Single cell type - PAXX - The Human Protein Atlas

PAXX

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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.	PAXX
Gene descriptionⁱ Full gene name according to HGNC.	PAXX non-homologous end joining factor
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.	1

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.	NK-cells - Adaptive 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.	Cell type enhanced (Dendritic cells, NK-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.	0.34
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 (Dendritic cells, NK-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: 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

PAXX is part of cluster 19 NK-cells - Adaptive immune response with confidenceⁱ 1
266 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.
CD7	CD7 molecule	0.7750	19
TMIGD2	Transmembrane and immunoglobulin domain containing 2	0.7390	19
IL2RB	Interleukin 2 receptor subunit beta	0.7372	19
GZMA	Granzyme A	0.7262	19
TSEN54	TRNA splicing endonuclease subunit 54	0.7258	19
GZMB	Granzyme B	0.7156	19
CD8A	CD8a molecule	0.7117	7
FASLG	Fas ligand	0.7099	19
KLRC2	Killer cell lectin like receptor C2	0.7043	19
GZMM	Granzyme M	0.6975	19
CCL5	C-C motif chemokine ligand 5	0.6970	19
KLRC1	Killer cell lectin like receptor C1	0.6963	19
CD247	CD247 molecule	0.6963	19
CTSW	Cathepsin W	0.6962	19
LAG3	Lymphocyte activating 3	0.6874	78

IMMUNE CELLS

PAXX is part of cluster 8 Plasmacytoid DCs - Unknown function with confidenceⁱ 0.66
236 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.
TRMT44	TRNA methyltransferase 44 homolog	0.9762	8
LARP1B	La ribonucleoprotein 1B	0.9762	8
NPRL3	NPR3 like, GATOR1 complex subunit	0.9524	8
RMDN3	Regulator of microtubule dynamics 3	0.9524	8
LTV1	LTV1 ribosome biogenesis factor	0.9524	8
MGP	Matrix Gla protein	0.9524	8
RAI1	Retinoic acid induced 1	0.9524	8
PALD1	Phosphatase domain containing paladin 1	0.9524	8
PPP6R1	Protein phosphatase 6 regulatory subunit 1	0.9524	8
UBXN8	UBX domain protein 8	0.9524	30
PDK2	Pyruvate dehydrogenase kinase 2	0.9524	8
MMP11	Matrix metallopeptidase 11	0.9524	8
ACOT7	Acyl-CoA thioesterase 7	0.9524	8
LTBP4	Latent transforming growth factor beta binding protein 4	0.9524	8
DDX24	DEAD-box helicase 24	0.9524	8

Adipocytes	63.2 nTPM
Breast	87.1 nTPM
Adipose tissue	39.3 nTPM

Alveolar cells type 1	57.9 nTPM
Lung	57.9 nTPM

Alveolar cells type 2	68.6 nTPM
Lung	68.6 nTPM

Astrocytes	18.0 nTPM
Brain	18.0 nTPM

B-cells	83.8 nTPM
Lung	155.6 nTPM
Bone marrow	126.7 nTPM
Stomach	117.7 nTPM
Skin	105.0 nTPM
Spleen	90.4 nTPM
Lymph node	75.2 nTPM
PBMC	73.9 nTPM
Esophagus	70.8 nTPM
Thymus	70.3 nTPM
Adipose tissue	56.0 nTPM
Liver	53.1 nTPM
Salivary gland	52.9 nTPM
Kidney	41.6 nTPM

Ciliated cells	38.8 nTPM
Fallopian tube	46.3 nTPM
Endometrium	45.2 nTPM
Lung	37.0 nTPM
Bronchus	26.6 nTPM

Club cells	42.8 nTPM
Lung	50.4 nTPM
Prostate	40.9 nTPM
Bronchus	37.0 nTPM

Dendritic cells	322.6 nTPM
PBMC	334.6 nTPM
Adipose tissue	310.7 nTPM

Endothelial cells	60.7 nTPM
Esophagus	123.1 nTPM
Lung	98.9 nTPM
Thymus	77.8 nTPM
Vascular	72.9 nTPM
Fallopian tube	71.3 nTPM
Ovary	68.3 nTPM
Placenta	65.9 nTPM
Testis	65.3 nTPM
Pancreas	62.0 nTPM
Tongue	60.2 nTPM
Skin	54.9 nTPM
Endometrium	54.3 nTPM
Prostate	53.0 nTPM
Skeletal muscle	40.6 nTPM
Salivary gland	38.0 nTPM
Liver	32.8 nTPM
Heart muscle	32.2 nTPM
Breast	21.1 nTPM

