Single cell type - CTSA - 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.	CTSA
Gene descriptionⁱ Full gene name according to HGNC.	Cathepsin A
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Enzymes Human disease related genes Metabolic 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
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	9

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	Myeloid cells - Hemostasis (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, Proximal enterocytes)
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 (ASC diff)
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 (Distal enterocytes, Proximal enterocytes)

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

CTSA is part of cluster 51 Myeloid cells - Hemostasis with confidenceⁱ 1
155 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
NT5C3A	5'-nucleotidase, cytosolic IIIA	0.7720	51
LAMTOR1	Late endosomal/lysosomal adaptor, MAPK and MTOR activator 1	0.6713	51
ARF3	ADP ribosylation factor 3	0.6547	53
LGALS12	Galectin 12	0.6212	51
RUFY1	RUN and FYVE domain containing 1	0.6199	51
PTCRA	Pre T cell antigen receptor alpha	0.6107	51
RGS18	Regulator of G protein signaling 18	0.6098	51
PPBP	Pro-platelet basic protein	0.6098	51
TREML1	Triggering receptor expressed on myeloid cells like 1	0.6067	51
ITGB3	Integrin subunit beta 3	0.6043	51
SLC35D3	Solute carrier family 35 member D3	0.6031	51
TUBB1	Tubulin beta 1 class VI	0.6030	51
NCOA4	Nuclear receptor coactivator 4	0.6023	51
HBG1	Hemoglobin subunit gamma 1	0.6016	51
PF4	Platelet factor 4	0.6008	51

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	53.7 nTPM
Adipose tissue	54.6 nTPM
Breast	52.7 nTPM

Alveolar cells type 1	35.3 nTPM
Lung	35.3 nTPM

Alveolar cells type 2	32.6 nTPM
Lung	32.6 nTPM

Astrocytes	26.1 nTPM
Brain	26.1 nTPM

B-cells	38.2 nTPM
Colon	54.3 nTPM
Stomach	47.7 nTPM
Liver	47.4 nTPM
Kidney	38.1 nTPM
Breast	37.5 nTPM
Spleen	37.4 nTPM
PBMC	37.1 nTPM
Bone marrow	30.2 nTPM
Adipose tissue	29.1 nTPM
Lymph node	23.0 nTPM

Dendritic cells	27.5 nTPM
Breast	39.8 nTPM
Adipose tissue	26.6 nTPM
PBMC	16.0 nTPM

Endothelial cells	56.0 nTPM
Pancreas	100.4 nTPM
Eye	96.3 nTPM
Placenta	88.1 nTPM
Ovary	72.4 nTPM
Esophagus	67.4 nTPM
Endometrium	51.3 nTPM
Breast	50.2 nTPM
Liver	48.6 nTPM
Skin	45.7 nTPM
Prostate	45.5 nTPM
Skeletal muscle	41.6 nTPM
Testis	40.9 nTPM
Lung	21.8 nTPM
Heart muscle	13.8 nTPM

Fibroblasts	86.8 nTPM
Stomach	210.9 nTPM
Esophagus	171.3 nTPM
Placenta	123.1 nTPM
Adipose tissue	122.5 nTPM
Breast	73.3 nTPM
Skeletal muscle	71.7 nTPM
Ovary	52.5 nTPM
Skin	48.9 nTPM
Prostate	44.7 nTPM
Lung	22.4 nTPM
Heart muscle	13.5 nTPM

Intestinal goblet cells	74.5 nTPM
Colon	80.7 nTPM
Rectum	80.6 nTPM
Small intestine	62.3 nTPM

Macrophages	273.1 nTPM
PBMC	1445.8 nTPM
Pancreas	719.7 nTPM
Ovary	423.9 nTPM
Bone marrow	192.5 nTPM
Kidney	186.8 nTPM
Prostate	180.0 nTPM
Spleen	173.1 nTPM
Stomach	164.1 nTPM
Endometrium	98.4 nTPM
Adipose tissue	92.4 nTPM
Esophagus	91.2 nTPM
Skeletal muscle	90.6 nTPM
Breast	88.3 nTPM
Lung	84.8 nTPM
Testis	64.4 nTPM

Paneth cells	216.0 nTPM
Colon	471.0 nTPM
Rectum	101.9 nTPM
Small intestine	75.1 nTPM

Plasma cells	41.9 nTPM
Stomach	52.1 nTPM
Esophagus	49.4 nTPM
Bone marrow	46.2 nTPM
Spleen	39.4 nTPM
Adipose tissue	22.5 nTPM

Respiratory ciliated cells	34.2 nTPM
Bronchus	43.6 nTPM
Lung	24.8 nTPM

Smooth muscle cells	54.5 nTPM
Pancreas	160.2 nTPM
Ovary	68.5 nTPM
Prostate	60.0 nTPM
Adipose tissue	58.1 nTPM
Skeletal muscle	53.4 nTPM
Esophagus	51.2 nTPM
Breast	44.0 nTPM
Skin	35.9 nTPM
Endometrium	32.1 nTPM
Bronchus	26.1 nTPM
Heart muscle	9.7 nTPM

T-cells	49.1 nTPM
Breast	83.5 nTPM
Kidney	75.3 nTPM
Stomach	61.3 nTPM
Skin	59.9 nTPM
Lung	59.2 nTPM
PBMC	57.9 nTPM
Liver	56.6 nTPM
Spleen	51.9 nTPM
Ovary	51.2 nTPM
Colon	48.5 nTPM
Bone marrow	45.9 nTPM
Lymph node	39.7 nTPM
Endometrium	35.1 nTPM
Adipose tissue	34.5 nTPM
Prostate	28.4 nTPM
Skeletal muscle	26.6 nTPM
Esophagus	19.7 nTPM

Basal keratinocytes	24.2 nTPM
Skin	24.2 nTPM

Basal prostatic cells	38.9 nTPM
Prostate	38.9 nTPM

Basal respiratory cells	88.8 nTPM
Bronchus	88.8 nTPM

Basal squamous epithelial cells	17.6 nTPM
Esophagus	17.6 nTPM

Undifferentiated cells	113.9 nTPM
Colon	148.6 nTPM
Rectum	116.8 nTPM
Small intestine	76.2 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