Single cell type - TMEM258 - The Human Protein Atlas

TMEM258

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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.	TMEM258
Gene descriptionⁱ Full gene name according to HGNC.	Transmembrane protein 258
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Transporters
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
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	2

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.	Plasma cells - Protein processing (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.	Low cell type specificity
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.	0.23
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: Low cell type specificity

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

TMEM258 is part of cluster 77 Plasma cells - Protein processing with confidenceⁱ 1
324 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.
MYDGF	Myeloid derived growth factor	0.6429	77
PDIA6	Protein disulfide isomerase family A member 6	0.6265	77
SSR3	Signal sequence receptor subunit 3	0.6262	77
PDIA4	Protein disulfide isomerase family A member 4	0.6139	77
TMED2	Transmembrane p24 trafficking protein 2	0.6110	77
SDF2L1	Stromal cell derived factor 2 like 1	0.6028	77
SPCS2	Signal peptidase complex subunit 2	0.5836	77
LMAN1	Lectin, mannose binding 1	0.5814	77
DDOST	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase non-catalytic subunit	0.5804	77
MANF	Mesencephalic astrocyte derived neurotrophic factor	0.5789	77
SPCS3	Signal peptidase complex subunit 3	0.5766	77
ERLEC1	Endoplasmic reticulum lectin 1	0.5713	77
HSP90B1	Heat shock protein 90 beta family member 1	0.5657	77
FKBP11	FKBP prolyl isomerase 11	0.5638	77
GMPPB	GDP-mannose pyrophosphorylase B	0.5609	77

IMMUNE CELLS

TMEM258 is part of cluster 10 Non-specific - Membrane trafficking with confidenceⁱ 0.75
408 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.
ARMH1	Armadillo like helical domain containing 1	0.9762	10
ZDHHC17	Zinc finger DHHC-type palmitoyltransferase 17	0.9762	10
MPND	MPN domain containing	0.9762	10
GPATCH11	G-patch domain containing 11	0.9524	41
WDR45	WD repeat domain 45	0.9524	10
OR2C3	Olfactory receptor family 2 subfamily C member 3	0.9524	41
TCP11L1	T-complex 11 like 1	0.9524	10
ZNF608	Zinc finger protein 608	0.9524	32
ECI1	Enoyl-CoA delta isomerase 1	0.9524	10
ZNF618	Zinc finger protein 618	0.9524	41
DBI	Diazepam binding inhibitor, acyl-CoA binding protein	0.9524	41
DSN1	DSN1 component of MIS12 kinetochore complex	0.9524	41
ARHGAP18	Rho GTPase activating protein 18	0.9524	41
GAS8	Growth arrest specific 8	0.9524	10
CTCF	CCCTC-binding factor	0.9524	41

Adipocytes	214.5 nTPM
Breast	231.9 nTPM
Adipose tissue	197.1 nTPM

Alveolar cells type 1	183.0 nTPM
Lung	183.0 nTPM

Alveolar cells type 2	304.1 nTPM
Lung	304.1 nTPM

Astrocytes	6.5 nTPM
Brain	6.5 nTPM

B-cells	207.6 nTPM
Skin	553.9 nTPM
Adipose tissue	328.4 nTPM
Kidney	260.0 nTPM
Liver	251.2 nTPM
PBMC	220.1 nTPM
Spleen	164.9 nTPM
Stomach	161.6 nTPM
Thymus	157.5 nTPM
Lung	151.6 nTPM
Bone marrow	135.9 nTPM
Lymph node	113.5 nTPM
Esophagus	100.3 nTPM
Salivary gland	100.3 nTPM

Basal squamous epithelial cells	193.7 nTPM
Esophagus	193.7 nTPM

Ciliated cells	316.1 nTPM
Bronchus	428.8 nTPM
Endometrium	343.3 nTPM
Fallopian tube	301.6 nTPM
Lung	190.6 nTPM

