Single cell type - VARS2 - The Human Protein Atlas

VARS2

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Pathway

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.	VARS2
Gene descriptionⁱ Full gene name according to HGNC.	Valyl-tRNA synthetase 2, mitochondrial
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Enzymes Human disease related genes Potential drug targets
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.	7

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 (Astrocytes, Inhibitory neurons, Excitatory neurons, Oligodendrocyte precursor cells, Oligodendrocytes, Plasma cells, Microglial 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.	0.90
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.	Not detected in immune cells
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 (Astrocytes, Inhibitory neurons, Excitatory neurons, Oligodendrocyte precursor cells, Oligodendrocytes, Plasma cells, Microglial 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: Not detected in immune cells
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

VARS2 is part of cluster 49 Non-specific - Transcription with confidenceⁱ 1
378 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.
BORCS8-MEF2B	BORCS8-MEF2B readthrough	0.7307	47
CRELD1	Cysteine rich with EGF like domains 1	0.6658	49
PAGR1	PAXIP1 associated glutamate rich protein 1	0.6503	49
GET4	Guided entry of tail-anchored proteins factor 4	0.6248	49
SPOUT1	SPOUT domain containing methyltransferase 1	0.6122	47
ZNF23	Zinc finger protein 23	0.6113	49
ZNF410	Zinc finger protein 410	0.5901	49
BCKDHA	Branched chain keto acid dehydrogenase E1 subunit alpha	0.5860	49
PIRT	Phosphoinositide interacting regulator of transient receptor potential channels	0.5739	47
ATG9A	Autophagy related 9A	0.5739	49
TREX1	Three prime repair exonuclease 1	0.5672	49
WDR83OS	WD repeat domain 83 opposite strand	0.5648	49
SMPD4	Sphingomyelin phosphodiesterase 4	0.5558	49
NDOR1	NADPH dependent diflavin oxidoreductase 1	0.5480	49
ZGPAT	Zinc finger CCCH-type and G-patch domain containing	0.5451	49

IMMUNE CELLS

VARS2 is part of cluster 33 Non-specific - ATP binding with confidenceⁱ 1
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.
PTCD2	Pentatricopeptide repeat domain 2	1.0000	33
PDZD11	PDZ domain containing 11	1.0000	33
ULK3	Unc-51 like kinase 3	1.0000	33
IARS2	Isoleucyl-tRNA synthetase 2, mitochondrial	0.9762	33
H2BC26	H2B clustered histone 26	0.9762	33
ATP1A1	ATPase Na+/K+ transporting subunit alpha 1	0.9762	33
NUP205	Nucleoporin 205	0.9762	33
DUSP10	Dual specificity phosphatase 10	0.9762	33
IL10RA	Interleukin 10 receptor subunit alpha	0.9762	33
RTCA	RNA 3'-terminal phosphate cyclase	0.9524	33
MTA2	Metastasis associated 1 family member 2	0.9524	9
MOV10	Mov10 RISC complex RNA helicase	0.9524	33
LANCL2	LanC like glutathione S-transferase 2	0.9524	33
PARS2	Prolyl-tRNA synthetase 2, mitochondrial	0.9524	33
DNAAF5	Dynein axonemal assembly factor 5	0.9524	33

Adipocytes	0.0 nTPM
Breast	0.1 nTPM
Adipose tissue	0.0 nTPM

Alveolar cells type 1	0.1 nTPM
Lung	0.1 nTPM

Alveolar cells type 2	0.1 nTPM
Lung	0.1 nTPM

B-cells	1.3 nTPM
Spleen	5.4 nTPM
Bone marrow	4.1 nTPM
Stomach	3.8 nTPM
Lymph node	2.5 nTPM
Thymus	1.4 nTPM
Salivary gland	0.2 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM

Basal keratinocytes	0.1 nTPM
Tongue	0.1 nTPM
Skin	0.0 nTPM

Ciliated cells	0.1 nTPM
Endometrium	0.2 nTPM
Lung	0.2 nTPM
Fallopian tube	0.1 nTPM
Bronchus	0.0 nTPM

