Single cell type - TMEM123 - The Human Protein Atlas

TMEM123

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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.	TMEM123
Gene descriptionⁱ Full gene name according to HGNC.	Transmembrane protein 123
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.	Membrane, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	6

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 (Langerhans 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.	0.31
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 (Ependymal cell, Endothelial cell)
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 (Langerhans 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: Cell type enhanced (Ependymal cell, Endothelial cell)

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

TMEM123 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.
ST6GAL1	ST6 beta-galactoside alpha-2,6-sialyltransferase 1	0.5379	62
TNFRSF10B	TNF receptor superfamily member 10b	0.5236	29
INSIG1	Insulin induced gene 1	0.5133	28
BID	BH3 interacting domain death agonist	0.5062	14
SAT1	Spermidine/spermine N1-acetyltransferase 1	0.4890	35
KYNU	Kynureninase	0.4807	29
IRAK2	Interleukin 1 receptor associated kinase 2	0.4690	29
SAA2	Serum amyloid A2	0.4689	62
SAA1	Serum amyloid A1	0.4642	62
CXCL8	C-X-C motif chemokine ligand 8	0.4603	29
H6PD	Hexose-6-phosphate dehydrogenase/glucose 1-dehydrogenase	0.4602	75
CXCL3	C-X-C motif chemokine ligand 3	0.4592	29
CD4	CD4 molecule	0.4546	41
SLC13A5	Solute carrier family 13 member 5	0.4519	75
PABPC1	Poly(A) binding protein cytoplasmic 1	0.4455	64

IMMUNE CELLS

TMEM123 is part of cluster 11 T-cells - Unknown function with confidenceⁱ 1
119 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.
SUSD4	Sushi domain containing 4	0.9762	11
BEX5	Brain expressed X-linked 5	0.9762	11
KCNA3	Potassium voltage-gated channel subfamily A member 3	0.9762	11
RFESD	Rieske Fe-S domain containing	0.9762	11
FAM241B	Family with sequence similarity 241 member B	0.9762	11
NSG1	Neuronal vesicle trafficking associated 1	0.9762	11
ACSL6	Acyl-CoA synthetase long chain family member 6	0.9762	11
HTR6	5-hydroxytryptamine receptor 6	0.9762	11
CD8A	CD8a molecule	0.9762	11
FAM171A1	Family with sequence similarity 171 member A1	0.9762	11
MID2	Midline 2	0.9762	11
SKAP1	Src kinase associated phosphoprotein 1	0.9762	11
CCDC65	Coiled-coil domain containing 65	0.9762	11
KCNH3	Potassium voltage-gated channel subfamily H member 3	0.9762	11
BCL11B	BAF chromatin remodeling complex subunit BCL11B	0.9762	11

Adipocytes	95.5 nTPM
Adipose tissue	100.2 nTPM
Breast	90.7 nTPM

Alveolar cells type 1	93.1 nTPM
Lung	93.1 nTPM

Alveolar cells type 2	77.3 nTPM
Lung	77.3 nTPM

Astrocytes	31.3 nTPM
Brain	31.3 nTPM

B-cells	142.0 nTPM
Adipose tissue	358.8 nTPM
Lymph node	194.4 nTPM
Skin	155.8 nTPM
PBMC	150.9 nTPM
Stomach	145.1 nTPM
Salivary gland	145.0 nTPM
Liver	140.1 nTPM
Spleen	133.7 nTPM
Kidney	130.0 nTPM
Lung	91.2 nTPM
Bone marrow	71.8 nTPM
Thymus	70.3 nTPM
Esophagus	59.0 nTPM

Basal squamous epithelial cells	167.8 nTPM
Esophagus	167.8 nTPM

Ciliated cells	185.6 nTPM
Bronchus	268.0 nTPM
Lung	184.0 nTPM
Endometrium	150.8 nTPM
Fallopian tube	139.5 nTPM

Club cells	180.1 nTPM
Bronchus	210.5 nTPM
Prostate	204.8 nTPM
Lung	125.1 nTPM

Dendritic cells	129.8 nTPM
Adipose tissue	144.4 nTPM
PBMC	115.1 nTPM

Endothelial cells	157.7 nTPM
Liver	576.9 nTPM
Skin	194.4 nTPM
Breast	182.8 nTPM
Pancreas	168.0 nTPM
Lung	161.1 nTPM
Salivary gland	160.5 nTPM
Heart muscle	156.8 nTPM
Endometrium	142.2 nTPM
Fallopian tube	134.8 nTPM
Esophagus	132.6 nTPM
Placenta	116.9 nTPM
Vascular	116.1 nTPM
Skeletal muscle	113.1 nTPM
Thymus	112.3 nTPM
Tongue	107.9 nTPM
Prostate	104.2 nTPM
Testis	91.3 nTPM
Ovary	65.6 nTPM

