Single cell type - NCSTN - 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.	NCSTN
Gene descriptionⁱ Full gene name according to HGNC.	Nicastrin
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Human 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,Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	7

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	Cytotrophoblasts - Unknown function (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 (Syncytiotrophoblasts)
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	Low cell line specificity
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 (Syncytiotrophoblasts)

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

NCSTN is part of cluster 47 Cytotrophoblasts - Unknown function with confidenceⁱ 0.87
226 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
RPN2	Ribophorin II	0.6754	55
BCAP31	B cell receptor associated protein 31	0.6501	47
TMX2	Thioredoxin related transmembrane protein 2	0.6246	26
MED20	Mediator complex subunit 20	0.5977	47
PIGO	Phosphatidylinositol glycan anchor biosynthesis class O	0.5953	55
CLN5	CLN5 intracellular trafficking protein	0.5789	26
ATP6AP1	ATPase H+ transporting accessory protein 1	0.5777	4
IL10RB	Interleukin 10 receptor subunit beta	0.5771	18
SLC43A2	Solute carrier family 43 member 2	0.5740	18
CLN3	CLN3 lysosomal/endosomal transmembrane protein, battenin	0.5682	47
TMED1	Transmembrane p24 trafficking protein 1	0.5676	55
TMEM9B	TMEM9 domain family member B	0.5655	26
MFSD5	Major facilitator superfamily domain containing 5	0.5632	47
COMT	Catechol-O-methyltransferase	0.5603	47
PTGES	Prostaglandin E synthase	0.5598	38

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	28.0 nTPM
Adipose tissue	34.2 nTPM
Breast	21.8 nTPM

Alveolar cells type 1	6.4 nTPM
Lung	6.4 nTPM

Alveolar cells type 2	9.3 nTPM
Lung	9.3 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	23.0 nTPM
Stomach	38.6 nTPM
Kidney	28.5 nTPM
Adipose tissue	26.1 nTPM
Liver	26.0 nTPM
Bone marrow	23.7 nTPM
Spleen	22.9 nTPM
Colon	22.3 nTPM
Lymph node	18.9 nTPM
Breast	13.4 nTPM
PBMC	9.9 nTPM

Dendritic cells	27.8 nTPM
PBMC	43.8 nTPM
Adipose tissue	21.4 nTPM
Breast	18.2 nTPM

Endothelial cells	23.9 nTPM
Placenta	47.7 nTPM
Eye	35.6 nTPM
Ovary	34.1 nTPM
Liver	26.6 nTPM
Breast	24.2 nTPM
Endometrium	24.1 nTPM
Testis	22.8 nTPM
Skeletal muscle	21.4 nTPM
Esophagus	20.7 nTPM
Pancreas	19.3 nTPM
Lung	15.6 nTPM
Heart muscle	15.4 nTPM
Skin	13.4 nTPM
Prostate	13.2 nTPM

Fibroblasts	33.7 nTPM
Adipose tissue	58.0 nTPM
Placenta	50.9 nTPM
Esophagus	42.7 nTPM
Stomach	41.6 nTPM
Skeletal muscle	33.5 nTPM
Breast	32.7 nTPM
Ovary	32.2 nTPM
Heart muscle	26.5 nTPM
Skin	21.0 nTPM
Prostate	20.3 nTPM
Lung	11.1 nTPM

Intestinal goblet cells	31.8 nTPM
Rectum	45.0 nTPM
Small intestine	28.8 nTPM
Colon	21.5 nTPM

Macrophages	33.4 nTPM
Ovary	52.5 nTPM
Kidney	49.9 nTPM
Pancreas	46.0 nTPM
Adipose tissue	46.0 nTPM
Esophagus	44.1 nTPM
Stomach	41.0 nTPM
Skeletal muscle	38.1 nTPM
Bone marrow	33.8 nTPM
Spleen	31.1 nTPM
Testis	29.7 nTPM
Endometrium	23.9 nTPM
Lung	23.7 nTPM
Breast	22.0 nTPM
Prostate	19.5 nTPM
PBMC	0.0 nTPM

Paneth cells	33.4 nTPM
Rectum	40.6 nTPM
Small intestine	30.0 nTPM
Colon	29.6 nTPM

Plasma cells	33.2 nTPM
Stomach	51.9 nTPM
Adipose tissue	34.9 nTPM
Bone marrow	31.3 nTPM
Esophagus	24.6 nTPM
Spleen	23.2 nTPM

Respiratory ciliated cells	28.7 nTPM
Bronchus	44.2 nTPM
Lung	13.1 nTPM

Smooth muscle cells	19.6 nTPM
Pancreas	35.3 nTPM
Adipose tissue	29.7 nTPM
Ovary	27.3 nTPM
Bronchus	23.6 nTPM
Skeletal muscle	18.7 nTPM
Prostate	16.8 nTPM
Esophagus	14.0 nTPM
Endometrium	13.6 nTPM
Breast	12.8 nTPM
Skin	12.2 nTPM
Heart muscle	11.0 nTPM

T-cells	16.5 nTPM
Stomach	26.6 nTPM
Kidney	26.0 nTPM
Bone marrow	23.1 nTPM
Liver	20.2 nTPM
Esophagus	19.7 nTPM
Spleen	19.5 nTPM
Lymph node	18.8 nTPM
Skin	15.7 nTPM
Lung	15.2 nTPM
Adipose tissue	15.2 nTPM
Colon	13.3 nTPM
PBMC	13.1 nTPM
Breast	13.0 nTPM
Skeletal muscle	12.7 nTPM
Endometrium	12.6 nTPM
Ovary	11.1 nTPM
Prostate	4.7 nTPM

Basal keratinocytes	10.5 nTPM
Skin	10.5 nTPM

Basal prostatic cells	23.8 nTPM
Prostate	23.8 nTPM

Basal respiratory cells	59.5 nTPM
Bronchus	59.5 nTPM

Basal squamous epithelial cells	15.9 nTPM
Esophagus	15.9 nTPM

Undifferentiated cells	29.6 nTPM
Rectum	38.3 nTPM
Small intestine	29.8 nTPM
Colon	20.7 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