Single cell type - NPC1 - The Human Protein Atlas

NPC1

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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.	NPC1
Gene descriptionⁱ Full gene name according to HGNC.	NPC intracellular cholesterol transporter 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Human disease related genes Metabolic 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.	Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	6

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.	Alveolar cells - Lung 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.	Cell type enhanced (Oligodendrocytes)
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.	0.50
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 enhanced (Oligodendrocyte)
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.	Immune cell enhanced (plasmacytoid 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

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 (Oligodendrocytes)

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 enhanced (Oligodendrocyte)

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: Immune cell enhanced (plasmacytoid 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

NPC1 is part of cluster 72 Alveolar cells - Lung function with confidenceⁱ 1
121 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.
USP54	Ubiquitin specific peptidase 54	0.5697	51
ATP11A	ATPase phospholipid transporting 11A	0.5588	72
HHIP	Hedgehog interacting protein	0.5527	72
KIF13B	Kinesin family member 13B	0.5154	37
DLG1	Discs large MAGUK scaffold protein 1	0.4941	51
SNX30	Sorting nexin family member 30	0.4888	72
CUEDC1	CUE domain containing 1	0.4873	51
TMEM63A	Transmembrane protein 63A	0.4817	58
SLC34A2	Solute carrier family 34 member 2	0.4770	72
ROS1	ROS proto-oncogene 1, receptor tyrosine kinase	0.4672	72
TMEM181	Transmembrane protein 181	0.4660	78
TBC1D2	TBC1 domain family member 2	0.4618	58
PALS1	Protein associated with LIN7 1, MAGUK p55 family member	0.4534	72
TJP1	Tight junction protein 1	0.4509	37
ST3GAL5	ST3 beta-galactoside alpha-2,3-sialyltransferase 5	0.4479	72

IMMUNE CELLS

NPC1 is part of cluster 44 Plasmacytoid DCs - Plasma membrane proteins with confidenceⁱ 1
112 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.
SLC25A39	Solute carrier family 25 member 39	1.0000	44
C12orf75	Chromosome 12 open reading frame 75	1.0000	44
AMIGO3	Adhesion molecule with Ig like domain 3	1.0000	44
HCFC1	Host cell factor C1	1.0000	44
E2F7	E2F transcription factor 7	1.0000	44
MCOLN2	Mucolipin TRP cation channel 2	1.0000	44
SMARCAL1	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1	1.0000	44
MORF4L2	Mortality factor 4 like 2	1.0000	44
SCT	Secretin	0.9762	44
SLC12A3	Solute carrier family 12 member 3	0.9762	44
TRAF4	TNF receptor associated factor 4	0.9762	13
CAPN6	Calpain 6	0.9762	44
DRD4	Dopamine receptor D4	0.9762	44
HHAT	Hedgehog acyltransferase	0.9762	8
GPM6B	Glycoprotein M6B	0.9762	44

Adipocytes	16.7 nTPM
Adipose tissue	22.9 nTPM
Breast	10.5 nTPM

Alveolar cells type 1	22.8 nTPM
Lung	22.8 nTPM

Alveolar cells type 2	64.2 nTPM
Lung	64.2 nTPM

Astrocytes	31.0 nTPM
Brain	31.0 nTPM

B-cells	8.9 nTPM
Lung	28.2 nTPM
Stomach	12.2 nTPM
Adipose tissue	11.9 nTPM
PBMC	10.8 nTPM
Liver	9.7 nTPM
Thymus	9.2 nTPM
Salivary gland	8.8 nTPM
Spleen	8.0 nTPM
Bone marrow	7.9 nTPM
Lymph node	7.3 nTPM
Skin	1.7 nTPM
Kidney	0.0 nTPM
Esophagus	0.0 nTPM

Ciliated cells	13.6 nTPM
Endometrium	20.2 nTPM
Bronchus	19.8 nTPM
Lung	7.9 nTPM
Fallopian tube	6.3 nTPM

Club cells	16.5 nTPM
Bronchus	25.2 nTPM
Lung	18.1 nTPM
Prostate	6.1 nTPM

Dendritic cells	69.1 nTPM
PBMC	111.5 nTPM
Adipose tissue	26.8 nTPM

Endothelial cells	12.8 nTPM
Lung	19.2 nTPM
Heart muscle	18.3 nTPM
Fallopian tube	17.7 nTPM
Salivary gland	17.2 nTPM
Prostate	15.5 nTPM
Skeletal muscle	15.0 nTPM
Tongue	14.3 nTPM
Thymus	12.2 nTPM
Vascular	11.7 nTPM
Testis	11.6 nTPM
Placenta	11.4 nTPM
Liver	11.3 nTPM
Skin	11.3 nTPM
Endometrium	10.9 nTPM
Ovary	10.6 nTPM
Esophagus	10.3 nTPM
Pancreas	7.8 nTPM
Breast	4.4 nTPM

