Single cell type - HCST - 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.	HCST
Gene descriptionⁱ Full gene name according to HGNC.	Hematopoietic cell signal transducer
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Metabolic proteins
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.	2

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	NK-cells & T-cells - 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. Read more	Cell type enhanced (NK-cells, dendritic cells, T-cells, Langerhans cells, Hofbauer cells, Kupffer cells, Macrophages)
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 (HEL, HL-60, HMC-1, THP-1, U-937)
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 (NK-cells, dendritic cells, T-cells, Langerhans cells, Hofbauer cells, Kupffer cells, Macrophages)

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

HCST is part of cluster 63 NK-cells & T-cells - Immune response with confidenceⁱ 1
362 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
IL12RB1	Interleukin 12 receptor subunit beta 1	0.9300	63
MATK	Megakaryocyte-associated tyrosine kinase	0.9174	63
IFNL1	Interferon lambda 1	0.9075	63
GZMH	Granzyme H	0.8987	63
CD247	CD247 molecule	0.8900	63
PTGER2	Prostaglandin E receptor 2	0.8882	63
FASLG	Fas ligand	0.8842	63
FCRL6	Fc receptor like 6	0.8839	63
KLRC1	Killer cell lectin like receptor C1	0.8826	63
GZMM	Granzyme M	0.8824	63
CD160	CD160 molecule	0.8811	63
TRDC	T cell receptor delta constant	0.8802	63
NKG7	Natural killer cell granule protein 7	0.8783	63
EOMES	Eomesodermin	0.8763	63
PYHIN1	Pyrin and HIN domain family member 1	0.8749	63

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	12.3 nTPM
Breast	21.0 nTPM
Adipose tissue	3.5 nTPM

Alveolar cells type 1	6.4 nTPM
Lung	6.4 nTPM

Alveolar cells type 2	43.3 nTPM
Lung	43.3 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	85.3 nTPM
PBMC	119.9 nTPM
Adipose tissue	107.3 nTPM
Colon	100.6 nTPM
Liver	97.9 nTPM
Kidney	85.7 nTPM
Stomach	84.5 nTPM
Breast	74.9 nTPM
Lymph node	66.2 nTPM
Spleen	60.2 nTPM
Bone marrow	55.6 nTPM

Dendritic cells	993.2 nTPM
Breast	1557.7 nTPM
Adipose tissue	1027.4 nTPM
PBMC	394.5 nTPM

Endothelial cells	18.3 nTPM
Eye	127.0 nTPM
Skin	32.6 nTPM
Lung	31.2 nTPM
Liver	23.8 nTPM
Placenta	9.7 nTPM
Breast	8.6 nTPM
Esophagus	7.8 nTPM
Heart muscle	4.9 nTPM
Skeletal muscle	4.6 nTPM
Endometrium	2.9 nTPM
Ovary	1.1 nTPM
Testis	0.9 nTPM
Prostate	0.7 nTPM
Pancreas	0.0 nTPM

Fibroblasts	9.5 nTPM
Skin	23.1 nTPM
Lung	22.4 nTPM
Stomach	17.8 nTPM
Breast	17.1 nTPM
Placenta	11.7 nTPM
Ovary	4.8 nTPM
Skeletal muscle	2.7 nTPM
Esophagus	2.5 nTPM
Adipose tissue	1.6 nTPM
Prostate	0.7 nTPM
Heart muscle	0.4 nTPM

Intestinal goblet cells	0.9 nTPM
Small intestine	1.1 nTPM
Rectum	0.8 nTPM
Colon	0.7 nTPM

Macrophages	392.7 nTPM
Kidney	723.8 nTPM
Adipose tissue	639.1 nTPM
Testis	576.9 nTPM
Skeletal muscle	465.4 nTPM
Breast	460.7 nTPM
Stomach	404.3 nTPM
Bone marrow	402.3 nTPM
Esophagus	344.6 nTPM
Spleen	326.6 nTPM
Lung	321.9 nTPM
Pancreas	301.2 nTPM
Endometrium	281.5 nTPM
Prostate	275.2 nTPM
Ovary	270.6 nTPM
PBMC	95.5 nTPM

Paneth cells	1.4 nTPM
Colon	3.3 nTPM
Rectum	1.0 nTPM
Small intestine	0.0 nTPM

Plasma cells	97.7 nTPM
Adipose tissue	165.7 nTPM
Bone marrow	138.5 nTPM
Spleen	107.8 nTPM
Stomach	51.7 nTPM
Esophagus	24.6 nTPM

Respiratory ciliated cells	5.1 nTPM
Lung	8.7 nTPM
Bronchus	1.4 nTPM

Smooth muscle cells	6.2 nTPM
Breast	27.8 nTPM
Skin	21.0 nTPM
Esophagus	4.6 nTPM
Skeletal muscle	3.6 nTPM
Endometrium	3.2 nTPM
Heart muscle	2.1 nTPM
Ovary	1.6 nTPM
Pancreas	1.4 nTPM
Adipose tissue	1.2 nTPM
Prostate	0.9 nTPM
Bronchus	0.9 nTPM

T-cells	769.9 nTPM
Kidney	1269.1 nTPM
Liver	1266.9 nTPM
Ovary	1156.7 nTPM
Skin	924.2 nTPM
Bone marrow	892.9 nTPM
PBMC	868.5 nTPM
Adipose tissue	851.0 nTPM
Stomach	838.0 nTPM
Breast	809.7 nTPM
Skeletal muscle	768.2 nTPM
Spleen	656.6 nTPM
Endometrium	624.3 nTPM
Colon	584.5 nTPM
Lung	530.0 nTPM
Esophagus	491.3 nTPM
Lymph node	357.1 nTPM
Prostate	198.9 nTPM

Basal keratinocytes	28.6 nTPM
Skin	28.6 nTPM

Basal prostatic cells	1.3 nTPM
Prostate	1.3 nTPM

Basal respiratory cells	1.7 nTPM
Bronchus	1.7 nTPM

Basal squamous epithelial cells	2.8 nTPM
Esophagus	2.8 nTPM

Undifferentiated cells	2.7 nTPM
Colon	4.7 nTPM
Small intestine	1.8 nTPM
Rectum	1.6 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