Single cell type - YTHDF3 - The Human Protein Atlas

YTHDF3

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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.	YTHDF3
Gene descriptionⁱ Full gene name according to HGNC.	YTH N6-methyladenosine RNA binding protein 3
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.	12

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.	Monocytes - Innate 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 (Monocytes)
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.	0.33
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 (Monocytes)

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

YTHDF3 is part of cluster 29 Monocytes - Innate immune response with confidenceⁱ 0.95
447 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.
ATP13A3	ATPase 13A3	0.6823	29
NRIP1	Nuclear receptor interacting protein 1	0.6195	29
CSGALNACT2	Chondroitin sulfate N-acetylgalactosaminyltransferase 2	0.6075	29
NOCT	Nocturnin	0.6066	29
DENND5A	DENN domain containing 5A	0.6052	29
SP3	Sp3 transcription factor	0.6014	29
NUP153	Nucleoporin 153	0.5976	37
CHSY1	Chondroitin sulfate synthase 1	0.5948	29
PPP1R15B	Protein phosphatase 1 regulatory subunit 15B	0.5948	29
PNPLA8	Patatin like phospholipase domain containing 8	0.5877	29
POLR1F	RNA polymerase I subunit F	0.5813	29
RLIM	Ring finger protein, LIM domain interacting	0.5794	29
DCTN4	Dynactin subunit 4	0.5781	55
ATF6	Activating transcription factor 6	0.5550	29
TSC22D2	TSC22 domain family member 2	0.5486	37

IMMUNE CELLS

YTHDF3 is part of cluster 42 Non-specific - Vesicular transport with confidenceⁱ 1
519 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.
EXOC1	Exocyst complex component 1	0.9762	42
ABHD3	Abhydrolase domain containing 3, phospholipase	0.9762	42
TPM1	Tropomyosin 1	0.9762	42
TMOD3	Tropomodulin 3	0.9524	42
BLOC1S3	Biogenesis of lysosomal organelles complex 1 subunit 3	0.9524	42
BROX	BRO1 domain and CAAX motif containing	0.9524	42
CACUL1	CDK2 associated cullin domain 1	0.9524	42
FLI1	Fli-1 proto-oncogene, ETS transcription factor	0.9524	42
IL15RA	Interleukin 15 receptor subunit alpha	0.9524	42
ITFG1	Integrin alpha FG-GAP repeat containing 1	0.9524	42
XRCC5	X-ray repair cross complementing 5	0.9524	42
ELMO2	Engulfment and cell motility 2	0.9286	42
XAF1	XIAP associated factor 1	0.9286	28
MAP1LC3B	Microtubule associated protein 1 light chain 3 beta	0.9286	42
TIPRL	TOR signaling pathway regulator	0.9286	42

Adipocytes	33.5 nTPM
Adipose tissue	42.5 nTPM
Breast	24.6 nTPM

Alveolar cells type 1	35.3 nTPM
Lung	35.3 nTPM

Alveolar cells type 2	27.2 nTPM
Lung	27.2 nTPM

Astrocytes	39.6 nTPM
Brain	39.6 nTPM

B-cells	24.8 nTPM
Adipose tissue	46.1 nTPM
Spleen	40.6 nTPM
Stomach	38.4 nTPM
Lymph node	37.8 nTPM
Salivary gland	27.6 nTPM
Thymus	26.1 nTPM
Skin	25.4 nTPM
Bone marrow	24.1 nTPM
PBMC	20.0 nTPM
Liver	19.3 nTPM
Lung	10.7 nTPM
Esophagus	5.9 nTPM
Kidney	0.0 nTPM

Ciliated cells	26.0 nTPM
Endometrium	34.6 nTPM
Bronchus	28.8 nTPM
Lung	20.3 nTPM
Fallopian tube	20.3 nTPM

Club cells	24.8 nTPM
Bronchus	26.0 nTPM
Lung	24.4 nTPM
Prostate	24.0 nTPM

Dendritic cells	44.3 nTPM
Adipose tissue	70.6 nTPM
PBMC	18.0 nTPM

Endothelial cells	28.0 nTPM
Endometrium	55.0 nTPM
Skin	41.6 nTPM
Salivary gland	41.2 nTPM
Fallopian tube	38.3 nTPM
Thymus	36.7 nTPM
Esophagus	31.0 nTPM
Vascular	30.7 nTPM
Prostate	30.2 nTPM
Placenta	29.0 nTPM
Tongue	28.2 nTPM
Liver	25.2 nTPM
Skeletal muscle	24.3 nTPM
Lung	21.8 nTPM
Testis	16.2 nTPM
Heart muscle	15.5 nTPM
Ovary	13.6 nTPM
Pancreas	12.9 nTPM
Breast	12.3 nTPM