Enteroendocrine cells	6.6 nTPM
Colon	9.5 nTPM
Small intestine	6.9 nTPM
Rectum	3.4 nTPM

Fibroblasts	8.4 nTPM
Salivary gland	13.3 nTPM
Placenta	12.8 nTPM
Lung	10.8 nTPM
Thymus	10.7 nTPM
Stomach	10.1 nTPM
Fallopian tube	9.8 nTPM
Skeletal muscle	9.4 nTPM
Vascular	9.1 nTPM
Pancreas	8.5 nTPM
Adipose tissue	8.5 nTPM
Liver	7.1 nTPM
Prostate	6.6 nTPM
Skin	5.7 nTPM
Breast	5.5 nTPM
Esophagus	5.2 nTPM
Heart muscle	2.0 nTPM

Granulocytes	9.9 nTPM
Tongue	19.4 nTPM
Lung	5.5 nTPM
Fallopian tube	4.8 nTPM

Intestinal goblet cells	5.3 nTPM
Colon	7.4 nTPM
Small intestine	5.2 nTPM
Rectum	3.4 nTPM

Lymphatic endothelial cells	11.1 nTPM
Fallopian tube	16.7 nTPM
Ovary	5.5 nTPM

Macrophages	22.6 nTPM
Pancreas	41.1 nTPM
Lung	40.7 nTPM
Fallopian tube	38.5 nTPM
Salivary gland	36.6 nTPM
Prostate	34.5 nTPM
Vascular	29.9 nTPM
Thymus	27.6 nTPM
Endometrium	20.9 nTPM
Skeletal muscle	19.1 nTPM
Spleen	19.0 nTPM
Adipose tissue	18.4 nTPM
Stomach	18.0 nTPM
Kidney	15.0 nTPM
Breast	14.7 nTPM
Skin	14.5 nTPM
Tongue	14.0 nTPM
Bone marrow	13.2 nTPM
Testis	10.5 nTPM
Esophagus	3.9 nTPM

Basal prostatic cells	8.1 nTPM
Prostate	8.1 nTPM

Basal respiratory cells	17.1 nTPM
Bronchus	17.1 nTPM

Basal squamous epithelial cells	11.5 nTPM
Esophagus	11.5 nTPM

Bipolar cells	6.2 nTPM
Eye	6.2 nTPM

Paneth cells	12.7 nTPM
Colon	18.1 nTPM
Small intestine	13.8 nTPM
Rectum	6.1 nTPM

Plasma cells	7.0 nTPM
Esophagus	15.6 nTPM
Salivary gland	11.6 nTPM
Fallopian tube	6.8 nTPM
Liver	6.0 nTPM
Thymus	5.5 nTPM
Stomach	3.8 nTPM
Spleen	3.4 nTPM
Bone marrow	3.0 nTPM

Schwann cells	13.8 nTPM
Vascular	27.2 nTPM
Esophagus	12.0 nTPM
Adipose tissue	2.3 nTPM

Serous glandular cells	31.9 nTPM
Salivary gland	41.7 nTPM
Tongue	22.1 nTPM

Smooth muscle cells	12.1 nTPM
Salivary gland	27.8 nTPM
Lung	17.6 nTPM
Thymus	16.3 nTPM
Skeletal muscle	14.4 nTPM
Fallopian tube	14.0 nTPM
Vascular	11.9 nTPM
Adipose tissue	11.8 nTPM
Placenta	11.3 nTPM
Esophagus	10.8 nTPM
Breast	9.6 nTPM
Endometrium	9.5 nTPM
Skin	9.1 nTPM
Tongue	8.7 nTPM
Ovary	7.4 nTPM
Prostate	7.3 nTPM
Liver	5.9 nTPM

