Single cell type - MITF - The Human Protein Atlas

MITF

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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.	MITF
Gene descriptionⁱ Full gene name according to HGNC.	Melanocyte inducing transcription factor
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Cancer-related genes Disease related genes Human disease related genes Transcription factors
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.	15

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.	Neurons - Neuronal signaling (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 (Melanocytes, Oligodendrocytes, Oligodendrocyte precursor cells, Cardiomyocytes)
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.	0.65
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.	Cell type enhanced (Choroid plexus epithelial cell, Oligodendrocyte)
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 (classical monocyte, myeloid DC, non-classical monocyte, basophil, intermediate monocyte)
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 (Melanocytes, Oligodendrocytes, Oligodendrocyte precursor cells, Cardiomyocytes)

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: Cell type enhanced (Choroid plexus epithelial cell, Oligodendrocyte)

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 (classical monocyte, myeloid DC, non-classical monocyte, basophil, intermediate monocyte)
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

MITF is part of cluster 8 Neurons - Neuronal signaling with confidenceⁱ 0.99
265 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.
TDRD3	Tudor domain containing 3	0.5273	58
ARMCX4	Armadillo repeat containing X-linked 4	0.5081	8
DIP2C	Disco interacting protein 2 homolog C	0.4817	69
PPP2R3A	Protein phosphatase 2 regulatory subunit B''alpha	0.4703	68
ZC3H12C	Zinc finger CCCH-type containing 12C	0.4582	47
PRNP	Prion protein	0.4535	26
TMEM132C	Transmembrane protein 132C	0.4529	76
KLHL13	Kelch like family member 13	0.4489	76
KCTD8	Potassium channel tetramerization domain containing 8	0.4388	8
TYRP1	Tyrosinase related protein 1	0.4342	26
USP13	Ubiquitin specific peptidase 13	0.4314	68
TAFA5	TAFA chemokine like family member 5	0.4282	10
ASB11	Ankyrin repeat and SOCS box containing 11	0.4268	68
S100G	S100 calcium binding protein G	0.4262	22
PLCXD3	Phosphatidylinositol specific phospholipase C X domain containing 3	0.4232	8

IMMUNE CELLS

MITF is part of cluster 38 Monocytes & Neutrophils - Degranulation with confidenceⁱ 0.99
501 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.
GPR162	G protein-coupled receptor 162	0.9762	38
RNF130	Ring finger protein 130	0.9762	38
RPN1	Ribophorin I	0.9762	38
ANKRD50	Ankyrin repeat domain containing 50	0.9762	38
MGAT1	Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase	0.9524	38
GABARAP	GABA type A receptor-associated protein	0.9524	38
NDUFB6	NADH:ubiquinone oxidoreductase subunit B6	0.9524	38
FAM151B	Family with sequence similarity 151 member B	0.9524	38
DGKZ	Diacylglycerol kinase zeta	0.9524	38
GLIPR1	GLI pathogenesis related 1	0.9524	38
MYO7A	Myosin VIIA	0.9524	38
SCARF1	Scavenger receptor class F member 1	0.9524	38
CD68	CD68 molecule	0.9524	38
CD93	CD93 molecule	0.9524	38
PLXDC2	Plexin domain containing 2	0.9524	38

Adipocytes	3.4 nTPM
Breast	3.6 nTPM
Adipose tissue	3.2 nTPM

Alveolar cells type 1	40.4 nTPM
Lung	40.4 nTPM

Alveolar cells type 2	17.4 nTPM
Lung	17.4 nTPM

Astrocytes	32.5 nTPM
Brain	32.5 nTPM

B-cells	2.0 nTPM
Skin	22.0 nTPM
Lung	1.3 nTPM
Thymus	1.1 nTPM
Adipose tissue	0.4 nTPM
Salivary gland	0.4 nTPM
Lymph node	0.1 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Ciliated cells	17.0 nTPM
Endometrium	25.4 nTPM
Lung	23.8 nTPM
Bronchus	9.4 nTPM
Fallopian tube	9.2 nTPM

Club cells	18.8 nTPM
Bronchus	24.2 nTPM
Lung	20.8 nTPM
Prostate	11.4 nTPM

Endothelial cells	5.6 nTPM
Breast	17.6 nTPM
Heart muscle	15.2 nTPM
Endometrium	9.0 nTPM
Prostate	7.2 nTPM
Ovary	6.4 nTPM
Skin	6.0 nTPM
Salivary gland	5.5 nTPM
Esophagus	5.2 nTPM
Tongue	4.9 nTPM
Vascular	4.2 nTPM
Thymus	3.9 nTPM
Liver	3.8 nTPM
Lung	3.6 nTPM
Testis	3.4 nTPM
Skeletal muscle	2.9 nTPM
Fallopian tube	2.4 nTPM
Placenta	0.0 nTPM
Pancreas	0.0 nTPM

