Single cell type - NCF4 - The Human Protein Atlas

NCF4

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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.	NCF4
Gene descriptionⁱ Full gene name according to HGNC.	Neutrophil cytosolic factor 4
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	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.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	5

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.	Neutrophils - Degranulation (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 (Hofbauer cells, Macrophages, Granulocytes, Plasma cells, B-cells, Kupffer cells, Langerhans cells)
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.	0.79
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.	Group enriched (Central nervous system macrophage, Leukocyte)
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.	Group enriched (neutrophil, eosinophil, basophil)
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 (Hofbauer cells, Macrophages, Granulocytes, Plasma cells, B-cells, Kupffer cells, Langerhans cells)

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: Group enriched (Central nervous system macrophage, Leukocyte)

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: Group enriched (neutrophil, eosinophil, basophil)
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

NCF4 is part of cluster 74 Neutrophils - Degranulation with confidenceⁱ 1
174 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.
TLR6	Toll like receptor 6	0.8390	74
ARL11	ADP ribosylation factor like GTPase 11	0.7921	74
TLR1	Toll like receptor 1	0.7821	74
DOK3	Docking protein 3	0.7796	74
GCA	Grancalcin	0.7718	74
CR1	Complement C3b/C4b receptor 1 (Knops blood group)	0.7640	74
VNN2	Vanin 2	0.7209	74
FCGR2A	Fc gamma receptor IIa	0.6964	58
CXCR2	C-X-C motif chemokine receptor 2	0.6962	74
FCGR3B	Fc gamma receptor IIIb	0.6889	74
LINC02218	Long intergenic non-protein coding RNA 2218	0.6884	74
MMP8	Matrix metallopeptidase 8	0.6841	74
FPR1	Formyl peptide receptor 1	0.6833	74
LILRB3	Leukocyte immunoglobulin like receptor B3	0.6807	74
RUBCNL	Rubicon like autophagy enhancer	0.6797	74

IMMUNE CELLS

NCF4 is part of cluster 21 Neutrophils - Unknown function with confidenceⁱ 1
492 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.
TOM1L2	Target of myb1 like 2 membrane trafficking protein	1.0000	21
ZNF658	Zinc finger protein 658	0.9524	21
WBP2	WW domain binding protein 2	0.9524	21
PPP1R21	Protein phosphatase 1 regulatory subunit 21	0.9524	21
CNN2	Calponin 2	0.9524	21
REPS2	RALBP1 associated Eps domain containing 2	0.9524	21
POLR2J3	RNA polymerase II subunit J3	0.9286	21
CCPG1	Cell cycle progression 1	0.9286	21
ZNF350	Zinc finger protein 350	0.9286	21
CKLF	Chemokine like factor	0.9286	21
CCDC125	Coiled-coil domain containing 125	0.9286	21
CRLF3	Cytokine receptor like factor 3	0.9286	21
MSL2	MSL complex subunit 2	0.9286	21
RPGR	Retinitis pigmentosa GTPase regulator	0.9286	21
C4orf19	Chromosome 4 open reading frame 19	0.9286	21

Adipocytes	1.0 nTPM
Breast	1.7 nTPM
Adipose tissue	0.4 nTPM

Alveolar cells type 1	0.6 nTPM
Lung	0.6 nTPM

Alveolar cells type 2	1.6 nTPM
Lung	1.6 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	71.8 nTPM
Thymus	184.0 nTPM
Stomach	86.5 nTPM
Bone marrow	86.1 nTPM
Lymph node	79.7 nTPM
Spleen	77.5 nTPM
Salivary gland	69.1 nTPM
Lung	68.4 nTPM
Liver	67.6 nTPM
PBMC	55.4 nTPM
Adipose tissue	47.7 nTPM
Esophagus	41.3 nTPM
Kidney	36.4 nTPM
Skin	33.9 nTPM

Ciliated cells	2.9 nTPM
Lung	6.8 nTPM
Fallopian tube	4.2 nTPM
Bronchus	0.4 nTPM
Endometrium	0.2 nTPM