Enteroendocrine cells	33.0 nTPM
Small intestine	34.3 nTPM
Colon	32.7 nTPM
Rectum	31.9 nTPM

Fibroblasts	31.5 nTPM
Fallopian tube	45.5 nTPM
Liver	41.5 nTPM
Salivary gland	35.9 nTPM
Skin	35.6 nTPM
Stomach	34.6 nTPM
Vascular	34.4 nTPM
Esophagus	33.1 nTPM
Adipose tissue	32.9 nTPM
Heart muscle	31.5 nTPM
Prostate	30.4 nTPM
Skeletal muscle	30.2 nTPM
Thymus	28.6 nTPM
Lung	26.3 nTPM
Breast	23.3 nTPM
Placenta	22.1 nTPM
Pancreas	19.0 nTPM

Granulocytes	31.4 nTPM
Tongue	43.7 nTPM
Fallopian tube	36.1 nTPM
Lung	14.6 nTPM

Intestinal goblet cells	30.0 nTPM
Rectum	38.1 nTPM
Colon	29.0 nTPM
Small intestine	22.8 nTPM

Lymphatic endothelial cells	26.9 nTPM
Fallopian tube	48.3 nTPM
Ovary	5.5 nTPM

Macrophages	66.1 nTPM
Fallopian tube	149.2 nTPM
Skin	138.2 nTPM
Adipose tissue	136.7 nTPM
Spleen	106.3 nTPM
Vascular	72.4 nTPM
Skeletal muscle	67.3 nTPM
Tongue	65.8 nTPM
Endometrium	64.0 nTPM
Salivary gland	58.7 nTPM
Stomach	56.6 nTPM
Esophagus	53.9 nTPM
Bone marrow	49.7 nTPM
Thymus	45.9 nTPM
Kidney	43.4 nTPM
Prostate	43.4 nTPM
Lung	42.6 nTPM
Breast	28.1 nTPM
Testis	17.4 nTPM
Pancreas	16.4 nTPM

Basal keratinocytes	34.8 nTPM
Skin	42.3 nTPM
Tongue	27.3 nTPM

Basal prostatic cells	31.6 nTPM
Prostate	31.6 nTPM

Basal respiratory cells	18.3 nTPM
Bronchus	18.3 nTPM

Basal squamous epithelial cells	29.7 nTPM
Esophagus	29.7 nTPM

Paneth cells	27.8 nTPM
Rectum	30.4 nTPM
Small intestine	27.6 nTPM
Colon	25.3 nTPM

Plasma cells	22.1 nTPM
Salivary gland	32.7 nTPM
Stomach	31.4 nTPM
Fallopian tube	27.7 nTPM
Spleen	25.7 nTPM
Thymus	21.3 nTPM
Liver	17.0 nTPM
Bone marrow	10.6 nTPM
Esophagus	10.4 nTPM

Schwann cells	41.2 nTPM
Adipose tissue	69.9 nTPM
Vascular	41.8 nTPM
Esophagus	12.0 nTPM

Serous glandular cells	39.8 nTPM
Salivary gland	44.2 nTPM
Tongue	35.4 nTPM

Smooth muscle cells	31.8 nTPM
Endometrium	46.5 nTPM
Esophagus	39.6 nTPM
Prostate	38.9 nTPM
Salivary gland	37.1 nTPM
Fallopian tube	36.2 nTPM
Skin	35.1 nTPM
Tongue	34.1 nTPM
Adipose tissue	33.8 nTPM
Vascular	33.8 nTPM
Lung	32.9 nTPM
Thymus	32.4 nTPM
Placenta	26.5 nTPM
Skeletal muscle	24.8 nTPM
Liver	24.6 nTPM
Ovary	17.6 nTPM
Breast	14.7 nTPM

Suprabasal keratinocytes	29.3 nTPM
Skin	30.6 nTPM
Tongue	28.0 nTPM

T-cells	30.5 nTPM
Endometrium	51.1 nTPM
Adipose tissue	50.8 nTPM
Fallopian tube	43.6 nTPM
Skin	38.2 nTPM
Vascular	37.8 nTPM
Spleen	37.7 nTPM
Esophagus	36.5 nTPM
Prostate	35.9 nTPM
Tongue	34.5 nTPM
Stomach	33.5 nTPM
Lymph node	32.8 nTPM
Salivary gland	32.7 nTPM
Thymus	31.1 nTPM
Bone marrow	28.1 nTPM
Breast	27.8 nTPM
Skeletal muscle	21.2 nTPM
Lung	17.9 nTPM
Liver	16.9 nTPM
Colon	12.7 nTPM
PBMC	11.3 nTPM
Kidney	8.0 nTPM