Enteroendocrine cells	0.7 nTPM
Rectum	1.7 nTPM
Colon	0.4 nTPM
Small intestine	0.0 nTPM

Fibroblasts	39.1 nTPM
Adipose tissue	100.3 nTPM
Fallopian tube	79.4 nTPM
Skin	72.1 nTPM
Esophagus	61.5 nTPM
Prostate	61.4 nTPM
Breast	53.5 nTPM
Heart muscle	44.0 nTPM
Salivary gland	30.5 nTPM
Skeletal muscle	26.5 nTPM
Thymus	25.0 nTPM
Lung	22.5 nTPM
Stomach	20.2 nTPM
Vascular	20.2 nTPM
Pancreas	5.4 nTPM
Liver	2.4 nTPM
Placenta	0.2 nTPM

Granulocytes	113.1 nTPM
Lung	176.0 nTPM
Fallopian tube	85.7 nTPM
Tongue	77.6 nTPM

Intestinal goblet cells	0.6 nTPM
Colon	1.0 nTPM
Rectum	0.8 nTPM
Small intestine	0.0 nTPM

Lymphatic endothelial cells	18.0 nTPM
Fallopian tube	30.6 nTPM
Ovary	5.5 nTPM

Macrophages	33.3 nTPM
Lung	101.4 nTPM
Vascular	64.6 nTPM
Skin	56.8 nTPM
Thymus	52.5 nTPM
Salivary gland	44.0 nTPM
Adipose tissue	39.4 nTPM
Pancreas	32.9 nTPM
Esophagus	32.1 nTPM
Fallopian tube	29.0 nTPM
Testis	27.3 nTPM
Prostate	23.1 nTPM
Stomach	20.6 nTPM
Skeletal muscle	19.4 nTPM
Breast	17.5 nTPM
Spleen	17.0 nTPM
Tongue	16.6 nTPM
Endometrium	15.4 nTPM
Bone marrow	12.2 nTPM
Kidney	11.5 nTPM

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

Basal prostatic cells	7.0 nTPM
Prostate	7.0 nTPM

Basal respiratory cells	16.7 nTPM
Bronchus	16.7 nTPM

Bipolar cells	0.5 nTPM
Eye	0.5 nTPM

Cholangiocytes	15.3 nTPM
Liver	15.3 nTPM

Plasma cells	2.5 nTPM
Fallopian tube	9.6 nTPM
Esophagus	5.2 nTPM
Salivary gland	2.7 nTPM
Thymus	1.2 nTPM
Liver	1.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Schwann cells	5.7 nTPM
Esophagus	12.0 nTPM
Vascular	3.7 nTPM
Adipose tissue	1.6 nTPM

Serous glandular cells	3.1 nTPM
Salivary gland	6.1 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	22.3 nTPM
Placenta	44.0 nTPM
Adipose tissue	36.3 nTPM
Tongue	35.3 nTPM
Skin	28.3 nTPM
Esophagus	26.4 nTPM
Thymus	23.9 nTPM
Vascular	22.8 nTPM
Endometrium	22.6 nTPM
Prostate	22.5 nTPM
Ovary	19.6 nTPM
Breast	17.6 nTPM
Fallopian tube	15.9 nTPM
Skeletal muscle	14.8 nTPM
Salivary gland	11.1 nTPM
Lung	10.6 nTPM
Liver	4.2 nTPM

Suprabasal keratinocytes	10.7 nTPM
Skin	17.9 nTPM
Tongue	3.4 nTPM

T-cells	1.8 nTPM
Endometrium	9.6 nTPM
Vascular	5.6 nTPM
Colon	3.9 nTPM
Kidney	2.7 nTPM
Salivary gland	2.7 nTPM
Lung	2.6 nTPM
Skin	2.5 nTPM
Esophagus	2.4 nTPM
Skeletal muscle	1.5 nTPM
Prostate	1.1 nTPM
Stomach	0.6 nTPM
Breast	0.6 nTPM
Fallopian tube	0.6 nTPM
Tongue	0.2 nTPM
PBMC	0.1 nTPM
Adipose tissue	0.1 nTPM
Thymus	0.1 nTPM
Liver	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Undifferentiated cells	1.3 nTPM
Colon	2.0 nTPM
Small intestine	0.9 nTPM
Rectum	0.9 nTPM