Enteroendocrine cells	86.5 nTPM
Colon	91.5 nTPM
Small intestine	89.3 nTPM
Rectum	78.8 nTPM

Fibroblasts	40.3 nTPM
Placenta	86.0 nTPM
Breast	58.0 nTPM
Fallopian tube	53.0 nTPM
Pancreas	48.6 nTPM
Stomach	47.6 nTPM
Skin	47.3 nTPM
Lung	45.2 nTPM
Liver	42.7 nTPM
Esophagus	35.4 nTPM
Thymus	34.8 nTPM
Adipose tissue	33.7 nTPM
Prostate	30.4 nTPM
Vascular	29.5 nTPM
Salivary gland	21.2 nTPM
Skeletal muscle	20.5 nTPM
Heart muscle	11.3 nTPM

Granulocytes	36.7 nTPM
Lung	43.9 nTPM
Fallopian tube	37.1 nTPM
Tongue	29.1 nTPM

Intestinal goblet cells	63.9 nTPM
Colon	89.6 nTPM
Small intestine	54.1 nTPM
Rectum	48.2 nTPM

Lymphatic endothelial cells	11.6 nTPM
Ovary	16.4 nTPM
Fallopian tube	6.7 nTPM

Macrophages	67.2 nTPM
Breast	143.2 nTPM
Endometrium	101.5 nTPM
Kidney	99.1 nTPM
Stomach	84.9 nTPM
Bone marrow	83.1 nTPM
Spleen	77.2 nTPM
Adipose tissue	75.7 nTPM
Fallopian tube	70.7 nTPM
Testis	63.9 nTPM
Skeletal muscle	60.1 nTPM
Prostate	59.0 nTPM
Lung	54.8 nTPM
Esophagus	53.9 nTPM
Skin	51.3 nTPM
Tongue	46.1 nTPM
Pancreas	45.2 nTPM
Salivary gland	44.0 nTPM
Thymus	39.7 nTPM
Vascular	23.4 nTPM

Basal keratinocytes	46.0 nTPM
Tongue	50.1 nTPM
Skin	41.9 nTPM

Basal prostatic cells	29.9 nTPM
Prostate	29.9 nTPM

Basal respiratory cells	45.4 nTPM
Bronchus	45.4 nTPM

Basal squamous epithelial cells	52.1 nTPM
Esophagus	52.1 nTPM

Paneth cells	66.5 nTPM
Colon	76.0 nTPM
Small intestine	65.6 nTPM
Rectum	57.8 nTPM

Plasma cells	50.0 nTPM
Stomach	66.2 nTPM
Fallopian tube	59.8 nTPM
Thymus	58.4 nTPM
Spleen	54.6 nTPM
Bone marrow	52.9 nTPM
Liver	43.1 nTPM
Salivary gland	33.6 nTPM
Esophagus	31.2 nTPM

Schwann cells	62.7 nTPM
Adipose tissue	109.7 nTPM
Vascular	78.4 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	42.4 nTPM
Tongue	48.6 nTPM
Salivary gland	36.2 nTPM

Smooth muscle cells	42.4 nTPM
Breast	71.5 nTPM
Placenta	69.7 nTPM
Lung	52.9 nTPM
Ovary	52.6 nTPM
Endometrium	47.6 nTPM
Skin	44.8 nTPM
Adipose tissue	43.6 nTPM
Liver	42.9 nTPM
Fallopian tube	40.9 nTPM
Thymus	36.2 nTPM
Esophagus	36.0 nTPM
Skeletal muscle	33.2 nTPM
Vascular	32.9 nTPM
Tongue	25.1 nTPM
Prostate	24.9 nTPM
Salivary gland	23.4 nTPM

Suprabasal keratinocytes	50.5 nTPM
Skin	56.1 nTPM
Tongue	44.9 nTPM

T-cells	171.5 nTPM
Stomach	302.0 nTPM
Breast	276.4 nTPM
Kidney	246.5 nTPM
Colon	237.9 nTPM
Bone marrow	230.4 nTPM
Lung	230.2 nTPM
Spleen	205.6 nTPM
Liver	193.0 nTPM
Fallopian tube	191.2 nTPM
Esophagus	187.4 nTPM
Prostate	154.5 nTPM
Skeletal muscle	149.7 nTPM
Adipose tissue	147.9 nTPM
Endometrium	130.1 nTPM
PBMC	128.0 nTPM
Thymus	111.4 nTPM
Lymph node	110.3 nTPM
Skin	105.5 nTPM
Vascular	105.3 nTPM
Tongue	89.5 nTPM
Salivary gland	68.1 nTPM