Undifferentiated cells	22.6 nTPM
Rectum	26.9 nTPM
Small intestine	20.8 nTPM
Colon	20.1 nTPM

Amygdala excitatory	66.2 nTPM
Thalamus	71.2 nTPM
Amygdala	66.6 nTPM
Hypothalamus	65.8 nTPM
Hippocampus	65.1 nTPM
Basal ganglia	64.7 nTPM
Cerebral cortex	63.9 nTPM

Astrocyte	62.7 nTPM
Amygdala	81.0 nTPM
Hypothalamus	74.2 nTPM
Basal ganglia	69.3 nTPM
Cerebral cortex	68.6 nTPM
Hippocampus	63.9 nTPM
Thalamus	60.0 nTPM
Midbrain	57.9 nTPM
Pons	56.9 nTPM
Medulla oblongata	54.7 nTPM
Spinal cord	53.5 nTPM
Cerebellum	50.4 nTPM

Bergmann glia	84.8 nTPM
Cerebellum	92.8 nTPM
Pons	84.9 nTPM
Medulla oblongata	76.7 nTPM

Central nervous system macrophage	134.3 nTPM
Hypothalamus	158.9 nTPM
Amygdala	153.0 nTPM
Basal ganglia	139.6 nTPM
Spinal cord	137.2 nTPM
Pons	137.0 nTPM
Thalamus	130.9 nTPM
Midbrain	130.6 nTPM
Medulla oblongata	128.3 nTPM
Hippocampus	120.9 nTPM
Cerebellum	120.3 nTPM
Cerebral cortex	120.2 nTPM

Cerebellar inhibitory	67.9 nTPM
Midbrain	77.1 nTPM
Spinal cord	68.7 nTPM
Pons	66.9 nTPM
Medulla oblongata	65.9 nTPM
Cerebellum	60.8 nTPM

Cge interneuron	62.1 nTPM
Thalamus	67.8 nTPM
Amygdala	66.5 nTPM
Hypothalamus	64.7 nTPM
Midbrain	60.1 nTPM
Basal ganglia	59.3 nTPM
Hippocampus	58.9 nTPM
Cerebral cortex	57.7 nTPM

Choroid plexus epithelial cell	91.7 nTPM
Basal ganglia	112.8 nTPM
Medulla oblongata	96.8 nTPM
Hippocampus	94.3 nTPM
Thalamus	63.0 nTPM

Committed oligodendrocyte precursor	63.6 nTPM
Hypothalamus	76.5 nTPM
Thalamus	73.8 nTPM
Amygdala	72.7 nTPM
Cerebellum	68.2 nTPM
Hippocampus	66.5 nTPM
Basal ganglia	65.2 nTPM
Cerebral cortex	60.2 nTPM
Midbrain	56.3 nTPM
Pons	54.9 nTPM
Medulla oblongata	54.2 nTPM
Spinal cord	51.5 nTPM

Deep-layer corticothalamic and 6b	60.5 nTPM
Amygdala	69.6 nTPM
Hypothalamus	63.5 nTPM
Cerebral cortex	60.5 nTPM
Basal ganglia	58.7 nTPM
Hippocampus	56.6 nTPM
Midbrain	54.4 nTPM

Deep-layer intratelencephalic	63.3 nTPM
Amygdala	69.8 nTPM
Hypothalamus	68.8 nTPM
Hippocampus	60.9 nTPM
Cerebral cortex	60.6 nTPM
Basal ganglia	56.5 nTPM

Deep-layer near-projecting	56.6 nTPM
Amygdala	66.7 nTPM
Cerebral cortex	55.2 nTPM
Hypothalamus	55.2 nTPM
Hippocampus	54.3 nTPM
Basal ganglia	51.7 nTPM

Eccentric medium spiny neuron	79.8 nTPM
Thalamus	90.0 nTPM
Amygdala	83.4 nTPM
Basal ganglia	83.4 nTPM
Cerebral cortex	78.3 nTPM
Hypothalamus	73.5 nTPM
Hippocampus	70.1 nTPM