Amygdala excitatory	25.2 nTPM
Thalamus	46.3 nTPM
Basal ganglia	26.3 nTPM
Hypothalamus	23.1 nTPM
Hippocampus	21.6 nTPM
Amygdala	20.9 nTPM
Cerebral cortex	13.4 nTPM

Astrocyte	79.7 nTPM
Basal ganglia	105.9 nTPM
Thalamus	95.3 nTPM
Midbrain	94.9 nTPM
Hypothalamus	86.8 nTPM
Amygdala	85.6 nTPM
Pons	80.9 nTPM
Cerebellum	75.4 nTPM
Hippocampus	69.7 nTPM
Cerebral cortex	66.7 nTPM
Spinal cord	59.0 nTPM
Medulla oblongata	56.0 nTPM

Bergmann glia	212.7 nTPM
Cerebellum	260.9 nTPM
Medulla oblongata	204.6 nTPM
Pons	172.6 nTPM

Central nervous system macrophage	195.8 nTPM
Amygdala	256.7 nTPM
Hypothalamus	249.5 nTPM
Hippocampus	236.1 nTPM
Spinal cord	229.6 nTPM
Basal ganglia	202.7 nTPM
Midbrain	170.6 nTPM
Thalamus	170.4 nTPM
Cerebral cortex	166.2 nTPM
Pons	165.9 nTPM
Medulla oblongata	155.0 nTPM
Cerebellum	151.4 nTPM

Cerebellar inhibitory	49.2 nTPM
Pons	57.7 nTPM
Midbrain	51.9 nTPM
Medulla oblongata	51.6 nTPM
Cerebellum	46.2 nTPM
Spinal cord	38.5 nTPM

Cge interneuron	79.3 nTPM
Hypothalamus	107.9 nTPM
Amygdala	100.0 nTPM
Cerebral cortex	79.3 nTPM
Hippocampus	74.1 nTPM
Basal ganglia	72.1 nTPM
Thalamus	61.1 nTPM
Midbrain	60.4 nTPM

Choroid plexus epithelial cell	511.7 nTPM
Medulla oblongata	662.5 nTPM
Basal ganglia	571.3 nTPM
Thalamus	433.0 nTPM
Hippocampus	379.9 nTPM

Committed oligodendrocyte precursor	197.0 nTPM
Hypothalamus	290.9 nTPM
Amygdala	240.8 nTPM
Thalamus	207.1 nTPM
Cerebral cortex	198.9 nTPM
Spinal cord	198.7 nTPM
Medulla oblongata	192.4 nTPM
Cerebellum	188.7 nTPM
Basal ganglia	186.7 nTPM
Pons	160.2 nTPM
Hippocampus	156.0 nTPM
Midbrain	147.0 nTPM

Deep-layer corticothalamic and 6b	17.0 nTPM
Midbrain	28.8 nTPM
Cerebral cortex	23.9 nTPM
Basal ganglia	21.7 nTPM
Amygdala	13.0 nTPM
Hippocampus	7.2 nTPM
Hypothalamus	7.2 nTPM

Deep-layer intratelencephalic	11.0 nTPM
Amygdala	21.3 nTPM
Hippocampus	10.9 nTPM
Basal ganglia	8.6 nTPM
Cerebral cortex	8.0 nTPM
Hypothalamus	6.0 nTPM

Deep-layer near-projecting	25.6 nTPM
Hippocampus	46.5 nTPM
Cerebral cortex	30.5 nTPM
Basal ganglia	24.0 nTPM
Amygdala	20.2 nTPM
Hypothalamus	6.8 nTPM

Eccentric medium spiny neuron	35.2 nTPM
Hippocampus	46.8 nTPM
Basal ganglia	42.6 nTPM
Thalamus	41.7 nTPM
Cerebral cortex	32.9 nTPM
Hypothalamus	24.1 nTPM
Amygdala	22.8 nTPM

Endothelial cell	20.7 nTPM
Basal ganglia	36.4 nTPM
Pons	25.6 nTPM
Midbrain	22.7 nTPM
Thalamus	20.3 nTPM
Medulla oblongata	19.5 nTPM
Cerebellum	19.4 nTPM
Hippocampus	18.6 nTPM
Spinal cord	17.3 nTPM
Cerebral cortex	16.6 nTPM
Hypothalamus	16.1 nTPM
Amygdala	15.6 nTPM