Single cell type - NXF1 - The Human Protein Atlas

NXF1

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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.	NXF1
Gene descriptionⁱ Full gene name according to HGNC.	Nuclear RNA export factor 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	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.	Intracellular
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.	Non-specific - Transcription (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 (Syncytiotrophoblasts)
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.	0.34
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.	Low cell type specificity
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.	Low immune cell specificity
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 (Syncytiotrophoblasts)

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: Low cell type specificity

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: Low immune cell specificity
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

NXF1 is part of cluster 80 Non-specific - Transcription with confidenceⁱ 1
184 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.
HEXIM1	HEXIM P-TEFb complex subunit 1	0.7835	80
PPP1R10	Protein phosphatase 1 regulatory subunit 10	0.7554	80
RSRP1	Arginine and serine rich protein 1	0.7209	80
INTS6	Integrator complex subunit 6	0.7089	80
IQCN	IQ motif containing N	0.7011	80
NEU1	Neuraminidase 1	0.6954	80
H2AX	H2A.X variant histone	0.6915	80
CBX4	Chromobox 4	0.6646	80
IER2	Immediate early response 2	0.6644	80
TNF	Tumor necrosis factor	0.6640	80
NUFIP2	Nuclear FMR1 interacting protein 2	0.6607	80
BRD2	Bromodomain containing 2	0.6569	80
SNAI1	Snail family transcriptional repressor 1	0.6553	80
GLA	Galactosidase alpha	0.6552	80
POU3F1	POU class 3 homeobox 1	0.6504	80

IMMUNE CELLS

NXF1 is part of cluster 33 Non-specific - ATP binding with confidenceⁱ 0.87
757 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.
CRYL1	Crystallin lambda 1	0.9762	33
MGST3	Microsomal glutathione S-transferase 3	0.9524	33
ENSG00000273155	Novel LIPT1-MRPL30 readthrough	0.9524	33
SGSH	N-sulfoglucosamine sulfohydrolase	0.9524	33
LRRC8C	Leucine rich repeat containing 8 VRAC subunit C	0.9524	33
USP38	Ubiquitin specific peptidase 38	0.9524	33
GPRC5B	G protein-coupled receptor class C group 5 member B	0.9524	33
PAN2	Poly(A) specific ribonuclease subunit PAN2	0.9524	33
USP5	Ubiquitin specific peptidase 5	0.9524	33
BCL2L13	BCL2 like 13	0.9524	33
TUBGCP2	Tubulin gamma complex associated protein 2	0.9286	33
DCLRE1B	DNA cross-link repair 1B	0.9286	33
SMARCD2	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	0.9286	33
ORC1	Origin recognition complex subunit 1	0.9286	33
DIABLO	Diablo IAP-binding mitochondrial protein	0.9286	33

Adipocytes	46.8 nTPM
Breast	64.3 nTPM
Adipose tissue	29.3 nTPM

Alveolar cells type 1	12.9 nTPM
Lung	12.9 nTPM

Alveolar cells type 2	19.6 nTPM
Lung	19.6 nTPM

Astrocytes	13.9 nTPM
Brain	13.9 nTPM

B-cells	29.8 nTPM
Lymph node	65.3 nTPM
Esophagus	47.2 nTPM
Kidney	41.6 nTPM
Skin	39.0 nTPM
Spleen	31.7 nTPM
Lung	26.8 nTPM
Liver	24.2 nTPM
Adipose tissue	23.9 nTPM
Stomach	21.9 nTPM
Thymus	19.9 nTPM
Salivary gland	17.3 nTPM
Bone marrow	15.0 nTPM
PBMC	13.9 nTPM

Ciliated cells	19.0 nTPM
Endometrium	26.4 nTPM
Bronchus	25.8 nTPM
Lung	12.5 nTPM
Fallopian tube	11.4 nTPM

Club cells	20.5 nTPM
Bronchus	29.1 nTPM
Prostate	16.5 nTPM
Lung	15.8 nTPM

Dendritic cells	27.9 nTPM
Adipose tissue	41.4 nTPM
PBMC	14.4 nTPM

Endothelial cells	29.6 nTPM
Esophagus	68.9 nTPM
Endometrium	43.2 nTPM
Liver	41.6 nTPM
Skin	36.5 nTPM
Heart muscle	35.4 nTPM
Placenta	32.4 nTPM
Thymus	29.5 nTPM
Skeletal muscle	29.3 nTPM
Testis	29.0 nTPM
Breast	28.1 nTPM
Prostate	24.9 nTPM
Ovary	24.2 nTPM
Tongue	21.4 nTPM
Salivary gland	19.6 nTPM
Vascular	18.5 nTPM
Pancreas	18.1 nTPM
Fallopian tube	17.3 nTPM
Lung	14.4 nTPM

