Single cell type - CMC1 - The Human Protein Atlas

CMC1

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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.	CMC1
Gene descriptionⁱ Full gene name according to HGNC.	C-X9-C motif containing 1
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.	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.	NK-cells - Adaptive 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 (NK-cells, Early spermatids, 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.	0.42
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.	Immune cell enhanced (NK-cell)
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 (NK-cells, Early spermatids, 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: 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: Immune cell enhanced (NK-cell)
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

CMC1 is part of cluster 19 NK-cells - Adaptive immune response with confidenceⁱ 1
266 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.
KLRF1	Killer cell lectin like receptor F1	0.9310	19
NKG7	Natural killer cell granule protein 7	0.9267	19
FGFBP2	Fibroblast growth factor binding protein 2	0.9208	19
GNLY	Granulysin	0.9144	19
LIM2	Lens intrinsic membrane protein 2	0.9091	19
KLRD1	Killer cell lectin like receptor D1	0.9051	19
KIR2DL3	Killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3	0.9046	19
GZMH	Granzyme H	0.9046	19
EOMES	Eomesodermin	0.9040	19
NCR1	Natural cytotoxicity triggering receptor 1	0.9019	19
FCRL6	Fc receptor like 6	0.8961	19
PRF1	Perforin 1	0.8929	19
S1PR5	Sphingosine-1-phosphate receptor 5	0.8918	19
SH2D1B	SH2 domain containing 1B	0.8898	19
KIR2DL1	Killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1	0.8881	19

IMMUNE CELLS

CMC1 is part of cluster 15 NK-cells - Unknown function with confidenceⁱ 0.97
158 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.
PCNX4	Pecanex 4	1.0000	15
IL18R1	Interleukin 18 receptor 1	1.0000	15
HOXA10	Homeobox A10	0.9762	15
FUT11	Fucosyltransferase 11	0.9762	15
JAKMIP2	Janus kinase and microtubule interacting protein 2	0.9762	15
CLSTN3	Calsyntenin 3	0.9762	15
IL12RB2	Interleukin 12 receptor subunit beta 2	0.9762	15
GPR68	G protein-coupled receptor 68	0.9762	15
ABCG2	ATP binding cassette subfamily G member 2 (Junior blood group)	0.9762	15
NCALD	Neurocalcin delta	0.9524	15
NKG7	Natural killer cell granule protein 7	0.9524	15
COPZ2	COPI coat complex subunit zeta 2	0.9524	15
STMN2	Stathmin 2	0.9524	15
IL2RB	Interleukin 2 receptor subunit beta	0.9524	15
CLASP1	Cytoplasmic linker associated protein 1	0.9524	15

Adipocytes	47.0 nTPM
Breast	49.0 nTPM
Adipose tissue	45.1 nTPM

Alveolar cells type 1	35.2 nTPM
Lung	35.2 nTPM

Alveolar cells type 2	47.1 nTPM
Lung	47.1 nTPM

Astrocytes	25.1 nTPM
Brain	25.1 nTPM

B-cells	24.3 nTPM
Liver	38.6 nTPM
Lung	37.6 nTPM
Adipose tissue	34.2 nTPM
PBMC	32.3 nTPM
Bone marrow	29.0 nTPM
Skin	28.8 nTPM
Kidney	26.0 nTPM
Thymus	24.2 nTPM
Salivary gland	21.3 nTPM
Spleen	16.7 nTPM
Stomach	13.9 nTPM
Lymph node	12.9 nTPM
Esophagus	0.0 nTPM

Ciliated cells	50.8 nTPM
Endometrium	63.2 nTPM
Fallopian tube	48.7 nTPM
Lung	46.7 nTPM
Bronchus	44.4 nTPM

Club cells	41.6 nTPM
Bronchus	48.7 nTPM
Lung	39.9 nTPM
Prostate	36.2 nTPM

Dendritic cells	38.3 nTPM
PBMC	61.2 nTPM
Adipose tissue	15.4 nTPM

Endothelial cells	41.9 nTPM
Liver	73.1 nTPM
Heart muscle	69.1 nTPM
Pancreas	64.6 nTPM
Breast	51.0 nTPM
Placenta	48.8 nTPM
Lung	42.3 nTPM
Skeletal muscle	40.6 nTPM
Testis	39.1 nTPM
Tongue	37.3 nTPM
Thymus	37.1 nTPM
Ovary	37.0 nTPM
Endometrium	36.9 nTPM
Prostate	35.0 nTPM
Fallopian tube	34.7 nTPM
Vascular	27.9 nTPM
Skin	27.7 nTPM
Salivary gland	26.5 nTPM
Esophagus	25.0 nTPM

