Single cell type - ERCC6 - The Human Protein Atlas

ERCC6

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Pathway

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.	ERCC6
Gene descriptionⁱ Full gene name according to HGNC.	ERCC excision repair 6, chromatin remodeling factor
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Cancer-related genes Disease related genes Human disease related genes Plasma proteins
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.	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.	Non-specific - Transcription (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.	0.29
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

ERCC6 is part of cluster 55 Non-specific - Transcription with confidenceⁱ 1
709 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.
ENSG00000286185	Novel protein, identical to neuroblastoma breakpoint family, member 19 NBPF19	0.5484	29
ZC3H7A	Zinc finger CCCH-type containing 7A	0.5381	55
MIA3	MIA SH3 domain ER export factor 3	0.5377	55
GOLGB1	Golgin B1	0.5318	55
MTX3	Metaxin 3	0.5047	66
GOLGA3	Golgin A3	0.4884	77
ROCK1	Rho associated coiled-coil containing protein kinase 1	0.4824	32
TRIP11	Thyroid hormone receptor interactor 11	0.4805	55
DYNC1H1	Dynein cytoplasmic 1 heavy chain 1	0.4782	55
RPAP2	RNA polymerase II associated protein 2	0.4717	55
ASH1L	ASH1 like histone lysine methyltransferase	0.4645	55
VIRMA	Vir like m6A methyltransferase associated	0.4613	55
BOD1L1	Biorientation of chromosomes in cell division 1 like 1	0.4525	55
ZNF510	Zinc finger protein 510	0.4416	55
ZNF605	Zinc finger protein 605	0.4393	55

IMMUNE CELLS

ERCC6 is part of cluster 7 Non-specific - Innate immune response with confidenceⁱ 0.99
237 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.
UBE2M	Ubiquitin conjugating enzyme E2 M	0.9762	7
ARF3	ADP ribosylation factor 3	0.9762	7
HOOK3	Hook microtubule tethering protein 3	0.9524	7
CPSF7	Cleavage and polyadenylation specific factor 7	0.9524	7
PIP5K1A	Phosphatidylinositol-4-phosphate 5-kinase type 1 alpha	0.9524	7
SETD1B	SET domain containing 1B, histone lysine methyltransferase	0.9524	7
ENSG00000272980	Novel protein	0.9286	7
GTPBP2	GTP binding protein 2	0.9286	7
TRAPPC8	Trafficking protein particle complex subunit 8	0.9286	7
ATG10	Autophagy related 10	0.9286	7
TIRAP	TIR domain containing adaptor protein	0.9286	7
MAP1S	Microtubule associated protein 1S	0.9286	7
PHF20L1	PHD finger protein 20 like 1	0.9286	7
PYCARD	PYD and CARD domain containing	0.9286	7
EXTL3	Exostosin like glycosyltransferase 3	0.9286	7

Adipocytes	9.3 nTPM
Breast	9.5 nTPM
Adipose tissue	9.1 nTPM

Alveolar cells type 1	12.1 nTPM
Lung	12.1 nTPM

Alveolar cells type 2	11.7 nTPM
Lung	11.7 nTPM

Astrocytes	13.9 nTPM
Brain	13.9 nTPM

B-cells	12.6 nTPM
Salivary gland	30.5 nTPM
Thymus	17.4 nTPM
Stomach	17.3 nTPM
PBMC	16.9 nTPM
Adipose tissue	16.9 nTPM
Lung	12.1 nTPM
Esophagus	11.8 nTPM
Lymph node	11.4 nTPM
Spleen	11.0 nTPM
Kidney	10.4 nTPM
Bone marrow	8.3 nTPM
Liver	0.0 nTPM
Skin	0.0 nTPM

Ciliated cells	10.1 nTPM
Endometrium	11.1 nTPM
Fallopian tube	10.3 nTPM
Lung	9.9 nTPM
Bronchus	9.1 nTPM

Club cells	13.0 nTPM
Prostate	19.2 nTPM
Lung	10.6 nTPM
Bronchus	9.3 nTPM

Endothelial cells	10.2 nTPM
Heart muscle	27.5 nTPM
Salivary gland	17.6 nTPM
Vascular	14.4 nTPM
Prostate	12.5 nTPM
Tongue	11.9 nTPM
Breast	11.4 nTPM
Ovary	10.7 nTPM
Endometrium	9.5 nTPM
Esophagus	9.5 nTPM
Skeletal muscle	9.3 nTPM
Thymus	9.2 nTPM
Liver	8.8 nTPM
Testis	7.0 nTPM
Fallopian tube	6.4 nTPM
Lung	5.4 nTPM
Skin	5.3 nTPM
Placenta	5.1 nTPM
Pancreas	2.6 nTPM