Suprabasal keratinocytes	13.8 nTPM
Tongue	16.1 nTPM
Skin	11.6 nTPM

T-cells	19.3 nTPM
Adipose tissue	42.2 nTPM
Fallopian tube	31.5 nTPM
Tongue	29.0 nTPM
Skeletal muscle	28.0 nTPM
Lung	25.5 nTPM
Vascular	22.5 nTPM
Liver	20.0 nTPM
Bone marrow	20.0 nTPM
Spleen	18.6 nTPM
Prostate	17.8 nTPM
Esophagus	17.0 nTPM
Stomach	16.3 nTPM
Endometrium	15.3 nTPM
Salivary gland	15.3 nTPM
Thymus	15.3 nTPM
Breast	15.1 nTPM
Kidney	14.2 nTPM
Skin	13.0 nTPM
Lymph node	11.9 nTPM
Colon	8.8 nTPM
PBMC	7.7 nTPM

Undifferentiated cells	4.0 nTPM
Colon	4.5 nTPM
Rectum	3.9 nTPM
Small intestine	3.5 nTPM

Amygdala excitatory	34.2 nTPM
Amygdala	42.7 nTPM
Cerebral cortex	37.6 nTPM
Hypothalamus	35.2 nTPM
Hippocampus	34.2 nTPM
Basal ganglia	31.2 nTPM
Thalamus	24.5 nTPM

Astrocyte	67.3 nTPM
Hippocampus	86.6 nTPM
Amygdala	77.7 nTPM
Cerebral cortex	77.6 nTPM
Spinal cord	73.0 nTPM
Hypothalamus	69.5 nTPM
Thalamus	65.4 nTPM
Medulla oblongata	63.1 nTPM
Pons	59.5 nTPM
Midbrain	59.1 nTPM
Cerebellum	55.4 nTPM
Basal ganglia	53.6 nTPM

Bergmann glia	53.2 nTPM
Medulla oblongata	68.2 nTPM
Cerebellum	51.2 nTPM
Pons	40.3 nTPM

Central nervous system macrophage	214.8 nTPM
Amygdala	254.3 nTPM
Midbrain	238.9 nTPM
Hippocampus	223.7 nTPM
Hypothalamus	221.1 nTPM
Thalamus	220.1 nTPM
Cerebral cortex	216.4 nTPM
Pons	210.9 nTPM
Basal ganglia	209.7 nTPM
Medulla oblongata	193.7 nTPM
Cerebellum	191.5 nTPM
Spinal cord	182.8 nTPM

Cerebellar inhibitory	32.1 nTPM
Spinal cord	38.5 nTPM
Midbrain	33.3 nTPM
Cerebellum	31.0 nTPM
Pons	29.8 nTPM
Medulla oblongata	27.8 nTPM

Cge interneuron	37.0 nTPM
Amygdala	39.3 nTPM
Basal ganglia	39.3 nTPM
Thalamus	38.1 nTPM
Cerebral cortex	38.0 nTPM
Hippocampus	37.0 nTPM
Midbrain	36.5 nTPM
Hypothalamus	31.0 nTPM

Choroid plexus epithelial cell	65.5 nTPM
Basal ganglia	77.7 nTPM
Medulla oblongata	65.9 nTPM
Thalamus	65.8 nTPM
Hippocampus	52.7 nTPM

Committed oligodendrocyte precursor	112.1 nTPM
Hypothalamus	225.3 nTPM
Thalamus	201.7 nTPM
Amygdala	155.6 nTPM
Basal ganglia	119.4 nTPM
Midbrain	115.1 nTPM
Cerebral cortex	91.8 nTPM
Pons	91.2 nTPM
Hippocampus	88.2 nTPM
Cerebellum	71.3 nTPM
Medulla oblongata	43.9 nTPM
Spinal cord	29.4 nTPM

Deep-layer corticothalamic and 6b	36.5 nTPM
Basal ganglia	42.0 nTPM
Amygdala	40.1 nTPM
Hippocampus	37.2 nTPM
Cerebral cortex	36.9 nTPM
Hypothalamus	35.2 nTPM
Midbrain	27.7 nTPM

Deep-layer intratelencephalic	38.3 nTPM
Basal ganglia	44.6 nTPM
Cerebral cortex	41.6 nTPM
Hippocampus	37.3 nTPM
Amygdala	34.4 nTPM
Hypothalamus	33.6 nTPM

Deep-layer near-projecting	37.7 nTPM
Hippocampus	42.6 nTPM
Amygdala	39.1 nTPM
Basal ganglia	38.6 nTPM
Cerebral cortex	37.8 nTPM
Hypothalamus	30.4 nTPM

Eccentric medium spiny neuron	19.8 nTPM
Cerebral cortex	22.1 nTPM
Amygdala	21.6 nTPM
Basal ganglia	21.3 nTPM
Thalamus	19.7 nTPM
Hypothalamus	17.5 nTPM
Hippocampus	16.6 nTPM