Club cells	292.2 nTPM
Bronchus	496.3 nTPM
Prostate	193.3 nTPM
Lung	186.9 nTPM

Dendritic cells	378.1 nTPM
PBMC	438.9 nTPM
Adipose tissue	317.2 nTPM

Endothelial cells	240.8 nTPM
Pancreas	424.0 nTPM
Heart muscle	361.0 nTPM
Placenta	340.1 nTPM
Skin	320.3 nTPM
Liver	306.1 nTPM
Breast	297.9 nTPM
Ovary	287.3 nTPM
Tongue	229.6 nTPM
Testis	218.2 nTPM
Esophagus	209.9 nTPM
Lung	196.6 nTPM
Endometrium	191.9 nTPM
Fallopian tube	184.8 nTPM
Thymus	175.9 nTPM
Skeletal muscle	171.3 nTPM
Vascular	159.8 nTPM
Prostate	151.9 nTPM
Salivary gland	107.8 nTPM

Enteroendocrine cells	300.9 nTPM
Small intestine	336.4 nTPM
Rectum	288.5 nTPM
Colon	277.7 nTPM

Erythroid cells	194.3 nTPM
Bone marrow	199.8 nTPM
Liver	188.8 nTPM

Fibroblasts	335.7 nTPM
Placenta	531.2 nTPM
Heart muscle	516.9 nTPM
Skin	434.2 nTPM
Pancreas	433.1 nTPM
Adipose tissue	383.9 nTPM
Breast	380.1 nTPM
Liver	336.8 nTPM
Stomach	327.1 nTPM
Esophagus	294.4 nTPM
Fallopian tube	292.9 nTPM
Vascular	286.2 nTPM
Lung	279.1 nTPM
Thymus	271.6 nTPM
Prostate	225.7 nTPM
Skeletal muscle	218.1 nTPM
Salivary gland	159.6 nTPM

Granulocytes	192.6 nTPM
Fallopian tube	237.5 nTPM
Lung	190.1 nTPM
Tongue	150.4 nTPM

Intestinal goblet cells	488.4 nTPM
Colon	551.9 nTPM
Rectum	539.1 nTPM
Small intestine	374.1 nTPM

Bipolar cells	47.3 nTPM
Eye	47.3 nTPM

Cholangiocytes	398.7 nTPM
Liver	398.7 nTPM

Collecting duct cells	285.9 nTPM
Kidney	285.9 nTPM

Cone photoreceptor cells	64.6 nTPM
Eye	64.6 nTPM

Lymphatic endothelial cells	242.1 nTPM
Ovary	272.8 nTPM
Fallopian tube	211.5 nTPM

Macrophages	237.1 nTPM
Kidney	520.4 nTPM
Pancreas	396.7 nTPM
Testis	316.2 nTPM
Adipose tissue	286.0 nTPM
Skin	277.5 nTPM
Endometrium	243.5 nTPM
Breast	228.8 nTPM
Bone marrow	221.9 nTPM
Spleen	220.6 nTPM
Lung	216.1 nTPM
Fallopian tube	211.6 nTPM
Stomach	198.1 nTPM
Thymus	194.2 nTPM
Skeletal muscle	185.5 nTPM
Esophagus	181.1 nTPM
Tongue	172.2 nTPM
Prostate	159.3 nTPM
Vascular	141.9 nTPM
Salivary gland	134.1 nTPM

Paneth cells	346.9 nTPM
Rectum	421.1 nTPM
Small intestine	359.2 nTPM
Colon	260.5 nTPM

Plasma cells	938.0 nTPM
Liver	1353.4 nTPM
Spleen	1154.9 nTPM
Fallopian tube	1102.6 nTPM
Stomach	862.3 nTPM
Bone marrow	809.4 nTPM
Thymus	786.2 nTPM
Esophagus	738.1 nTPM
Salivary gland	697.0 nTPM

Schwann cells	294.6 nTPM
Adipose tissue	349.0 nTPM
Vascular	283.1 nTPM
Esophagus	251.6 nTPM

Serous glandular cells	311.0 nTPM
Salivary gland	396.7 nTPM
Tongue	225.4 nTPM

Smooth muscle cells	201.6 nTPM
Placenta	441.7 nTPM
Liver	363.4 nTPM
Ovary	262.1 nTPM
Skin	191.6 nTPM
Adipose tissue	188.2 nTPM
Fallopian tube	185.9 nTPM
Endometrium	183.1 nTPM
Salivary gland	175.7 nTPM
Breast	172.3 nTPM
Prostate	166.0 nTPM
Vascular	166.0 nTPM
Tongue	163.8 nTPM
Thymus	156.3 nTPM
Esophagus	152.6 nTPM
Skeletal muscle	146.1 nTPM
Lung	111.7 nTPM

