Single cell type - SGCE - The Human Protein Atlas

SGCE

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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.	SGCE
Gene descriptionⁱ Full gene name according to HGNC.	Sarcoglycan epsilon
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Human disease related genes
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.	45

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.	Fibroblasts - ECM organization (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 (Ovarian stromal 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.	0.49
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.	Group enriched (naive B-cell, memory B-cell, gdT-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 (Ovarian stromal 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: 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: Group enriched (naive B-cell, memory B-cell, gdT-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

SGCE is part of cluster 53 Fibroblasts - ECM organization with confidenceⁱ 1
305 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.
OLFML1	Olfactomedin like 1	0.6394	53
GLT8D2	Glycosyltransferase 8 domain containing 2	0.6294	53
NOVA1	NOVA alternative splicing regulator 1	0.6196	53
ITIH5	Inter-alpha-trypsin inhibitor heavy chain 5	0.6049	53
COL6A6	Collagen type VI alpha 6 chain	0.5988	53
PDGFRL	Platelet derived growth factor receptor like	0.5806	53
HTRA3	HtrA serine peptidase 3	0.5668	53
ABCA9	ATP binding cassette subfamily A member 9	0.5598	53
SSPN	Sarcospan	0.5595	53
LAMB2	Laminin subunit beta 2	0.5587	53
ANGPTL2	Angiopoietin like 2	0.5578	53
CPQ	Carboxypeptidase Q	0.5570	53
LRRN4CL	LRRN4 C-terminal like	0.5537	53
LTBP4	Latent transforming growth factor beta binding protein 4	0.5535	53
TNXB	Tenascin XB	0.5471	53

IMMUNE CELLS

SGCE is part of cluster 34 B-cells - Unknown function with confidenceⁱ 1
112 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.
CELSR1	Cadherin EGF LAG seven-pass G-type receptor 1	1.0000	34
LARGE2	LARGE xylosyl- and glucuronyltransferase 2	0.9762	34
PEG10	Paternally expressed 10	0.9762	14
L3MBTL3	L3MBTL histone methyl-lysine binding protein 3	0.9762	14
ZNF665	Zinc finger protein 665	0.9762	34
SAXO2	Stabilizer of axonemal microtubules 2	0.9762	34
PCDH9	Protocadherin 9	0.9762	34
ZBED2	Zinc finger BED-type containing 2	0.9762	14
PAWR	Pro-apoptotic WT1 regulator	0.9762	34
C19orf18	Chromosome 19 open reading frame 18	0.9762	14
CEP135	Centrosomal protein 135	0.9762	14
STRBP	Spermatid perinuclear RNA binding protein	0.9762	14
AUTS2	Activator of transcription and developmental regulator AUTS2	0.9762	14
LARGE1	LARGE xylosyl- and glucuronyltransferase 1	0.9762	34
TERF2	Telomeric repeat binding factor 2	0.9762	34

Adipocytes	31.1 nTPM
Adipose tissue	34.6 nTPM
Breast	27.7 nTPM

Alveolar cells type 1	82.2 nTPM
Lung	82.2 nTPM

Alveolar cells type 2	34.2 nTPM
Lung	34.2 nTPM

Astrocytes	63.5 nTPM
Brain	63.5 nTPM

B-cells	8.0 nTPM
Liver	24.2 nTPM
Kidney	10.4 nTPM
Adipose tissue	9.9 nTPM
PBMC	9.2 nTPM
Bone marrow	8.8 nTPM
Lymph node	7.8 nTPM
Stomach	7.6 nTPM
Skin	6.8 nTPM
Salivary gland	6.2 nTPM
Thymus	6.2 nTPM
Spleen	4.5 nTPM
Lung	2.7 nTPM
Esophagus	0.0 nTPM

Ciliated cells	13.3 nTPM
Lung	24.7 nTPM
Fallopian tube	20.5 nTPM
Bronchus	4.4 nTPM
Endometrium	3.7 nTPM

Club cells	13.3 nTPM
Lung	25.0 nTPM
Bronchus	11.7 nTPM
Prostate	3.2 nTPM

Endothelial cells	21.0 nTPM
Breast	108.1 nTPM
Liver	46.6 nTPM
Placenta	30.1 nTPM
Ovary	25.3 nTPM
Salivary gland	24.0 nTPM
Heart muscle	22.7 nTPM
Thymus	21.9 nTPM
Skeletal muscle	20.5 nTPM
Prostate	14.5 nTPM
Tongue	10.9 nTPM
Esophagus	10.2 nTPM
Lung	8.0 nTPM
Vascular	8.0 nTPM
Pancreas	7.8 nTPM
Testis	7.6 nTPM
Skin	5.2 nTPM
Fallopian tube	5.2 nTPM
Endometrium	1.6 nTPM