Enteroendocrine cells	74.5 nTPM
Colon	124.0 nTPM
Rectum	78.8 nTPM
Small intestine	20.6 nTPM

Fibroblasts	97.0 nTPM
Liver	383.0 nTPM
Skin	124.5 nTPM
Placenta	124.0 nTPM
Esophagus	103.0 nTPM
Salivary gland	88.9 nTPM
Adipose tissue	84.0 nTPM
Skeletal muscle	79.2 nTPM
Heart muscle	72.6 nTPM
Fallopian tube	69.7 nTPM
Vascular	69.4 nTPM
Pancreas	67.1 nTPM
Stomach	66.3 nTPM
Breast	58.3 nTPM
Lung	54.9 nTPM
Thymus	54.3 nTPM
Prostate	52.8 nTPM

Granulocytes	77.1 nTPM
Fallopian tube	80.5 nTPM
Lung	78.2 nTPM
Tongue	72.8 nTPM

Intestinal goblet cells	134.3 nTPM
Rectum	205.1 nTPM
Colon	125.0 nTPM
Small intestine	72.8 nTPM

Lymphatic endothelial cells	168.8 nTPM
Fallopian tube	228.5 nTPM
Ovary	109.1 nTPM

Bipolar cells	1.2 nTPM
Eye	1.2 nTPM

Cholangiocytes	141.2 nTPM
Liver	141.2 nTPM

Collecting duct cells	157.5 nTPM
Kidney	157.5 nTPM

Cone photoreceptor cells	0.0 nTPM
Eye	0.0 nTPM

Macrophages	196.0 nTPM
Adipose tissue	507.6 nTPM
Fallopian tube	279.5 nTPM
Skeletal muscle	265.6 nTPM
Spleen	257.6 nTPM
Tongue	248.7 nTPM
Skin	231.8 nTPM
Esophagus	224.8 nTPM
Testis	202.7 nTPM
Endometrium	175.3 nTPM
Stomach	156.9 nTPM
Bone marrow	156.1 nTPM
Kidney	146.0 nTPM
Pancreas	141.8 nTPM
Lung	133.0 nTPM
Salivary gland	131.0 nTPM
Vascular	127.3 nTPM
Prostate	125.1 nTPM
Thymus	108.5 nTPM
Breast	105.1 nTPM

Paneth cells	65.8 nTPM
Rectum	115.3 nTPM
Colon	54.3 nTPM
Small intestine	27.6 nTPM

Plasma cells	112.4 nTPM
Stomach	175.1 nTPM
Fallopian tube	147.0 nTPM
Esophagus	129.9 nTPM
Spleen	126.8 nTPM
Salivary gland	98.0 nTPM
Liver	93.1 nTPM
Bone marrow	71.0 nTPM
Thymus	58.6 nTPM

Schwann cells	177.7 nTPM
Adipose tissue	261.9 nTPM
Vascular	151.5 nTPM
Esophagus	119.8 nTPM

Serous glandular cells	197.6 nTPM
Salivary gland	253.7 nTPM
Tongue	141.4 nTPM

Smooth muscle cells	77.2 nTPM
Liver	146.5 nTPM
Salivary gland	125.8 nTPM
Skin	105.9 nTPM
Tongue	105.1 nTPM
Fallopian tube	83.9 nTPM
Esophagus	80.5 nTPM
Skeletal muscle	78.8 nTPM
Vascular	70.6 nTPM
Adipose tissue	65.7 nTPM
Prostate	65.7 nTPM
Thymus	57.2 nTPM
Ovary	55.2 nTPM
Placenta	49.5 nTPM
Lung	49.4 nTPM
Endometrium	48.2 nTPM
Breast	48.0 nTPM

