Single cell type - CGNL1 - 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.	CGNL1
Gene descriptionⁱ Full gene name according to HGNC.	Cingulin like 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	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
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	Alveolar cells - Smell perception (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 (Microglial cells, Alveolar cells type 2, Astrocytes, Hepatocytes, Hepatic stellate 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 (HUVEC TERT2, SuSa, TIME)
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 (Microglial cells, Alveolar cells type 2, Astrocytes, Hepatocytes, Hepatic stellate 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

CGNL1 is part of cluster 11 Alveolar cells - Smell perception with confidenceⁱ 1
281 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
PALM3	Paralemmin 3	0.5740	11
LRRN4	Leucine rich repeat neuronal 4	0.5737	11
AC092329.3	Zinc finger protein 724	0.5669	11
AQP4	Aquaporin 4	0.5652	11
NAPSA	Napsin A aspartic peptidase	0.5595	11
VEPH1	Ventricular zone expressed PH domain containing 1	0.5399	11
FAM189A2	Family with sequence similarity 189 member A2	0.5356	64
CST5	Cystatin D	0.5356	11
FGGY	FGGY carbohydrate kinase domain containing	0.5293	11
AL132780.3	Novel protein	0.5288	11
SEC14L6	SEC14 like lipid binding 6	0.5274	5
SYT15	Synaptotagmin 15	0.5266	11
AGER	Advanced glycosylation end-product specific receptor	0.5243	11
SFTA2	Surfactant associated 2	0.5103	11
ACSS3	Acyl-CoA synthetase short chain family member 3	0.5050	64

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	3.9 nTPM
Adipose tissue	4.3 nTPM
Breast	3.4 nTPM

Alveolar cells type 1	51.3 nTPM
Lung	51.3 nTPM

B-cells	0.2 nTPM
Liver	1.3 nTPM
Stomach	0.5 nTPM
Colon	0.0 nTPM
Kidney	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
Breast	0.0 nTPM

Basal keratinocytes	4.6 nTPM
Skin	4.6 nTPM

Basal prostatic cells	13.4 nTPM
Prostate	13.4 nTPM

Dendritic cells	1.6 nTPM
PBMC	4.0 nTPM
Breast	0.7 nTPM
Adipose tissue	0.0 nTPM

Endothelial cells	21.8 nTPM
Endometrium	78.1 nTPM
Placenta	59.1 nTPM
Heart muscle	43.1 nTPM
Lung	34.3 nTPM
Eye	33.2 nTPM
Prostate	10.1 nTPM
Ovary	8.9 nTPM
Esophagus	8.2 nTPM
Skin	7.2 nTPM
Breast	6.9 nTPM
Liver	5.5 nTPM
Pancreas	3.9 nTPM
Testis	3.3 nTPM
Skeletal muscle	3.0 nTPM

Fibroblasts	17.1 nTPM
Heart muscle	55.4 nTPM
Lung	48.0 nTPM
Prostate	25.3 nTPM
Skin	22.9 nTPM
Ovary	9.4 nTPM
Placenta	9.2 nTPM
Skeletal muscle	5.1 nTPM
Esophagus	4.8 nTPM
Breast	4.5 nTPM
Stomach	3.0 nTPM
Adipose tissue	0.6 nTPM

Intestinal goblet cells	3.7 nTPM
Rectum	5.9 nTPM
Small intestine	3.0 nTPM
Colon	2.2 nTPM

Macrophages	0.9 nTPM
Kidney	3.0 nTPM
Lung	2.9 nTPM
Prostate	2.2 nTPM
Esophagus	1.6 nTPM
Testis	1.2 nTPM
Breast	1.2 nTPM
Endometrium	1.0 nTPM
Skeletal muscle	0.2 nTPM
Ovary	0.2 nTPM
PBMC	0.0 nTPM
Pancreas	0.0 nTPM
Adipose tissue	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	1.2 nTPM
Rectum	3.6 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Plasma cells	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

Respiratory ciliated cells	2.2 nTPM
Lung	2.9 nTPM
Bronchus	1.5 nTPM

Smooth muscle cells	2.3 nTPM
Heart muscle	5.9 nTPM
Ovary	3.7 nTPM
Prostate	3.2 nTPM
Skin	3.1 nTPM
Endometrium	3.0 nTPM
Breast	2.9 nTPM
Pancreas	2.7 nTPM
Skeletal muscle	0.3 nTPM
Bronchus	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM

T-cells	1.2 nTPM
Kidney	8.2 nTPM
Skin	4.6 nTPM
Endometrium	3.0 nTPM
Liver	1.5 nTPM
Lung	1.5 nTPM
Breast	1.0 nTPM
Colon	0.5 nTPM
Skeletal muscle	0.3 nTPM
PBMC	0.1 nTPM
Prostate	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

Astrocytes	79.7 nTPM
Brain	79.7 nTPM

Cholangiocytes	10.0 nTPM
Liver	10.0 nTPM

Collecting duct cells	22.0 nTPM
Kidney	22.0 nTPM

Distal tubular cells	41.1 nTPM
Kidney	41.1 nTPM

Undifferentiated cells	2.2 nTPM
Rectum	3.7 nTPM
Colon	2.0 nTPM
Small intestine	1.0 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