Club cells	0.1 nTPM
Lung	0.4 nTPM
Bronchus	0.0 nTPM
Prostate	0.0 nTPM

Endothelial cells	0.1 nTPM
Esophagus	0.5 nTPM
Thymus	0.3 nTPM
Skin	0.2 nTPM
Salivary gland	0.2 nTPM
Endometrium	0.1 nTPM
Skeletal muscle	0.1 nTPM
Lung	0.1 nTPM
Ovary	0.1 nTPM
Testis	0.0 nTPM
Heart muscle	0.0 nTPM
Liver	0.0 nTPM
Placenta	0.0 nTPM
Pancreas	0.0 nTPM
Prostate	0.0 nTPM
Tongue	0.0 nTPM
Vascular	0.0 nTPM
Breast	0.0 nTPM
Fallopian tube	0.0 nTPM

Enteroendocrine cells	0.0 nTPM
Colon	0.1 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Fibroblasts	0.2 nTPM
Stomach	1.4 nTPM
Thymus	0.6 nTPM
Esophagus	0.5 nTPM
Vascular	0.2 nTPM
Skin	0.1 nTPM
Skeletal muscle	0.1 nTPM
Adipose tissue	0.1 nTPM
Salivary gland	0.1 nTPM
Breast	0.1 nTPM
Fallopian tube	0.1 nTPM
Heart muscle	0.0 nTPM
Liver	0.0 nTPM
Placenta	0.0 nTPM
Pancreas	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM

Granulocytes	0.2 nTPM
Fallopian tube	0.6 nTPM
Lung	0.0 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Lymphatic endothelial cells	0.0 nTPM
Fallopian tube	0.1 nTPM
Ovary	0.0 nTPM

Macrophages	0.3 nTPM
Bone marrow	2.0 nTPM
Esophagus	1.3 nTPM
Spleen	1.0 nTPM
Thymus	0.4 nTPM
Prostate	0.2 nTPM
Tongue	0.2 nTPM
Breast	0.2 nTPM
Vascular	0.1 nTPM
Testis	0.0 nTPM
Kidney	0.0 nTPM
Endometrium	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Adipose tissue	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Salivary gland	0.0 nTPM
Fallopian tube	0.0 nTPM

Paneth cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Astrocytes	13.9 nTPM
Brain	13.9 nTPM

Plasma cells	4.2 nTPM
Spleen	14.0 nTPM
Bone marrow	9.1 nTPM
Stomach	7.1 nTPM
Thymus	2.8 nTPM
Fallopian tube	0.6 nTPM
Liver	0.0 nTPM
Esophagus	0.0 nTPM
Salivary gland	0.0 nTPM

Schwann cells	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Vascular	0.0 nTPM

Serous glandular cells	0.0 nTPM
Salivary gland	0.1 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	0.2 nTPM
Esophagus	2.4 nTPM
Thymus	0.5 nTPM
Endometrium	0.3 nTPM
Skeletal muscle	0.2 nTPM
Adipose tissue	0.2 nTPM
Vascular	0.1 nTPM
Ovary	0.1 nTPM
Liver	0.0 nTPM
Placenta	0.0 nTPM
Skin	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Salivary gland	0.0 nTPM
Tongue	0.0 nTPM
Breast	0.0 nTPM
Fallopian tube	0.0 nTPM

T-cells	0.8 nTPM
Spleen	4.0 nTPM
Lymph node	3.6 nTPM
Stomach	3.4 nTPM
Bone marrow	2.3 nTPM
Thymus	0.5 nTPM
Skeletal muscle	0.4 nTPM
Vascular	0.4 nTPM
Liver	0.2 nTPM
Endometrium	0.2 nTPM
PBMC	0.2 nTPM
Salivary gland	0.2 nTPM
Adipose tissue	0.1 nTPM
Breast	0.1 nTPM
Fallopian tube	0.1 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
Skin	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Tongue	0.0 nTPM

Undifferentiated cells	0.0 nTPM
Small intestine	0.1 nTPM
Colon	0.0 nTPM
Rectum	0.0 nTPM

Amygdala excitatory	15.7 nTPM
Hypothalamus	17.7 nTPM
Amygdala	16.3 nTPM
Thalamus	16.3 nTPM
Basal ganglia	16.0 nTPM
Hippocampus	15.9 nTPM
Cerebral cortex	11.8 nTPM

