Single cell type - CTSB - The Human Protein Atlas

CTSB

Search result

Field

Term

Cluster

Pathway

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.	CTSB
Gene descriptionⁱ Full gene name according to HGNC.	Cathepsin B
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Cancer-related genes Candidate cardiovascular disease genes 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.	Secreted, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	52

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.	Macrophages - Innate immune response (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.	Cell type enhanced (Hofbauer cells, Kupffer cells, Macrophages)
Tau specificity scoreⁱ Tau specificity score is a numerical indicator of the specificity of the gene expression across cells or tissues. The value ranges from 0 and 1, where 0 indicates identical expression across all cells/tissue types, while 1 indicates expression in a single cell/tissue type.	0.39
Brain cluster specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell cluster types based on snRNA-seq data from brain samples. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. "cell type" refer to one of the 34 cluster names used to summarize the 2.5 million cells included in the brain cell representation.	Cell type enriched (Central nervous system macrophage)
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.	Group enriched (classical monocyte, intermediate monocyte, plasmacytoid DC, basophil, non-classical monocyte, myeloid DC)
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); neXtProt protein existence (neXtProt evidence);and a Human Protein Atlas antibody- or RNA based score (HPA evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable.	Evidence at protein level
Extracellular locationⁱ A possible secretion of the protein was predicted based on N-terminal signal sequence (signal peptide) predictions and transmembrane region predictions, and subsequently annotated for its local or systemic secretion based on literature, function, and protein and RNA expression data.	Protein predicted to be secreted

ASSAYSⁱ

SINGLE CELL TYPESⁱ A summary of normalized 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 RNA single cell type specificity: Cell type enhanced (Hofbauer cells, Kupffer cells, Macrophages)

TISSUE CELL TYPEⁱ The tissue cell type section provides a cell type specificity prediction for all protein coding genes. More information on the data available can be found here and a description of the analysis here.
	Core cell typesⁱ The core cell type table displays data for a panel of eight cell types that are found in many tissues. Colored dots indicate that the selected gene has core cell type specificity in the indicated tissue. Grey dots indicate that cell type is present within that tissue, but the selected gene is not predicted to be enriched there. Category Alphabetical Enrichment Tissue specific cell typesⁱ This plot shows the enrichment score of the selected gene in all non-core cell types found within the profiled tissues, allowing comparisons between different cell types within different tissues. An enlarged symbol indicates classification of the gene as cell type enriched in the corresponding cell type.

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Cell type enriched (Central nervous system macrophage)

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
HPA datasetⁱ The resulting transcript expression values calculated as nTPM, resulting from the internal normalization pipeline for 18 immune cell types and total peripheral blood mononuclear cells (PBMC). Lineage Expression Alphabetical Immune cell type specificity: Group enriched (classical monocyte, intermediate monocyte, plasmacytoid DC, basophil, non-classical monocyte, myeloid DC)
Monaco datasetⁱ The transcript expression values (nTPM) resulting from the internal normalization pipeline are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SINGLE CELL TYPE

CTSB is part of cluster 58 Macrophages - Innate immune response with confidenceⁱ 1
420 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
MS4A4A	Membrane spanning 4-domains A4A	0.8635	58
CD163	CD163 molecule	0.8596	58
LIPA	Lipase A, lysosomal acid type	0.8443	58
OTOA	Otoancorin	0.8434	58
GSDMA	Gasdermin A	0.8386	58
SIGLEC1	Sialic acid binding Ig like lectin 1	0.8326	58
CD14	CD14 molecule	0.8274	58
C1QC	Complement C1q C chain	0.8230	58
CREG1	Cellular repressor of E1A stimulated genes 1	0.8212	58
CCR1	C-C motif chemokine receptor 1	0.8197	58
RAB42	RAB42, member RAS oncogene family	0.8155	58
CD68	CD68 molecule	0.7951	58
GPR34	G protein-coupled receptor 34	0.7946	58
CRYBB1	Crystallin beta B1	0.7920	58
ADAP2	ArfGAP with dual PH domains 2	0.7870	58