Undifferentiated cells	98.3 nTPM
Colon	135.6 nTPM
Rectum	81.2 nTPM
Small intestine	78.1 nTPM

Amygdala excitatory	20.4 nTPM
Thalamus	25.4 nTPM
Cerebral cortex	24.9 nTPM
Basal ganglia	24.4 nTPM
Hippocampus	20.4 nTPM
Amygdala	16.8 nTPM
Hypothalamus	10.5 nTPM

Astrocyte	42.3 nTPM
Pons	61.2 nTPM
Cerebral cortex	50.0 nTPM
Spinal cord	49.9 nTPM
Medulla oblongata	48.4 nTPM
Cerebellum	48.2 nTPM
Hippocampus	45.0 nTPM
Thalamus	42.1 nTPM
Midbrain	39.5 nTPM
Basal ganglia	37.6 nTPM
Amygdala	21.9 nTPM
Hypothalamus	21.7 nTPM

Bergmann glia	48.7 nTPM
Pons	50.3 nTPM
Cerebellum	49.0 nTPM
Medulla oblongata	46.9 nTPM

Central nervous system macrophage	42.7 nTPM
Cerebral cortex	58.7 nTPM
Spinal cord	52.7 nTPM
Pons	48.4 nTPM
Cerebellum	47.7 nTPM
Medulla oblongata	47.5 nTPM
Basal ganglia	44.2 nTPM
Hippocampus	44.0 nTPM
Midbrain	40.2 nTPM
Thalamus	33.0 nTPM
Amygdala	27.2 nTPM
Hypothalamus	26.5 nTPM

Cerebellar inhibitory	29.1 nTPM
Pons	38.8 nTPM
Midbrain	34.5 nTPM
Cerebellum	27.7 nTPM
Medulla oblongata	22.6 nTPM
Spinal cord	22.0 nTPM

Cge interneuron	34.9 nTPM
Thalamus	43.1 nTPM
Midbrain	39.7 nTPM
Cerebral cortex	39.5 nTPM
Hippocampus	38.7 nTPM
Basal ganglia	36.7 nTPM
Amygdala	30.4 nTPM
Hypothalamus	15.8 nTPM

Choroid plexus epithelial cell	16.8 nTPM
Hippocampus	22.2 nTPM
Medulla oblongata	20.8 nTPM
Thalamus	13.7 nTPM
Basal ganglia	10.5 nTPM

Committed oligodendrocyte precursor	32.5 nTPM
Pons	49.6 nTPM
Midbrain	40.3 nTPM
Medulla oblongata	38.7 nTPM
Cerebral cortex	38.0 nTPM
Hippocampus	38.0 nTPM
Cerebellum	33.3 nTPM
Basal ganglia	27.4 nTPM
Spinal cord	25.8 nTPM
Amygdala	23.7 nTPM
Thalamus	22.5 nTPM
Hypothalamus	19.8 nTPM

Deep-layer corticothalamic and 6b	26.4 nTPM
Midbrain	36.6 nTPM
Cerebral cortex	30.2 nTPM
Basal ganglia	29.9 nTPM
Hippocampus	28.5 nTPM
Amygdala	25.4 nTPM
Hypothalamus	8.0 nTPM

Deep-layer intratelencephalic	25.2 nTPM
Basal ganglia	33.6 nTPM
Cerebral cortex	32.9 nTPM
Hippocampus	25.9 nTPM
Amygdala	23.9 nTPM
Hypothalamus	9.8 nTPM

Deep-layer near-projecting	35.0 nTPM
Hippocampus	54.6 nTPM
Cerebral cortex	41.1 nTPM
Basal ganglia	37.2 nTPM
Amygdala	28.9 nTPM
Hypothalamus	13.3 nTPM

Eccentric medium spiny neuron	20.3 nTPM
Basal ganglia	24.6 nTPM
Cerebral cortex	20.8 nTPM
Amygdala	20.0 nTPM
Hypothalamus	19.7 nTPM
Thalamus	19.6 nTPM
Hippocampus	17.0 nTPM