motif containing 31	0.9338	53
SIRT6	Sirtuin 6	0.9328	53
GCNT3	Glucosaminyl (N-acetyl) transferase 3, mucin type	0.9236	53
CLDN23	Claudin 23	0.9203	53
MS4A12	Membrane spanning 4-domains A12	0.9190	53
CD177	CD177 molecule	0.9181	53
SLC26A3	Solute carrier family 26 member 3	0.9158	53
CEACAM1	CEA cell adhesion molecule 1	0.8998	53
RSAD2	Radical S-adenosyl methionine domain containing 2	0.8935	53
TMEM54	Transmembrane protein 54	0.8819	53
CGN	Cingulin	0.8770	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	0.1 nTPM
Adipose tissue	0.2 nTPM
Breast	0.0 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	0.0 nTPM
Lung	0.0 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	2.9 nTPM
Colon	28.7 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	0.2 nTPM
Breast	0.7 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM

Endothelial cells	0.3 nTPM
Prostate	2.0 nTPM
Esophagus	1.5 nTPM
Breast	0.5 nTPM
Heart muscle	0.2 nTPM
Skin	0.1 nTPM
Eye	0.0 nTPM
Liver	0.0 nTPM
Lung	0.0 nTPM
Placenta	0.0 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Endometrium	0.0 nTPM
Skeletal muscle	0.0 nTPM
Ovary	0.0 nTPM

Fibroblasts	0.4 nTPM
Esophagus	2.4 nTPM
Prostate	1.2 nTPM
Heart muscle	0.2 nTPM
Skin	0.1 nTPM
Lung	0.0 nTPM
Placenta	0.0 nTPM
Skeletal muscle	0.0 nTPM
Ovary	0.0 nTPM
Adipose tissue	0.0 nTPM
Stomach	0.0 nTPM
Breast	0.0 nTPM

Intestinal goblet cells	9.8 nTPM
Colon	16.5 nTPM
Rectum	12.6 nTPM
Small intestine	0.4 nTPM

Macrophages	0.3 nTPM
Prostate	3.4 nTPM
Endometrium	0.4 nTPM
Breast	0.1 nTPM
Kidney	0.0 nTPM
Lung	0.0 nTPM
PBMC	0.0 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Skeletal muscle	0.0 nTPM
Ovary	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	183.2 nTPM
Colon	520.4 nTPM
Rectum	29.3 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	1.9 nTPM
Lung	2.9 nTPM
Bronchus	0.9 nTPM

Smooth muscle cells	0.4 nTPM
Prostate	1.9 nTPM
Esophagus	1.5 nTPM
Bronchus	1.0 nTPM
Skin	0.4 nTPM
Heart muscle	0.1 nTPM
Pancreas	0.0 nTPM
Endometrium	0.0 nTPM
Skeletal muscle	0.0 nTPM
Ovary	0.0 nTPM
Adipose tissue	0.0 nTPM
Breast	0.0 nTPM

T-cells	1.5 nTPM
Colon	20.5 nTPM
Prostate	4.7 nTPM
Endometrium	0.3 nTPM
Breast	0.1 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
Lung	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	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

Basal keratinocytes	3.3 nTPM
Skin	3.3 nTPM

Basal prostatic cells	40.3 nTPM
Prostate	40.3 nTPM

Basal respiratory cells	6.5 nTPM
Bronchus	6.5 nTPM

Collecting duct cells	1.8 nTPM
Kidney	1.8 nTPM

Undifferentiated cells	12.0 nTPM
Colon	31.3 nTPM
Rectum	4.5 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