Enteroendocrine cells	25.5 nTPM
Colon	29.1 nTPM
Small intestine	24.0 nTPM
Rectum	23.5 nTPM

Fibroblasts	26.3 nTPM
Esophagus	66.4 nTPM
Breast	42.4 nTPM
Stomach	40.3 nTPM
Skin	39.1 nTPM
Skeletal muscle	33.3 nTPM
Liver	27.3 nTPM
Placenta	26.0 nTPM
Fallopian tube	23.5 nTPM
Thymus	19.0 nTPM
Adipose tissue	18.2 nTPM
Pancreas	17.4 nTPM
Salivary gland	15.5 nTPM
Vascular	14.2 nTPM
Lung	13.7 nTPM
Prostate	12.5 nTPM
Heart muscle	11.5 nTPM

Granulocytes	15.1 nTPM
Lung	15.6 nTPM
Fallopian tube	15.2 nTPM
Tongue	14.6 nTPM

Intestinal goblet cells	28.7 nTPM
Colon	36.7 nTPM
Small intestine	28.3 nTPM
Rectum	21.3 nTPM

Lymphatic endothelial cells	22.6 nTPM
Ovary	32.7 nTPM
Fallopian tube	12.5 nTPM

Macrophages	56.9 nTPM
Breast	197.4 nTPM
Esophagus	165.7 nTPM
Endometrium	73.8 nTPM
Adipose tissue	65.5 nTPM
Spleen	63.2 nTPM
Skin	62.4 nTPM
Fallopian tube	55.3 nTPM
Skeletal muscle	50.8 nTPM
Stomach	46.3 nTPM
Lung	41.4 nTPM
Kidney	38.1 nTPM
Salivary gland	34.1 nTPM
Thymus	32.5 nTPM
Vascular	30.6 nTPM
Bone marrow	29.4 nTPM
Prostate	28.2 nTPM
Testis	27.9 nTPM
Tongue	24.5 nTPM
Pancreas	14.4 nTPM

Basal squamous epithelial cells	35.7 nTPM
Esophagus	35.7 nTPM

Bipolar cells	10.1 nTPM
Eye	10.1 nTPM

Cholangiocytes	24.8 nTPM
Liver	24.8 nTPM

Collecting duct cells	19.4 nTPM
Kidney	19.4 nTPM

Paneth cells	25.8 nTPM
Colon	39.8 nTPM
Small intestine	24.2 nTPM
Rectum	13.4 nTPM

Plasma cells	20.3 nTPM
Esophagus	52.0 nTPM
Stomach	22.2 nTPM
Liver	21.0 nTPM
Salivary gland	17.5 nTPM
Spleen	16.6 nTPM
Thymus	15.5 nTPM
Fallopian tube	11.3 nTPM
Bone marrow	6.0 nTPM

Schwann cells	18.7 nTPM
Adipose tissue	39.4 nTPM
Vascular	16.7 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	19.5 nTPM
Tongue	26.5 nTPM
Salivary gland	12.5 nTPM

Smooth muscle cells	30.7 nTPM
Esophagus	79.3 nTPM
Breast	62.5 nTPM
Skin	47.5 nTPM
Skeletal muscle	43.1 nTPM
Endometrium	36.2 nTPM
Placenta	29.7 nTPM
Liver	28.4 nTPM
Adipose tissue	21.8 nTPM
Thymus	21.4 nTPM
Tongue	21.0 nTPM
Ovary	21.0 nTPM
Salivary gland	19.6 nTPM
Prostate	19.5 nTPM
Fallopian tube	15.8 nTPM
Vascular	13.9 nTPM
Lung	10.6 nTPM

Suprabasal keratinocytes	58.7 nTPM
Skin	74.3 nTPM
Tongue	43.1 nTPM

T-cells	35.7 nTPM
Breast	114.5 nTPM
Endometrium	68.4 nTPM
Lymph node	64.1 nTPM
Esophagus	51.1 nTPM
Skin	41.0 nTPM
Adipose tissue	38.1 nTPM
Skeletal muscle	37.0 nTPM
Liver	35.2 nTPM
Kidney	34.6 nTPM
Colon	31.2 nTPM
Vascular	30.2 nTPM
Spleen	26.7 nTPM
Thymus	25.8 nTPM
PBMC	21.8 nTPM
Tongue	21.7 nTPM
Salivary gland	20.2 nTPM
Stomach	20.1 nTPM
Fallopian tube	18.9 nTPM
Prostate	18.0 nTPM
Lung	16.7 nTPM
Bone marrow	14.9 nTPM