Enteroendocrine cells	48.9 nTPM
Colon	92.7 nTPM
Rectum	33.5 nTPM
Small intestine	20.6 nTPM

Erythroid cells	135.3 nTPM
Liver	237.7 nTPM
Bone marrow	32.9 nTPM

Fibroblasts	42.1 nTPM
Heart muscle	121.6 nTPM
Pancreas	59.9 nTPM
Adipose tissue	43.5 nTPM
Prostate	42.2 nTPM
Liver	41.5 nTPM
Lung	40.9 nTPM
Thymus	38.7 nTPM
Placenta	38.3 nTPM
Breast	38.1 nTPM
Fallopian tube	37.6 nTPM
Skeletal muscle	37.2 nTPM
Vascular	32.4 nTPM
Salivary gland	28.1 nTPM
Esophagus	27.6 nTPM
Stomach	23.1 nTPM
Skin	22.2 nTPM

Granulocytes	29.6 nTPM
Lung	47.9 nTPM
Fallopian tube	31.3 nTPM
Tongue	9.7 nTPM

Intestinal goblet cells	67.9 nTPM
Colon	86.6 nTPM
Rectum	81.9 nTPM
Small intestine	35.3 nTPM

Lymphatic endothelial cells	34.3 nTPM
Fallopian tube	46.7 nTPM
Ovary	21.8 nTPM

Basal keratinocytes	29.4 nTPM
Tongue	40.3 nTPM
Skin	18.4 nTPM

Basal prostatic cells	40.1 nTPM
Prostate	40.1 nTPM

Basal respiratory cells	66.1 nTPM
Bronchus	66.1 nTPM

Basal squamous epithelial cells	19.5 nTPM
Esophagus	19.5 nTPM

Macrophages	38.4 nTPM
Lung	101.9 nTPM
Pancreas	67.8 nTPM
Testis	56.4 nTPM
Endometrium	47.4 nTPM
Breast	46.4 nTPM
Kidney	46.0 nTPM
Vascular	42.5 nTPM
Thymus	40.4 nTPM
Prostate	40.0 nTPM
Adipose tissue	35.3 nTPM
Skeletal muscle	28.5 nTPM
Salivary gland	26.9 nTPM
Fallopian tube	26.9 nTPM
Bone marrow	26.4 nTPM
Tongue	25.5 nTPM
Esophagus	21.8 nTPM
Skin	18.9 nTPM
Spleen	17.0 nTPM
Stomach	12.9 nTPM

Paneth cells	68.4 nTPM
Rectum	88.6 nTPM
Small intestine	58.7 nTPM
Colon	57.9 nTPM

Plasma cells	38.5 nTPM
Liver	92.1 nTPM
Thymus	43.8 nTPM
Fallopian tube	38.6 nTPM
Salivary gland	31.3 nTPM
Bone marrow	30.2 nTPM
Spleen	30.1 nTPM
Stomach	21.4 nTPM
Esophagus	20.8 nTPM

Schwann cells	18.8 nTPM
Adipose tissue	35.9 nTPM
Vascular	20.4 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	30.5 nTPM
Tongue	30.9 nTPM
Salivary gland	30.0 nTPM

Smooth muscle cells	36.5 nTPM
Liver	59.0 nTPM
Ovary	50.2 nTPM
Thymus	43.8 nTPM
Placenta	41.7 nTPM
Prostate	40.7 nTPM
Breast	40.4 nTPM
Skeletal muscle	39.3 nTPM
Fallopian tube	38.9 nTPM
Adipose tissue	37.0 nTPM
Vascular	35.0 nTPM
Esophagus	31.2 nTPM
Tongue	30.2 nTPM
Endometrium	28.4 nTPM
Salivary gland	24.5 nTPM
Lung	23.5 nTPM
Skin	20.6 nTPM