IMMUNE CELLS

CTSB is part of cluster 10 Non-specific - Membrane trafficking with confidenceⁱ 0.95
408 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
DAP	Death associated protein	0.9762	10
FPR3	Formyl peptide receptor 3	0.9762	10
ZEB2	Zinc finger E-box binding homeobox 2	0.9762	10
NKIRAS2	NFKB inhibitor interacting Ras like 2	0.9762	10
FADS1	Fatty acid desaturase 1	0.9762	10
DBNL	Drebrin like	0.9762	10
IGF2BP2	Insulin like growth factor 2 mRNA binding protein 2	0.9762	10
DUSP3	Dual specificity phosphatase 3	0.9762	10
GALK1	Galactokinase 1	0.9762	10
CPED1	Cadherin like and PC-esterase domain containing 1	0.9762	2
ALDH2	Aldehyde dehydrogenase 2 family member	0.9524	10
KCTD20	Potassium channel tetramerization domain containing 20	0.9524	10
MACROH2A1	MacroH2A.1 histone	0.9524	10
AKR1A1	Aldo-keto reductase family 1 member A1	0.9524	10
SERP1	Stress associated endoplasmic reticulum protein 1	0.9524	10

Adipocytes	83.1 nTPM
Adipose tissue	84.6 nTPM
Breast	81.5 nTPM

Alveolar cells type 1	84.1 nTPM
Lung	84.1 nTPM

Alveolar cells type 2	122.0 nTPM
Lung	122.0 nTPM

Astrocytes	16.7 nTPM
Brain	16.7 nTPM

B-cells	47.4 nTPM
Lung	120.7 nTPM
Thymus	89.5 nTPM
Salivary gland	60.4 nTPM
Stomach	48.9 nTPM
Spleen	42.3 nTPM
Liver	38.6 nTPM
Bone marrow	37.9 nTPM
PBMC	36.9 nTPM
Kidney	36.4 nTPM
Skin	30.5 nTPM
Adipose tissue	28.0 nTPM
Lymph node	27.8 nTPM
Esophagus	17.7 nTPM

Ciliated cells	151.1 nTPM
Bronchus	215.3 nTPM
Lung	150.0 nTPM
Fallopian tube	127.3 nTPM
Endometrium	111.6 nTPM

Club cells	322.1 nTPM
Bronchus	410.7 nTPM
Lung	285.2 nTPM
Prostate	270.4 nTPM

Dendritic cells	765.1 nTPM
Adipose tissue	1231.6 nTPM
PBMC	298.6 nTPM

Endothelial cells	145.7 nTPM
Liver	413.2 nTPM
Pancreas	403.3 nTPM
Fallopian tube	167.8 nTPM
Tongue	158.4 nTPM
Vascular	145.5 nTPM
Lung	143.4 nTPM
Salivary gland	139.3 nTPM
Thymus	128.1 nTPM
Endometrium	123.5 nTPM
Esophagus	123.3 nTPM
Placenta	111.3 nTPM
Heart muscle	98.6 nTPM
Breast	96.7 nTPM
Prostate	85.6 nTPM
Skeletal muscle	80.3 nTPM
Testis	68.7 nTPM
Ovary	68.6 nTPM
Skin	66.9 nTPM

Enteroendocrine cells	122.8 nTPM
Rectum	176.1 nTPM
Colon	109.8 nTPM
Small intestine	82.4 nTPM

Erythroid cells	122.3 nTPM
Liver	160.8 nTPM
Bone marrow	83.8 nTPM

Fibroblasts	182.3 nTPM
Pancreas	466.8 nTPM
Prostate	316.2 nTPM
Liver	231.3 nTPM
Esophagus	201.0 nTPM
Salivary gland	200.5 nTPM
Vascular	176.6 nTPM
Stomach	171.5 nTPM
Fallopian tube	166.8 nTPM
Placenta	147.9 nTPM
Skin	146.6 nTPM
Adipose tissue	132.2 nTPM
Thymus	128.2 nTPM
Skeletal muscle	113.5 nTPM
Breast	112.7 nTPM
Lung	108.3 nTPM
Heart muscle	96.8 nTPM