Suprabasal keratinocytes	320.0 nTPM
Tongue	362.2 nTPM
Skin	277.9 nTPM

T-cells	214.8 nTPM
Kidney	409.7 nTPM
Liver	340.0 nTPM
PBMC	309.4 nTPM
Skin	308.4 nTPM
Adipose tissue	239.5 nTPM
Fallopian tube	224.3 nTPM
Thymus	216.2 nTPM
Prostate	207.9 nTPM
Spleen	207.6 nTPM
Bone marrow	204.5 nTPM
Stomach	200.9 nTPM
Breast	199.2 nTPM
Vascular	183.3 nTPM
Colon	176.5 nTPM
Lung	173.6 nTPM
Endometrium	172.2 nTPM
Lymph node	169.1 nTPM
Skeletal muscle	153.5 nTPM
Tongue	150.8 nTPM
Esophagus	148.4 nTPM
Salivary gland	116.1 nTPM

Undifferentiated cells	403.2 nTPM
Small intestine	464.9 nTPM
Rectum	431.9 nTPM
Colon	312.8 nTPM

Amygdala excitatory	13.1 nTPM
Thalamus	26.8 nTPM
Basal ganglia	12.6 nTPM
Cerebral cortex	12.5 nTPM
Hippocampus	12.3 nTPM
Amygdala	9.0 nTPM
Hypothalamus	5.5 nTPM

Astrocyte	20.8 nTPM
Medulla oblongata	26.3 nTPM
Cerebellum	25.7 nTPM
Spinal cord	24.6 nTPM
Basal ganglia	23.8 nTPM
Pons	23.6 nTPM
Hippocampus	21.9 nTPM
Midbrain	21.8 nTPM
Thalamus	19.9 nTPM
Cerebral cortex	19.4 nTPM
Amygdala	11.2 nTPM
Hypothalamus	10.2 nTPM

Bergmann glia	32.3 nTPM
Pons	40.3 nTPM
Medulla oblongata	38.4 nTPM
Cerebellum	18.4 nTPM

Central nervous system macrophage	26.1 nTPM
Spinal cord	39.2 nTPM
Medulla oblongata	37.4 nTPM
Basal ganglia	32.1 nTPM
Pons	30.3 nTPM
Midbrain	28.5 nTPM
Cerebellum	28.0 nTPM
Thalamus	25.4 nTPM
Cerebral cortex	20.7 nTPM
Hippocampus	18.4 nTPM
Hypothalamus	15.2 nTPM
Amygdala	11.4 nTPM

Cerebellar inhibitory	36.1 nTPM
Spinal cord	55.0 nTPM
Medulla oblongata	42.9 nTPM
Pons	35.2 nTPM
Midbrain	25.2 nTPM
Cerebellum	22.3 nTPM

Cge interneuron	33.5 nTPM
Thalamus	49.2 nTPM
Midbrain	45.4 nTPM
Basal ganglia	40.4 nTPM
Hippocampus	33.3 nTPM
Cerebral cortex	29.5 nTPM
Amygdala	26.7 nTPM
Hypothalamus	10.2 nTPM

Choroid plexus epithelial cell	28.3 nTPM
Hippocampus	44.4 nTPM
Medulla oblongata	36.1 nTPM
Thalamus	24.7 nTPM
Basal ganglia	8.0 nTPM

Committed oligodendrocyte precursor	54.1 nTPM
Pons	76.1 nTPM
Basal ganglia	71.2 nTPM
Medulla oblongata	71.0 nTPM
Cerebellum	69.8 nTPM
Midbrain	66.4 nTPM
Spinal cord	51.5 nTPM
Thalamus	47.1 nTPM
Hippocampus	46.0 nTPM
Amygdala	39.5 nTPM
Cerebral cortex	35.5 nTPM
Hypothalamus	21.2 nTPM

Deep-layer corticothalamic and 6b	19.2 nTPM
Midbrain	28.8 nTPM
Basal ganglia	26.5 nTPM
Hippocampus	18.5 nTPM
Cerebral cortex	18.1 nTPM
Amygdala	16.5 nTPM
Hypothalamus	6.7 nTPM

Deep-layer intratelencephalic	17.5 nTPM
Basal ganglia	26.0 nTPM
Hippocampus	20.8 nTPM
Cerebral cortex	19.7 nTPM
Amygdala	14.3 nTPM
Hypothalamus	6.6 nTPM