Suprabasal keratinocytes	37.6 nTPM
Tongue	44.8 nTPM
Skin	30.3 nTPM

T-cells	166.5 nTPM
Liver	1216.2 nTPM
Skeletal muscle	226.8 nTPM
PBMC	215.2 nTPM
Spleen	187.7 nTPM
Lung	181.6 nTPM
Adipose tissue	180.5 nTPM
Endometrium	159.1 nTPM
Kidney	149.9 nTPM
Bone marrow	146.9 nTPM
Breast	137.1 nTPM
Prostate	103.4 nTPM
Fallopian tube	99.5 nTPM
Salivary gland	73.5 nTPM
Vascular	72.4 nTPM
Skin	67.3 nTPM
Colon	64.3 nTPM
Thymus	59.5 nTPM
Lymph node	45.9 nTPM
Tongue	39.8 nTPM
Esophagus	38.9 nTPM
Stomach	31.4 nTPM

Undifferentiated cells	74.4 nTPM
Colon	89.8 nTPM
Rectum	81.7 nTPM
Small intestine	51.8 nTPM

Amygdala excitatory	59.3 nTPM
Thalamus	77.6 nTPM
Amygdala	60.9 nTPM
Basal ganglia	58.8 nTPM
Hypothalamus	54.8 nTPM
Cerebral cortex	52.1 nTPM
Hippocampus	51.6 nTPM

Astrocyte	59.5 nTPM
Amygdala	92.7 nTPM
Cerebral cortex	72.2 nTPM
Hypothalamus	70.5 nTPM
Hippocampus	67.9 nTPM
Basal ganglia	67.1 nTPM
Thalamus	55.3 nTPM
Medulla oblongata	52.0 nTPM
Midbrain	51.2 nTPM
Pons	45.6 nTPM
Cerebellum	40.5 nTPM
Spinal cord	39.6 nTPM

Bergmann glia	74.0 nTPM
Medulla oblongata	81.0 nTPM
Cerebellum	76.4 nTPM
Pons	64.7 nTPM

Central nervous system macrophage	129.8 nTPM
Amygdala	186.3 nTPM
Hypothalamus	146.0 nTPM
Basal ganglia	136.0 nTPM
Thalamus	132.6 nTPM
Hippocampus	127.7 nTPM
Pons	127.2 nTPM
Midbrain	125.2 nTPM
Medulla oblongata	118.3 nTPM
Cerebellum	113.2 nTPM
Cerebral cortex	112.2 nTPM
Spinal cord	103.3 nTPM

Cerebellar inhibitory	87.5 nTPM
Spinal cord	110.0 nTPM
Medulla oblongata	84.5 nTPM
Midbrain	83.4 nTPM
Cerebellum	82.2 nTPM
Pons	77.5 nTPM

Cge interneuron	60.2 nTPM
Amygdala	68.5 nTPM
Thalamus	65.2 nTPM
Hypothalamus	61.5 nTPM
Hippocampus	58.0 nTPM
Basal ganglia	57.0 nTPM
Cerebral cortex	56.1 nTPM
Midbrain	55.2 nTPM

Choroid plexus epithelial cell	124.0 nTPM
Basal ganglia	192.3 nTPM
Medulla oblongata	121.7 nTPM
Thalamus	93.2 nTPM
Hippocampus	88.7 nTPM

Committed oligodendrocyte precursor	67.1 nTPM
Thalamus	82.6 nTPM
Amygdala	77.8 nTPM
Spinal cord	77.3 nTPM
Hypothalamus	73.7 nTPM
Basal ganglia	69.5 nTPM
Medulla oblongata	64.5 nTPM
Cerebral cortex	61.4 nTPM
Hippocampus	59.2 nTPM
Pons	58.4 nTPM
Midbrain	58.0 nTPM
Cerebellum	55.5 nTPM

Deep-layer corticothalamic and 6b	89.6 nTPM
Amygdala	116.3 nTPM
Hypothalamus	90.4 nTPM
Basal ganglia	85.4 nTPM
Hippocampus	85.3 nTPM
Cerebral cortex	81.5 nTPM
Midbrain	78.8 nTPM

Deep-layer intratelencephalic	66.1 nTPM
Hypothalamus	69.8 nTPM
Cerebral cortex	67.4 nTPM
Amygdala	66.8 nTPM
Hippocampus	65.3 nTPM
Basal ganglia	61.2 nTPM

Deep-layer near-projecting	108.5 nTPM
Amygdala	128.1 nTPM
Hypothalamus	119.6 nTPM
Hippocampus	98.9 nTPM
Basal ganglia	97.9 nTPM
Cerebral cortex	97.8 nTPM