Granulocytes	159.8 nTPM
Lung	217.3 nTPM
Fallopian tube	131.1 nTPM
Tongue	131.0 nTPM

Intestinal goblet cells	93.1 nTPM
Small intestine	130.8 nTPM
Rectum	75.9 nTPM
Colon	72.6 nTPM

Lymphatic endothelial cells	40.1 nTPM
Fallopian tube	58.4 nTPM
Ovary	21.8 nTPM

Basal keratinocytes	105.5 nTPM
Tongue	170.3 nTPM
Skin	40.7 nTPM

Basal prostatic cells	132.7 nTPM
Prostate	132.7 nTPM

Basal respiratory cells	510.3 nTPM
Bronchus	510.3 nTPM

Basal squamous epithelial cells	99.5 nTPM
Esophagus	99.5 nTPM

Macrophages	1463.1 nTPM
Pancreas	4758.6 nTPM
Vascular	3733.5 nTPM
Thymus	3506.3 nTPM
Lung	1543.8 nTPM
Fallopian tube	1447.3 nTPM
Salivary gland	1270.0 nTPM
Skin	1238.0 nTPM
Prostate	1215.6 nTPM
Spleen	1158.9 nTPM
Kidney	1074.4 nTPM
Adipose tissue	992.5 nTPM
Esophagus	960.7 nTPM
Bone marrow	870.6 nTPM
Stomach	838.5 nTPM
Tongue	789.1 nTPM
Testis	734.6 nTPM
Breast	617.2 nTPM
Skeletal muscle	531.3 nTPM
Endometrium	517.8 nTPM

Paneth cells	146.1 nTPM
Small intestine	176.1 nTPM
Colon	144.7 nTPM
Rectum	117.5 nTPM

Plasma cells	65.1 nTPM
Salivary gland	118.2 nTPM
Liver	107.6 nTPM
Esophagus	62.4 nTPM
Stomach	57.0 nTPM
Fallopian tube	52.7 nTPM
Thymus	45.3 nTPM
Bone marrow	39.3 nTPM
Spleen	38.5 nTPM

Schwann cells	46.5 nTPM
Vascular	90.9 nTPM
Adipose tissue	24.6 nTPM
Esophagus	24.0 nTPM

Serous glandular cells	272.1 nTPM
Salivary gland	336.4 nTPM
Tongue	207.7 nTPM

Smooth muscle cells	118.7 nTPM
Placenta	285.7 nTPM
Salivary gland	178.7 nTPM
Tongue	175.1 nTPM
Vascular	159.9 nTPM
Thymus	146.4 nTPM
Fallopian tube	145.7 nTPM
Endometrium	129.7 nTPM
Prostate	118.0 nTPM
Liver	115.5 nTPM
Esophagus	92.5 nTPM
Lung	82.3 nTPM
Ovary	62.0 nTPM
Skin	61.8 nTPM
Skeletal muscle	51.6 nTPM
Adipose tissue	49.2 nTPM
Breast	45.0 nTPM

Suprabasal keratinocytes	139.3 nTPM
Tongue	247.6 nTPM
Skin	31.2 nTPM

T-cells	51.1 nTPM
Vascular	119.0 nTPM
Lung	86.3 nTPM
Tongue	78.3 nTPM
Thymus	62.6 nTPM
Colon	62.4 nTPM
Endometrium	58.6 nTPM
Kidney	57.6 nTPM
Salivary gland	53.1 nTPM
Skin	47.0 nTPM
Adipose tissue	46.0 nTPM
Skeletal muscle	45.7 nTPM
PBMC	42.0 nTPM
Breast	41.2 nTPM
Spleen	39.4 nTPM
Bone marrow	38.5 nTPM
Stomach	38.3 nTPM
Prostate	37.7 nTPM
Lymph node	36.0 nTPM
Fallopian tube	34.3 nTPM
Liver	31.5 nTPM
Esophagus	17.0 nTPM