Club cells	5.9 nTPM
Lung	10.7 nTPM
Prostate	5.2 nTPM
Bronchus	1.6 nTPM

Dendritic cells	40.8 nTPM
PBMC	54.0 nTPM
Adipose tissue	27.6 nTPM

Endothelial cells	1.6 nTPM
Thymus	4.2 nTPM
Skin	3.9 nTPM
Liver	3.8 nTPM
Lung	3.0 nTPM
Tongue	2.7 nTPM
Salivary gland	2.2 nTPM
Fallopian tube	2.2 nTPM
Vascular	2.0 nTPM
Esophagus	1.3 nTPM
Prostate	1.2 nTPM
Heart muscle	1.0 nTPM
Breast	0.9 nTPM
Placenta	0.6 nTPM
Skeletal muscle	0.4 nTPM
Endometrium	0.3 nTPM
Ovary	0.1 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM

Enteroendocrine cells	0.3 nTPM
Colon	0.9 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Fibroblasts	1.3 nTPM
Lung	7.6 nTPM
Thymus	3.8 nTPM
Salivary gland	2.1 nTPM
Placenta	1.9 nTPM
Vascular	1.6 nTPM
Prostate	1.3 nTPM
Skin	1.2 nTPM
Breast	0.5 nTPM
Fallopian tube	0.5 nTPM
Pancreas	0.3 nTPM
Heart muscle	0.2 nTPM
Skeletal muscle	0.2 nTPM
Adipose tissue	0.2 nTPM
Esophagus	0.2 nTPM
Liver	0.0 nTPM
Stomach	0.0 nTPM

Granulocytes	75.1 nTPM
Lung	112.9 nTPM
Tongue	58.2 nTPM
Fallopian tube	54.2 nTPM

Intestinal goblet cells	0.9 nTPM
Rectum	1.2 nTPM
Small intestine	0.8 nTPM
Colon	0.7 nTPM

Lymphatic endothelial cells	0.2 nTPM
Fallopian tube	0.4 nTPM
Ovary	0.0 nTPM

Macrophages	101.4 nTPM
Skin	205.0 nTPM
Lung	161.5 nTPM
Esophagus	158.0 nTPM
Fallopian tube	125.1 nTPM
Testis	119.0 nTPM
Vascular	116.7 nTPM
Pancreas	111.0 nTPM
Breast	109.6 nTPM
Adipose tissue	98.2 nTPM
Thymus	89.8 nTPM
Skeletal muscle	86.9 nTPM
Spleen	77.2 nTPM
Tongue	75.1 nTPM
Endometrium	74.4 nTPM
Kidney	72.6 nTPM
Stomach	69.4 nTPM
Bone marrow	60.8 nTPM
Prostate	60.0 nTPM
Salivary gland	56.4 nTPM

Basal prostatic cells	3.3 nTPM
Prostate	3.3 nTPM

Paneth cells	21.2 nTPM
Small intestine	41.4 nTPM
Rectum	14.8 nTPM
Colon	7.2 nTPM

Plasma cells	71.9 nTPM
Stomach	109.7 nTPM
Esophagus	109.2 nTPM
Thymus	70.8 nTPM
Fallopian tube	68.5 nTPM
Salivary gland	67.6 nTPM
Spleen	57.5 nTPM
Liver	48.1 nTPM
Bone marrow	43.8 nTPM

Schwann cells	10.3 nTPM
Adipose tissue	29.3 nTPM
Vascular	1.6 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	12.6 nTPM
Salivary gland	16.5 nTPM
Tongue	8.8 nTPM

Smooth muscle cells	1.6 nTPM
Thymus	6.4 nTPM
Esophagus	2.4 nTPM
Lung	2.4 nTPM
Skin	2.3 nTPM
Placenta	1.7 nTPM
Breast	1.4 nTPM
Liver	1.3 nTPM
Salivary gland	1.3 nTPM
Prostate	1.2 nTPM
Tongue	1.2 nTPM
Vascular	1.1 nTPM
Skeletal muscle	1.0 nTPM
Fallopian tube	1.0 nTPM
Ovary	0.6 nTPM
Endometrium	0.5 nTPM
Adipose tissue	0.4 nTPM

