Single cell type - NOTCH3 - 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.	NOTCH3
Gene descriptionⁱ Full gene name according to HGNC.	Notch receptor 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes Disease related genes Human disease related genes Plasma 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	Intracellular,Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	3

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	Smooth muscle cells - ECM organization (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 (Sertoli cells, Smooth muscle cells, Skeletal myocytes)
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	Not detected in immune cells
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	Not detected
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 (AF22, MCF7, RT4, U-87 MG)
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 (Sertoli cells, Smooth muscle cells, Skeletal myocytes)

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

NOTCH3 is part of cluster 48 Smooth muscle cells - ECM organization with confidenceⁱ 1
270 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
COX4I2	Cytochrome c oxidase subunit 4I2	0.9077	48
HIGD1B	HIG1 hypoxia inducible domain family member 1B	0.9045	48
REM1	RRAD and GEM like GTPase 1	0.8932	48
RGS5	Regulator of G protein signaling 5	0.8815	48
GJA4	Gap junction protein alpha 4	0.8757	48
GPR20	G protein-coupled receptor 20	0.8639	48
RERGL	RERG like	0.8589	48
CSPG4	Chondroitin sulfate proteoglycan 4	0.8583	48
GJC1	Gap junction protein gamma 1	0.8583	48
MCAM	Melanoma cell adhesion molecule	0.8431	48
AOC3	Amine oxidase copper containing 3	0.8366	48
KCNJ8	Potassium inwardly rectifying channel subfamily J member 8	0.8279	48
NDUFA4L2	NDUFA4 mitochondrial complex associated like 2	0.8230	48
FAM162B	Family with sequence similarity 162 member B	0.8188	48
SCN4B	Sodium voltage-gated channel beta subunit 4	0.8059	48

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	39.6 nTPM
Breast	72.2 nTPM
Adipose tissue	7.1 nTPM

Alveolar cells type 1	9.6 nTPM
Lung	9.6 nTPM

Alveolar cells type 2	1.5 nTPM
Lung	1.5 nTPM

Astrocytes	5.9 nTPM
Brain	5.9 nTPM

B-cells	0.4 nTPM
Breast	4.0 nTPM
Lymph node	0.1 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Dendritic cells	1.0 nTPM
Breast	2.9 nTPM
Adipose tissue	0.1 nTPM
PBMC	0.0 nTPM

Endothelial cells	32.0 nTPM
Eye	150.5 nTPM
Heart muscle	89.7 nTPM
Breast	71.4 nTPM
Skeletal muscle	52.3 nTPM
Skin	33.4 nTPM
Testis	18.1 nTPM
Prostate	8.7 nTPM
Esophagus	7.7 nTPM
Endometrium	6.2 nTPM
Ovary	5.9 nTPM
Lung	3.1 nTPM
Placenta	1.1 nTPM
Liver	0.0 nTPM
Pancreas	0.0 nTPM

Fibroblasts	24.2 nTPM
Heart muscle	54.4 nTPM
Stomach	50.5 nTPM
Ovary	38.7 nTPM
Placenta	24.9 nTPM
Skin	24.8 nTPM
Breast	23.0 nTPM
Adipose tissue	16.3 nTPM
Skeletal muscle	13.1 nTPM
Lung	11.1 nTPM
Prostate	5.7 nTPM
Esophagus	3.3 nTPM

Intestinal goblet cells	0.3 nTPM
Small intestine	0.4 nTPM
Rectum	0.4 nTPM
Colon	0.0 nTPM

Macrophages	4.1 nTPM
Spleen	19.7 nTPM
Skeletal muscle	10.2 nTPM
Esophagus	9.4 nTPM
Pancreas	5.1 nTPM
Bone marrow	5.0 nTPM
Prostate	4.6 nTPM
Testis	3.5 nTPM
Breast	1.8 nTPM
Endometrium	1.4 nTPM
Adipose tissue	1.0 nTPM
Ovary	0.3 nTPM
Kidney	0.0 nTPM
Lung	0.0 nTPM
PBMC	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	0.1 nTPM
Rectum	0.2 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Plasma cells	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Respiratory ciliated cells	4.2 nTPM
Bronchus	8.4 nTPM
Lung	0.0 nTPM

Smooth muscle cells	317.0 nTPM
Skeletal muscle	650.6 nTPM
Adipose tissue	593.8 nTPM
Esophagus	410.9 nTPM
Breast	401.8 nTPM
Endometrium	360.6 nTPM
Skin	335.4 nTPM
Heart muscle	334.6 nTPM
Prostate	178.5 nTPM
Ovary	130.9 nTPM
Pancreas	83.7 nTPM
Bronchus	6.6 nTPM

T-cells	2.0 nTPM
Skin	12.9 nTPM
Esophagus	6.6 nTPM
Endometrium	3.3 nTPM
Skeletal muscle	3.3 nTPM
Lung	3.0 nTPM
Breast	2.5 nTPM
Colon	1.0 nTPM
Liver	0.3 nTPM
PBMC	0.3 nTPM
Adipose tissue	0.1 nTPM
Stomach	0.1 nTPM
Kidney	0.0 nTPM
Prostate	0.0 nTPM
Ovary	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Basal keratinocytes	24.1 nTPM
Skin	24.1 nTPM

Basal prostatic cells	7.8 nTPM
Prostate	7.8 nTPM

Basal respiratory cells	17.8 nTPM
Bronchus	17.8 nTPM

Collecting duct cells	16.5 nTPM
Kidney	16.5 nTPM

Undifferentiated cells	0.2 nTPM
Small intestine	0.5 nTPM
Rectum	0.1 nTPM
Colon	0.0 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