Single cell type - CTSC - 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.	CTSC
Gene descriptionⁱ Full gene name according to HGNC.	Cathepsin C
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Enzymes Human disease related genes Metabolic proteins Plasma proteins Potential drug targets
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.	13

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 (Hofbauer cells, Basal respiratory cells, Club 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	Low immune cell specificity
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 all
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 (BJ hTERT+)
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 all
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 (Hofbauer cells, Basal respiratory cells, Club 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

CTSC 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
MR1	Major histocompatibility complex, class I-related	0.6927	26
ATP6AP1	ATPase H+ transporting accessory protein 1	0.6861	4
IFNGR1	Interferon gamma receptor 1	0.6824	26
PLD3	Phospholipase D family member 3	0.6784	4
SERPINB3	Serpin family B member 3	0.6754	26
HEXA	Hexosaminidase subunit alpha	0.6752	4
ATP6AP2	ATPase H+ transporting accessory protein 2	0.6663	4
ATP12A	ATPase H+/K+ transporting non-gastric alpha2 subunit	0.6482	26
IKBKE	Inhibitor of nuclear factor kappa B kinase subunit epsilon	0.6481	26
PGLYRP4	Peptidoglycan recognition protein 4	0.6469	26
SERPINB4	Serpin family B member 4	0.6459	26
TREM2	Triggering receptor expressed on myeloid cells 2	0.6441	4
CXCL1	C-X-C motif chemokine ligand 1	0.6416	26
TMEM45A	Transmembrane protein 45A	0.6392	26
BPIFB1	BPI fold containing family B member 1	0.6390	26

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	78.6 nTPM
Breast	105.8 nTPM
Adipose tissue	51.3 nTPM

Alveolar cells type 1	22.4 nTPM
Lung	22.4 nTPM

Alveolar cells type 2	88.1 nTPM
Lung	88.1 nTPM

Astrocytes	0.3 nTPM
Brain	0.3 nTPM

B-cells	40.8 nTPM
Colon	71.9 nTPM
Liver	70.0 nTPM
Kidney	42.9 nTPM
Breast	36.0 nTPM
Spleen	35.7 nTPM
PBMC	34.3 nTPM
Adipose tissue	33.6 nTPM
Lymph node	31.8 nTPM
Stomach	28.6 nTPM
Bone marrow	22.9 nTPM

Dendritic cells	330.6 nTPM
PBMC	506.1 nTPM
Breast	262.8 nTPM
Adipose tissue	222.9 nTPM

Endothelial cells	94.8 nTPM
Esophagus	292.0 nTPM
Placenta	197.8 nTPM
Skin	177.1 nTPM
Breast	151.5 nTPM
Prostate	132.7 nTPM
Endometrium	79.9 nTPM
Eye	58.2 nTPM
Liver	54.1 nTPM
Lung	53.0 nTPM
Pancreas	38.6 nTPM
Skeletal muscle	35.5 nTPM
Testis	29.9 nTPM
Heart muscle	21.2 nTPM
Ovary	4.8 nTPM

Fibroblasts	114.4 nTPM
Placenta	619.8 nTPM
Stomach	150.0 nTPM
Prostate	124.1 nTPM
Lung	92.8 nTPM
Ovary	74.3 nTPM
Skin	54.9 nTPM
Esophagus	50.7 nTPM
Skeletal muscle	32.3 nTPM
Adipose tissue	26.8 nTPM
Heart muscle	19.0 nTPM
Breast	13.9 nTPM

Intestinal goblet cells	19.4 nTPM
Colon	24.3 nTPM
Rectum	17.3 nTPM
Small intestine	16.7 nTPM

Macrophages	391.7 nTPM
Ovary	1154.2 nTPM
Pancreas	650.8 nTPM
Lung	585.4 nTPM
Spleen	519.5 nTPM
Kidney	513.5 nTPM
Bone marrow	428.6 nTPM
Endometrium	340.6 nTPM
Prostate	291.2 nTPM
Adipose tissue	282.7 nTPM
Breast	263.0 nTPM
Skeletal muscle	238.2 nTPM
Testis	222.4 nTPM
Stomach	190.5 nTPM
Esophagus	180.9 nTPM
PBMC	13.6 nTPM

Paneth cells	72.3 nTPM
Rectum	134.1 nTPM
Colon	79.0 nTPM
Small intestine	3.7 nTPM

Plasma cells	78.5 nTPM
Spleen	84.8 nTPM
Bone marrow	84.1 nTPM
Adipose tissue	75.5 nTPM
Stomach	74.1 nTPM
Esophagus	74.0 nTPM

Respiratory ciliated cells	93.7 nTPM
Bronchus	100.0 nTPM
Lung	87.4 nTPM

Smooth muscle cells	150.8 nTPM
Pancreas	259.0 nTPM
Prostate	240.7 nTPM
Bronchus	211.5 nTPM
Ovary	203.3 nTPM
Endometrium	150.9 nTPM
Adipose tissue	148.9 nTPM
Esophagus	130.2 nTPM
Breast	118.2 nTPM
Skeletal muscle	100.3 nTPM
Skin	76.9 nTPM
Heart muscle	19.2 nTPM

T-cells	170.6 nTPM
Ovary	349.3 nTPM
Kidney	262.8 nTPM
Liver	228.1 nTPM
Bone marrow	197.5 nTPM
Skin	179.6 nTPM
Breast	176.8 nTPM
Lung	174.7 nTPM
Adipose tissue	159.6 nTPM
Stomach	157.9 nTPM
Colon	152.5 nTPM
Esophagus	137.6 nTPM
Endometrium	134.4 nTPM
Spleen	133.5 nTPM
Skeletal muscle	133.3 nTPM
Prostate	132.5 nTPM
PBMC	116.8 nTPM
Lymph node	73.5 nTPM

Cholangiocytes	52.9 nTPM
Liver	52.9 nTPM

Collecting duct cells	40.5 nTPM
Kidney	40.5 nTPM

Cone photoreceptor cells	0.0 nTPM
Eye	0.0 nTPM

Cytotrophoblasts	414.1 nTPM
Placenta	414.1 nTPM

Undifferentiated cells	44.9 nTPM
Colon	68.1 nTPM
Rectum	38.4 nTPM
Small intestine	28.3 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