Astrocyte	26.1 nTPM
Pons	35.1 nTPM
Spinal cord	33.9 nTPM
Cerebellum	32.2 nTPM
Hippocampus	29.2 nTPM
Midbrain	27.7 nTPM
Cerebral cortex	25.5 nTPM
Thalamus	24.5 nTPM
Medulla oblongata	23.8 nTPM
Basal ganglia	20.1 nTPM
Amygdala	18.2 nTPM
Hypothalamus	16.9 nTPM

Bergmann glia	10.8 nTPM
Cerebellum	12.5 nTPM
Pons	11.5 nTPM
Medulla oblongata	8.5 nTPM

Central nervous system macrophage	10.2 nTPM
Cerebellum	13.3 nTPM
Spinal cord	12.1 nTPM
Hippocampus	11.5 nTPM
Midbrain	10.5 nTPM
Pons	10.3 nTPM
Amygdala	10.0 nTPM
Cerebral cortex	9.8 nTPM
Thalamus	9.5 nTPM
Basal ganglia	9.4 nTPM
Hypothalamus	9.1 nTPM
Medulla oblongata	7.1 nTPM

Cerebellar inhibitory	13.8 nTPM
Spinal cord	24.7 nTPM
Cerebellum	12.6 nTPM
Midbrain	12.4 nTPM
Pons	9.7 nTPM
Medulla oblongata	9.6 nTPM

Cge interneuron	13.9 nTPM
Hypothalamus	20.2 nTPM
Amygdala	16.5 nTPM
Hippocampus	13.3 nTPM
Cerebral cortex	13.1 nTPM
Basal ganglia	12.8 nTPM
Thalamus	11.6 nTPM
Midbrain	10.1 nTPM

Choroid plexus epithelial cell	6.8 nTPM
Hippocampus	8.3 nTPM
Thalamus	8.2 nTPM
Basal ganglia	5.4 nTPM
Medulla oblongata	5.2 nTPM

Committed oligodendrocyte precursor	11.9 nTPM
Hippocampus	21.0 nTPM
Cerebellum	14.3 nTPM
Hypothalamus	14.3 nTPM
Basal ganglia	13.7 nTPM
Cerebral cortex	12.7 nTPM
Midbrain	11.8 nTPM
Thalamus	10.4 nTPM
Pons	9.7 nTPM
Medulla oblongata	9.0 nTPM
Spinal cord	7.4 nTPM
Amygdala	6.8 nTPM

Deep-layer corticothalamic and 6b	11.7 nTPM
Hypothalamus	16.3 nTPM
Amygdala	13.7 nTPM
Hippocampus	12.7 nTPM
Cerebral cortex	12.2 nTPM
Basal ganglia	9.8 nTPM
Midbrain	5.5 nTPM

Deep-layer intratelencephalic	12.9 nTPM
Hypothalamus	17.7 nTPM
Amygdala	12.7 nTPM
Hippocampus	12.7 nTPM
Cerebral cortex	11.0 nTPM
Basal ganglia	10.1 nTPM

Deep-layer near-projecting	12.6 nTPM
Hypothalamus	18.4 nTPM
Amygdala	15.7 nTPM
Cerebral cortex	12.9 nTPM
Basal ganglia	9.8 nTPM
Hippocampus	6.2 nTPM

Eccentric medium spiny neuron	17.4 nTPM
Hippocampus	22.4 nTPM
Thalamus	20.2 nTPM
Basal ganglia	17.0 nTPM
Amygdala	15.4 nTPM
Cerebral cortex	15.0 nTPM
Hypothalamus	14.3 nTPM

Endothelial cell	5.0 nTPM
Cerebral cortex	9.0 nTPM
Basal ganglia	8.4 nTPM
Hypothalamus	6.2 nTPM
Pons	6.2 nTPM
Spinal cord	5.2 nTPM
Hippocampus	4.8 nTPM
Thalamus	4.5 nTPM
Cerebellum	3.9 nTPM
Medulla oblongata	3.1 nTPM
Amygdala	2.2 nTPM
Midbrain	1.9 nTPM

Ependymal cell	11.3 nTPM
Hippocampus	16.0 nTPM
Basal ganglia	13.4 nTPM
Spinal cord	13.4 nTPM
Amygdala	12.5 nTPM
Pons	11.4 nTPM
Midbrain	10.2 nTPM
Medulla oblongata	10.1 nTPM
Thalamus	8.1 nTPM
Hypothalamus	6.2 nTPM