Undifferentiated cells	20.9 nTPM
Colon	26.4 nTPM
Small intestine	20.8 nTPM
Rectum	15.4 nTPM

Amygdala excitatory	13.7 nTPM
Basal ganglia	16.2 nTPM
Amygdala	15.3 nTPM
Thalamus	13.6 nTPM
Cerebral cortex	12.9 nTPM
Hippocampus	12.5 nTPM
Hypothalamus	11.7 nTPM

Astrocyte	21.0 nTPM
Cerebellum	30.4 nTPM
Pons	27.1 nTPM
Thalamus	27.1 nTPM
Midbrain	25.1 nTPM
Cerebral cortex	23.7 nTPM
Hippocampus	19.5 nTPM
Basal ganglia	18.3 nTPM
Spinal cord	17.8 nTPM
Medulla oblongata	16.3 nTPM
Amygdala	14.2 nTPM
Hypothalamus	11.9 nTPM

Bergmann glia	11.2 nTPM
Pons	15.8 nTPM
Cerebellum	13.5 nTPM
Medulla oblongata	4.3 nTPM

Central nervous system macrophage	23.1 nTPM
Hippocampus	29.7 nTPM
Cerebral cortex	26.9 nTPM
Cerebellum	26.2 nTPM
Pons	24.3 nTPM
Midbrain	23.3 nTPM
Thalamus	21.8 nTPM
Spinal cord	21.2 nTPM
Medulla oblongata	20.7 nTPM
Hypothalamus	20.5 nTPM
Amygdala	20.2 nTPM
Basal ganglia	19.8 nTPM

Cerebellar inhibitory	18.8 nTPM
Pons	24.3 nTPM
Midbrain	20.2 nTPM
Cerebellum	19.4 nTPM
Medulla oblongata	16.6 nTPM
Spinal cord	13.7 nTPM

Cge interneuron	14.4 nTPM
Midbrain	15.6 nTPM
Thalamus	15.0 nTPM
Basal ganglia	14.8 nTPM
Hypothalamus	14.3 nTPM
Cerebral cortex	14.2 nTPM
Amygdala	14.1 nTPM
Hippocampus	12.8 nTPM

Choroid plexus epithelial cell	16.0 nTPM
Thalamus	19.2 nTPM
Medulla oblongata	19.1 nTPM
Basal ganglia	14.7 nTPM
Hippocampus	11.1 nTPM

Committed oligodendrocyte precursor	14.8 nTPM
Cerebral cortex	19.0 nTPM
Hippocampus	16.6 nTPM
Hypothalamus	16.4 nTPM
Basal ganglia	15.9 nTPM
Cerebellum	15.9 nTPM
Pons	15.9 nTPM
Amygdala	15.8 nTPM
Thalamus	13.5 nTPM
Midbrain	11.8 nTPM
Medulla oblongata	11.6 nTPM
Spinal cord	11.0 nTPM

Deep-layer corticothalamic and 6b	11.3 nTPM
Cerebral cortex	11.6 nTPM
Hippocampus	11.5 nTPM
Basal ganglia	11.4 nTPM
Hypothalamus	11.3 nTPM
Midbrain	11.1 nTPM
Amygdala	10.9 nTPM

Deep-layer intratelencephalic	11.9 nTPM
Amygdala	14.2 nTPM
Cerebral cortex	13.1 nTPM
Basal ganglia	12.1 nTPM
Hippocampus	10.4 nTPM
Hypothalamus	9.8 nTPM

Deep-layer near-projecting	11.3 nTPM
Amygdala	13.7 nTPM
Cerebral cortex	13.2 nTPM
Basal ganglia	12.2 nTPM
Hypothalamus	12.2 nTPM
Hippocampus	5.2 nTPM

Eccentric medium spiny neuron	14.8 nTPM
Cerebral cortex	16.2 nTPM
Amygdala	15.6 nTPM
Basal ganglia	15.1 nTPM
Thalamus	14.8 nTPM
Hippocampus	13.7 nTPM
Hypothalamus	13.7 nTPM