Single cell type - NPC2 - 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.	NPC2
Gene descriptionⁱ Full gene name according to HGNC.	NPC intracellular cholesterol transporter 2
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Human disease related genes Plasma proteins Potential drug targets Transporters
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,Secreted
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	8

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	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. Read more	Cell type enhanced (Hofbauer cells, Kupffer cells, Alveolar cells type 2)
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	Group enriched (plasmacytoid DC, intermediate monocyte, classical monocyte, non-classical monocyte, neutrophil, basophil, myeloid DC)
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
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. Read more	Protein predicted to be secreted

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 (Hofbauer cells, Kupffer cells, Alveolar cells type 2)

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

NPC2 is part of cluster 4 Macrophages - Innate immune response with confidenceⁱ 1
228 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
CTSB	Cathepsin B	0.7855	4
GRN	Granulin precursor	0.7448	4
PLD3	Phospholipase D family member 3	0.7260	4
TREM2	Triggering receptor expressed on myeloid cells 2	0.7126	4
HEXA	Hexosaminidase subunit alpha	0.7095	4
CD68	CD68 molecule	0.7094	4
DNASE2	Deoxyribonuclease 2, lysosomal	0.6967	4
LILRB4	Leukocyte immunoglobulin like receptor B4	0.6862	4
ACP5	Acid phosphatase 5, tartrate resistant	0.6734	4
PLA2G7	Phospholipase A2 group VII	0.6617	4
LIPA	Lipase A, lysosomal acid type	0.6491	4
VSIG4	V-set and immunoglobulin domain containing 4	0.6477	4
CCL7	C-C motif chemokine ligand 7	0.6456	4
PSAP	Prosaposin	0.6416	4
CTSD	Cathepsin D	0.6409	4

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	154.9 nTPM
Adipose tissue	187.5 nTPM
Breast	122.2 nTPM

Alveolar cells type 1	381.4 nTPM
Lung	381.4 nTPM

Astrocytes	11.1 nTPM
Brain	11.1 nTPM

B-cells	160.2 nTPM
Colon	239.6 nTPM
Kidney	223.8 nTPM
Liver	223.2 nTPM
Breast	211.4 nTPM
PBMC	187.0 nTPM
Adipose tissue	122.3 nTPM
Lymph node	115.2 nTPM
Spleen	112.8 nTPM
Stomach	90.9 nTPM
Bone marrow	76.0 nTPM

Basal keratinocytes	374.9 nTPM
Skin	374.9 nTPM

Basal squamous epithelial cells	170.2 nTPM
Esophagus	170.2 nTPM

Dendritic cells	664.0 nTPM
PBMC	1853.0 nTPM
Adipose tissue	84.3 nTPM
Breast	54.6 nTPM

Endothelial cells	276.5 nTPM
Prostate	564.7 nTPM
Skin	478.9 nTPM
Liver	401.8 nTPM
Esophagus	347.5 nTPM
Testis	291.9 nTPM
Placenta	289.3 nTPM
Eye	259.7 nTPM
Pancreas	251.0 nTPM
Lung	246.4 nTPM
Breast	239.0 nTPM
Endometrium	155.9 nTPM
Skeletal muscle	150.7 nTPM
Ovary	105.5 nTPM
Heart muscle	89.4 nTPM

Enteroendocrine cells	119.7 nTPM
Rectum	150.5 nTPM
Colon	88.8 nTPM

Fibroblasts	318.1 nTPM
Esophagus	563.0 nTPM
Skin	521.4 nTPM
Stomach	449.9 nTPM
Prostate	447.3 nTPM
Adipose tissue	335.2 nTPM
Breast	328.5 nTPM
Placenta	254.0 nTPM
Lung	231.2 nTPM
Skeletal muscle	179.2 nTPM
Heart muscle	111.0 nTPM
Ovary	79.0 nTPM

Intestinal goblet cells	264.8 nTPM
Rectum	335.5 nTPM
Colon	269.4 nTPM
Small intestine	189.5 nTPM

Macrophages	1462.6 nTPM
Pancreas	4053.1 nTPM
Prostate	3812.7 nTPM
Kidney	2258.1 nTPM
Ovary	2015.5 nTPM
Testis	1578.4 nTPM
Esophagus	1321.8 nTPM
Adipose tissue	983.8 nTPM
Endometrium	949.6 nTPM
Spleen	889.6 nTPM
Breast	870.1 nTPM
Bone marrow	852.1 nTPM
Lung	782.6 nTPM
Skeletal muscle	756.5 nTPM
Stomach	665.2 nTPM
PBMC	150.1 nTPM

Paneth cells	405.1 nTPM
Colon	550.0 nTPM
Rectum	421.4 nTPM
Small intestine	244.0 nTPM

Plasma cells	287.4 nTPM
Esophagus	554.4 nTPM
Stomach	432.4 nTPM
Adipose tissue	210.9 nTPM
Spleen	138.8 nTPM
Bone marrow	100.6 nTPM

Respiratory ciliated cells	393.3 nTPM
Bronchus	566.6 nTPM
Lung	220.1 nTPM

Cholangiocytes	163.0 nTPM
Liver	163.0 nTPM

Collecting duct cells	331.1 nTPM
Kidney	331.1 nTPM

Cone photoreceptor cells	22.9 nTPM
Eye	22.9 nTPM

Cytotrophoblasts	228.3 nTPM
Placenta	228.3 nTPM

Smooth muscle cells	155.9 nTPM
Pancreas	449.2 nTPM
Bronchus	245.3 nTPM
Ovary	232.0 nTPM
Skin	150.7 nTPM
Prostate	149.7 nTPM
Adipose tissue	113.9 nTPM
Esophagus	89.9 nTPM
Skeletal muscle	80.0 nTPM
Breast	77.7 nTPM
Endometrium	72.1 nTPM
Heart muscle	54.8 nTPM

T-cells	109.9 nTPM
Prostate	383.5 nTPM
Lung	291.6 nTPM
Skin	170.9 nTPM
Kidney	154.0 nTPM
Liver	114.8 nTPM
PBMC	102.3 nTPM
Adipose tissue	80.9 nTPM
Skeletal muscle	78.7 nTPM
Lymph node	63.8 nTPM
Spleen	62.4 nTPM
Colon	60.3 nTPM
Bone marrow	55.5 nTPM
Endometrium	54.4 nTPM
Breast	54.1 nTPM
Esophagus	52.4 nTPM
Ovary	51.2 nTPM
Stomach	37.7 nTPM

Undifferentiated cells	298.5 nTPM
Rectum	358.2 nTPM
Small intestine	270.1 nTPM
Colon	267.1 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