Enteroendocrine cells	2.8 nTPM
Rectum	8.4 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Fibroblasts	105.2 nTPM
Adipose tissue	263.8 nTPM
Breast	228.0 nTPM
Skeletal muscle	201.1 nTPM
Heart muscle	155.4 nTPM
Esophagus	110.2 nTPM
Stomach	92.2 nTPM
Placenta	79.3 nTPM
Fallopian tube	76.6 nTPM
Prostate	71.3 nTPM
Skin	69.1 nTPM
Salivary gland	68.2 nTPM
Thymus	66.6 nTPM
Liver	59.3 nTPM
Vascular	56.6 nTPM
Lung	45.8 nTPM
Pancreas	39.9 nTPM

Granulocytes	2.0 nTPM
Fallopian tube	5.6 nTPM
Lung	0.5 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	0.3 nTPM
Rectum	0.7 nTPM
Colon	0.2 nTPM
Small intestine	0.0 nTPM

Lymphatic endothelial cells	95.5 nTPM
Ovary	120.0 nTPM
Fallopian tube	70.9 nTPM

Macrophages	1.9 nTPM
Skin	7.8 nTPM
Skeletal muscle	5.6 nTPM
Thymus	3.9 nTPM
Prostate	3.2 nTPM
Esophagus	2.6 nTPM
Breast	2.3 nTPM
Fallopian tube	2.2 nTPM
Vascular	2.1 nTPM
Testis	1.2 nTPM
Endometrium	1.2 nTPM
Salivary gland	1.1 nTPM
Kidney	0.9 nTPM
Adipose tissue	0.5 nTPM
Lung	0.4 nTPM
Tongue	0.3 nTPM
Pancreas	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

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

Basal prostatic cells	31.3 nTPM
Prostate	31.3 nTPM

Basal respiratory cells	16.7 nTPM
Bronchus	16.7 nTPM

Bipolar cells	44.3 nTPM
Eye	44.3 nTPM

Collecting duct cells	23.3 nTPM
Kidney	23.3 nTPM

Plasma cells	3.6 nTPM
Fallopian tube	9.3 nTPM
Esophagus	5.2 nTPM
Salivary gland	4.9 nTPM
Thymus	3.6 nTPM
Stomach	3.4 nTPM
Bone marrow	1.5 nTPM
Spleen	0.7 nTPM
Liver	0.0 nTPM

Schwann cells	57.4 nTPM
Vascular	88.3 nTPM
Esophagus	83.9 nTPM
Adipose tissue	0.0 nTPM

Serous glandular cells	11.6 nTPM
Salivary gland	14.4 nTPM
Tongue	8.8 nTPM

Smooth muscle cells	64.8 nTPM
Placenta	107.7 nTPM
Adipose tissue	99.1 nTPM
Ovary	96.9 nTPM
Breast	94.0 nTPM
Lung	91.7 nTPM
Skeletal muscle	76.3 nTPM
Fallopian tube	70.6 nTPM
Esophagus	58.9 nTPM
Liver	55.6 nTPM
Skin	54.9 nTPM
Thymus	51.9 nTPM
Vascular	48.8 nTPM
Tongue	42.5 nTPM
Prostate	36.5 nTPM
Salivary gland	30.4 nTPM
Endometrium	21.5 nTPM

T-cells	2.4 nTPM
Skeletal muscle	7.6 nTPM
Skin	4.9 nTPM
Lung	4.2 nTPM
Prostate	4.2 nTPM
Vascular	4.0 nTPM
Liver	2.7 nTPM
Endometrium	2.4 nTPM
Esophagus	2.4 nTPM
Fallopian tube	2.2 nTPM
Spleen	2.0 nTPM
Breast	2.0 nTPM
Colon	1.9 nTPM
Salivary gland	1.9 nTPM
Kidney	1.8 nTPM
Adipose tissue	1.3 nTPM
Bone marrow	0.9 nTPM
Tongue	0.9 nTPM
Lymph node	0.7 nTPM
Thymus	0.6 nTPM
Stomach	0.5 nTPM
PBMC	0.4 nTPM

Undifferentiated cells	0.5 nTPM
Colon	1.5 nTPM
Rectum	0.1 nTPM
Small intestine	0.0 nTPM

Amygdala excitatory	134.7 nTPM
Thalamus	164.7 nTPM
Basal ganglia	150.3 nTPM
Cerebral cortex	128.2 nTPM
Amygdala	124.6 nTPM
Hypothalamus	123.4 nTPM
Hippocampus	117.1 nTPM