T-cells	18.5 nTPM
Vascular	37.0 nTPM
Thymus	29.7 nTPM
Lung	29.4 nTPM
Colon	29.2 nTPM
Tongue	27.4 nTPM
Breast	25.8 nTPM
Skin	25.6 nTPM
Fallopian tube	23.9 nTPM
Prostate	18.7 nTPM
Esophagus	17.0 nTPM
Stomach	16.1 nTPM
Endometrium	15.3 nTPM
Skeletal muscle	14.4 nTPM
Liver	12.9 nTPM
Adipose tissue	12.4 nTPM
Kidney	11.5 nTPM
Salivary gland	10.9 nTPM
Lymph node	10.7 nTPM
Bone marrow	8.3 nTPM
Spleen	6.6 nTPM
PBMC	6.0 nTPM

Undifferentiated cells	1.6 nTPM
Rectum	3.2 nTPM
Colon	1.1 nTPM
Small intestine	0.6 nTPM

Amygdala excitatory	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Thalamus	0.0 nTPM

Astrocyte	0.2 nTPM
Spinal cord	0.5 nTPM
Cerebellum	0.3 nTPM
Midbrain	0.3 nTPM
Hippocampus	0.2 nTPM
Basal ganglia	0.1 nTPM
Cerebral cortex	0.1 nTPM
Medulla oblongata	0.1 nTPM
Pons	0.1 nTPM
Thalamus	0.1 nTPM
Amygdala	0.0 nTPM
Hypothalamus	0.0 nTPM

Bergmann glia	0.0 nTPM
Cerebellum	0.1 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	34.0 nTPM
Cerebral cortex	43.8 nTPM
Hippocampus	37.7 nTPM
Spinal cord	37.7 nTPM
Cerebellum	37.3 nTPM
Pons	34.1 nTPM
Midbrain	33.9 nTPM
Amygdala	32.6 nTPM
Medulla oblongata	31.7 nTPM
Thalamus	29.9 nTPM
Hypothalamus	28.2 nTPM
Basal ganglia	27.2 nTPM

Cerebellar inhibitory	1.2 nTPM
Spinal cord	5.5 nTPM
Midbrain	0.3 nTPM
Medulla oblongata	0.2 nTPM
Pons	0.1 nTPM
Cerebellum	0.0 nTPM

Cge interneuron	0.1 nTPM
Midbrain	0.2 nTPM
Hippocampus	0.1 nTPM
Hypothalamus	0.1 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Thalamus	0.0 nTPM

Choroid plexus epithelial cell	0.1 nTPM
Basal ganglia	0.2 nTPM
Hippocampus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	0.3 nTPM
Basal ganglia	1.1 nTPM
Hippocampus	1.0 nTPM
Cerebral cortex	0.6 nTPM
Amygdala	0.0 nTPM
Cerebellum	0.0 nTPM
Hypothalamus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM
Thalamus	0.0 nTPM

Deep-layer corticothalamic and 6b	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM

Deep-layer near-projecting	0.1 nTPM
Hippocampus	0.3 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hypothalamus	0.0 nTPM

Eccentric medium spiny neuron	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Thalamus	0.0 nTPM

Endothelial cell	0.8 nTPM
Cerebral cortex	1.9 nTPM
Spinal cord	1.7 nTPM
Hypothalamus	1.2 nTPM
Medulla oblongata	1.0 nTPM
Basal ganglia	0.9 nTPM
Midbrain	0.9 nTPM
Thalamus	0.6 nTPM
Amygdala	0.0 nTPM
Cerebellum	0.0 nTPM
Hippocampus	0.0 nTPM
Pons	0.0 nTPM