Suprabasal keratinocytes	130.8 nTPM
Skin	167.7 nTPM
Tongue	93.9 nTPM

T-cells	164.1 nTPM
PBMC	312.8 nTPM
Lymph node	281.5 nTPM
Salivary gland	270.4 nTPM
Skin	237.6 nTPM
Thymus	210.1 nTPM
Kidney	188.0 nTPM
Adipose tissue	173.8 nTPM
Spleen	169.4 nTPM
Colon	161.8 nTPM
Fallopian tube	156.7 nTPM
Skeletal muscle	147.4 nTPM
Stomach	146.4 nTPM
Bone marrow	132.4 nTPM
Tongue	130.9 nTPM
Vascular	112.2 nTPM
Endometrium	108.6 nTPM
Liver	107.5 nTPM
Breast	103.4 nTPM
Esophagus	102.2 nTPM
Lung	101.5 nTPM
Prostate	92.0 nTPM

Undifferentiated cells	144.8 nTPM
Rectum	172.8 nTPM
Colon	149.8 nTPM
Small intestine	111.9 nTPM

Amygdala excitatory	2.5 nTPM
Thalamus	4.5 nTPM
Cerebral cortex	2.8 nTPM
Amygdala	2.3 nTPM
Basal ganglia	2.2 nTPM
Hippocampus	2.0 nTPM
Hypothalamus	1.1 nTPM

Astrocyte	53.7 nTPM
Amygdala	67.5 nTPM
Thalamus	65.6 nTPM
Medulla oblongata	57.0 nTPM
Midbrain	57.0 nTPM
Hypothalamus	53.9 nTPM
Cerebral cortex	52.3 nTPM
Pons	52.3 nTPM
Hippocampus	51.4 nTPM
Spinal cord	48.3 nTPM
Basal ganglia	43.8 nTPM
Cerebellum	41.2 nTPM

Bergmann glia	26.7 nTPM
Medulla oblongata	29.8 nTPM
Cerebellum	27.4 nTPM
Pons	23.0 nTPM

Central nervous system macrophage	61.7 nTPM
Amygdala	92.2 nTPM
Hypothalamus	64.5 nTPM
Thalamus	64.5 nTPM
Hippocampus	63.5 nTPM
Midbrain	61.9 nTPM
Cerebral cortex	60.2 nTPM
Basal ganglia	58.4 nTPM
Cerebellum	57.8 nTPM
Pons	57.7 nTPM
Spinal cord	50.9 nTPM
Medulla oblongata	47.3 nTPM

Cerebellar inhibitory	1.9 nTPM
Medulla oblongata	3.3 nTPM
Pons	2.9 nTPM
Midbrain	1.9 nTPM
Cerebellum	1.7 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	10.6 nTPM
Hypothalamus	13.8 nTPM
Amygdala	12.5 nTPM
Hippocampus	12.2 nTPM
Basal ganglia	11.9 nTPM
Midbrain	9.4 nTPM
Thalamus	7.1 nTPM
Cerebral cortex	6.9 nTPM

Choroid plexus epithelial cell	76.9 nTPM
Thalamus	117.8 nTPM
Basal ganglia	73.6 nTPM
Hippocampus	69.3 nTPM
Medulla oblongata	46.9 nTPM

Committed oligodendrocyte precursor	110.3 nTPM
Amygdala	160.7 nTPM
Hypothalamus	156.4 nTPM
Spinal cord	136.1 nTPM
Thalamus	131.7 nTPM
Cerebral cortex	113.4 nTPM
Pons	103.6 nTPM
Hippocampus	96.5 nTPM
Basal ganglia	93.6 nTPM
Midbrain	89.9 nTPM
Cerebellum	87.2 nTPM
Medulla oblongata	43.9 nTPM

Deep-layer corticothalamic and 6b	2.1 nTPM
Hippocampus	3.2 nTPM
Basal ganglia	2.9 nTPM
Amygdala	2.7 nTPM
Cerebral cortex	2.2 nTPM
Midbrain	1.1 nTPM
Hypothalamus	0.7 nTPM

Deep-layer intratelencephalic	2.3 nTPM
Basal ganglia	3.1 nTPM
Hippocampus	2.7 nTPM
Amygdala	2.6 nTPM
Cerebral cortex	2.1 nTPM
Hypothalamus	1.0 nTPM

Deep-layer near-projecting	3.1 nTPM
Hippocampus	5.5 nTPM
Amygdala	4.8 nTPM
Basal ganglia	2.2 nTPM
Cerebral cortex	2.0 nTPM
Hypothalamus	1.1 nTPM