Astrocyte	110.3 nTPM
Hypothalamus	154.0 nTPM
Amygdala	149.8 nTPM
Basal ganglia	130.5 nTPM
Cerebral cortex	129.4 nTPM
Hippocampus	116.9 nTPM
Spinal cord	104.8 nTPM
Thalamus	101.7 nTPM
Medulla oblongata	95.3 nTPM
Pons	88.7 nTPM
Midbrain	86.1 nTPM
Cerebellum	56.5 nTPM

Bergmann glia	148.2 nTPM
Cerebellum	156.5 nTPM
Medulla oblongata	151.3 nTPM
Pons	136.7 nTPM

Central nervous system macrophage	44.1 nTPM
Hypothalamus	102.3 nTPM
Medulla oblongata	60.5 nTPM
Basal ganglia	58.5 nTPM
Thalamus	51.2 nTPM
Pons	40.7 nTPM
Spinal cord	33.0 nTPM
Amygdala	32.0 nTPM
Cerebral cortex	29.9 nTPM
Midbrain	27.4 nTPM
Cerebellum	27.2 nTPM
Hippocampus	22.3 nTPM

Cerebellar inhibitory	126.7 nTPM
Spinal cord	132.0 nTPM
Midbrain	131.3 nTPM
Pons	130.3 nTPM
Medulla oblongata	129.4 nTPM
Cerebellum	110.5 nTPM

Cge interneuron	108.7 nTPM
Amygdala	118.0 nTPM
Basal ganglia	115.8 nTPM
Thalamus	111.6 nTPM
Midbrain	109.1 nTPM
Cerebral cortex	105.4 nTPM
Hippocampus	103.0 nTPM
Hypothalamus	98.1 nTPM

Choroid plexus epithelial cell	156.2 nTPM
Basal ganglia	187.5 nTPM
Thalamus	158.9 nTPM
Medulla oblongata	139.7 nTPM
Hippocampus	138.7 nTPM

Committed oligodendrocyte precursor	132.4 nTPM
Amygdala	166.3 nTPM
Medulla oblongata	148.5 nTPM
Hypothalamus	145.4 nTPM
Basal ganglia	139.6 nTPM
Cerebral cortex	135.5 nTPM
Thalamus	135.5 nTPM
Cerebellum	134.8 nTPM
Hippocampus	122.1 nTPM
Pons	117.8 nTPM
Midbrain	108.4 nTPM
Spinal cord	103.0 nTPM

Deep-layer corticothalamic and 6b	106.8 nTPM
Midbrain	116.5 nTPM
Cerebral cortex	115.6 nTPM
Basal ganglia	115.0 nTPM
Hippocampus	104.6 nTPM
Amygdala	103.7 nTPM
Hypothalamus	85.5 nTPM

Deep-layer intratelencephalic	110.1 nTPM
Basal ganglia	113.5 nTPM
Amygdala	113.1 nTPM
Hippocampus	110.2 nTPM
Cerebral cortex	109.0 nTPM
Hypothalamus	104.5 nTPM

Deep-layer near-projecting	126.7 nTPM
Hippocampus	154.8 nTPM
Amygdala	126.2 nTPM
Basal ganglia	125.0 nTPM
Cerebral cortex	122.2 nTPM
Hypothalamus	105.5 nTPM

Eccentric medium spiny neuron	159.9 nTPM
Basal ganglia	177.0 nTPM
Cerebral cortex	165.8 nTPM
Amygdala	165.7 nTPM
Hypothalamus	160.4 nTPM
Thalamus	154.4 nTPM
Hippocampus	136.4 nTPM

Endothelial cell	31.1 nTPM
Hypothalamus	65.8 nTPM
Medulla oblongata	50.3 nTPM
Thalamus	37.8 nTPM
Cerebral cortex	28.8 nTPM
Spinal cord	25.9 nTPM
Cerebellum	24.8 nTPM
Pons	24.3 nTPM
Midbrain	23.6 nTPM
Hippocampus	23.4 nTPM
Basal ganglia	22.4 nTPM
Amygdala	14.5 nTPM

Ependymal cell	138.1 nTPM
Hypothalamus	185.6 nTPM
Thalamus	142.5 nTPM
Amygdala	137.7 nTPM
Basal ganglia	137.7 nTPM
Hippocampus	135.1 nTPM
Pons	134.0 nTPM
Midbrain	125.1 nTPM
Spinal cord	124.6 nTPM
Medulla oblongata	120.7 nTPM