Undifferentiated cells	115.7 nTPM
Small intestine	134.2 nTPM
Rectum	111.0 nTPM
Colon	102.0 nTPM

Amygdala excitatory	36.3 nTPM
Hippocampus	43.2 nTPM
Thalamus	38.6 nTPM
Basal ganglia	36.2 nTPM
Cerebral cortex	35.3 nTPM
Hypothalamus	34.1 nTPM
Amygdala	30.3 nTPM

Astrocyte	32.9 nTPM
Cerebellum	40.8 nTPM
Spinal cord	38.4 nTPM
Midbrain	37.9 nTPM
Cerebral cortex	37.0 nTPM
Basal ganglia	32.8 nTPM
Hippocampus	32.3 nTPM
Pons	31.2 nTPM
Thalamus	31.1 nTPM
Medulla oblongata	29.5 nTPM
Hypothalamus	25.6 nTPM
Amygdala	25.1 nTPM

Bergmann glia	17.0 nTPM
Pons	20.1 nTPM
Cerebellum	16.0 nTPM
Medulla oblongata	14.9 nTPM

Central nervous system macrophage	499.5 nTPM
Spinal cord	677.4 nTPM
Basal ganglia	600.7 nTPM
Medulla oblongata	587.1 nTPM
Pons	542.8 nTPM
Hypothalamus	521.8 nTPM
Midbrain	481.9 nTPM
Thalamus	454.3 nTPM
Cerebellum	426.6 nTPM
Cerebral cortex	425.2 nTPM
Hippocampus	391.8 nTPM
Amygdala	385.5 nTPM

Cerebellar inhibitory	52.0 nTPM
Midbrain	64.1 nTPM
Pons	57.2 nTPM
Cerebellum	56.4 nTPM
Medulla oblongata	43.8 nTPM
Spinal cord	38.5 nTPM

Cge interneuron	65.0 nTPM
Thalamus	74.4 nTPM
Midbrain	66.6 nTPM
Cerebral cortex	66.2 nTPM
Basal ganglia	64.3 nTPM
Hippocampus	63.3 nTPM
Hypothalamus	61.0 nTPM
Amygdala	58.8 nTPM

Choroid plexus epithelial cell	27.5 nTPM
Hippocampus	33.3 nTPM
Medulla oblongata	27.1 nTPM
Basal ganglia	24.8 nTPM
Thalamus	24.7 nTPM

Committed oligodendrocyte precursor	21.9 nTPM
Basal ganglia	31.8 nTPM
Midbrain	29.4 nTPM
Hypothalamus	24.6 nTPM
Thalamus	22.1 nTPM
Cerebral cortex	21.5 nTPM
Hippocampus	21.0 nTPM
Amygdala	20.9 nTPM
Medulla oblongata	20.7 nTPM
Cerebellum	19.0 nTPM
Pons	18.6 nTPM
Spinal cord	11.0 nTPM

Deep-layer corticothalamic and 6b	48.6 nTPM
Midbrain	69.9 nTPM
Cerebral cortex	50.0 nTPM
Hypothalamus	46.7 nTPM
Basal ganglia	44.4 nTPM
Hippocampus	41.7 nTPM
Amygdala	38.8 nTPM

Deep-layer intratelencephalic	42.3 nTPM
Hypothalamus	50.5 nTPM
Cerebral cortex	47.4 nTPM
Hippocampus	38.6 nTPM
Basal ganglia	37.9 nTPM
Amygdala	37.0 nTPM

Deep-layer near-projecting	64.2 nTPM
Hypothalamus	79.0 nTPM
Cerebral cortex	68.0 nTPM
Basal ganglia	59.7 nTPM
Amygdala	58.4 nTPM
Hippocampus	55.9 nTPM