Enteroendocrine cells	11.0 nTPM
Small intestine	20.6 nTPM
Colon	7.3 nTPM
Rectum	5.0 nTPM

Fibroblasts	11.7 nTPM
Vascular	22.3 nTPM
Heart muscle	19.2 nTPM
Salivary gland	18.5 nTPM
Prostate	17.8 nTPM
Adipose tissue	13.7 nTPM
Breast	13.0 nTPM
Skeletal muscle	11.6 nTPM
Esophagus	11.6 nTPM
Thymus	10.7 nTPM
Placenta	9.4 nTPM
Skin	8.6 nTPM
Liver	8.3 nTPM
Fallopian tube	8.3 nTPM
Lung	6.7 nTPM
Pancreas	5.2 nTPM
Stomach	2.9 nTPM

Granulocytes	11.8 nTPM
Fallopian tube	16.9 nTPM
Lung	13.6 nTPM
Tongue	4.9 nTPM

Intestinal goblet cells	7.9 nTPM
Rectum	8.6 nTPM
Small intestine	8.1 nTPM
Colon	7.1 nTPM

Lymphatic endothelial cells	12.1 nTPM
Fallopian tube	13.4 nTPM
Ovary	10.9 nTPM

Macrophages	14.6 nTPM
Adipose tissue	37.4 nTPM
Salivary gland	25.0 nTPM
Tongue	23.8 nTPM
Prostate	23.6 nTPM
Fallopian tube	22.2 nTPM
Endometrium	19.1 nTPM
Bone marrow	17.2 nTPM
Testis	14.9 nTPM
Breast	13.4 nTPM
Vascular	12.2 nTPM
Spleen	12.0 nTPM
Skeletal muscle	11.8 nTPM
Thymus	9.9 nTPM
Esophagus	9.0 nTPM
Lung	8.0 nTPM
Skin	5.6 nTPM
Stomach	5.1 nTPM
Pancreas	4.1 nTPM
Kidney	2.7 nTPM

Paneth cells	4.7 nTPM
Rectum	7.0 nTPM
Small intestine	6.9 nTPM
Colon	0.0 nTPM

Basal prostatic cells	16.0 nTPM
Prostate	16.0 nTPM

Bipolar cells	23.0 nTPM
Eye	23.0 nTPM

Collecting duct cells	15.6 nTPM
Kidney	15.6 nTPM

Cone photoreceptor cells	27.2 nTPM
Eye	27.2 nTPM

Plasma cells	8.9 nTPM
Salivary gland	19.7 nTPM
Stomach	13.0 nTPM
Fallopian tube	12.5 nTPM
Esophagus	10.4 nTPM
Thymus	6.5 nTPM
Spleen	4.6 nTPM
Liver	3.0 nTPM
Bone marrow	1.5 nTPM

Schwann cells	11.6 nTPM
Vascular	19.3 nTPM
Adipose tissue	15.6 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	13.1 nTPM
Salivary gland	21.8 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	10.4 nTPM
Vascular	25.9 nTPM
Placenta	15.8 nTPM
Liver	12.7 nTPM
Adipose tissue	12.5 nTPM
Endometrium	12.3 nTPM
Salivary gland	11.7 nTPM
Tongue	10.8 nTPM
Ovary	10.5 nTPM
Prostate	9.7 nTPM
Esophagus	9.6 nTPM
Skeletal muscle	8.6 nTPM
Thymus	8.1 nTPM
Breast	8.0 nTPM
Fallopian tube	6.0 nTPM
Skin	3.5 nTPM
Lung	1.2 nTPM

Suprabasal keratinocytes	11.9 nTPM
Tongue	16.4 nTPM
Skin	7.4 nTPM

T-cells	14.6 nTPM
Salivary gland	27.6 nTPM
Fallopian tube	22.2 nTPM
Prostate	20.0 nTPM
Vascular	18.5 nTPM
Adipose tissue	17.6 nTPM
Tongue	17.2 nTPM
Thymus	17.0 nTPM
Endometrium	15.2 nTPM
Lung	15.0 nTPM
Skeletal muscle	14.7 nTPM
Stomach	14.7 nTPM
Bone marrow	13.8 nTPM
Breast	13.4 nTPM
Esophagus	12.2 nTPM
Lymph node	12.2 nTPM
PBMC	11.4 nTPM
Liver	11.0 nTPM
Colon	10.7 nTPM
Kidney	8.0 nTPM
Spleen	7.8 nTPM
Skin	6.3 nTPM

Undifferentiated cells	6.0 nTPM
Small intestine	7.1 nTPM
Rectum	5.9 nTPM
Colon	4.9 nTPM

Amygdala excitatory	44.8 nTPM
Amygdala	52.0 nTPM
Hypothalamus	51.9 nTPM
Hippocampus	45.7 nTPM
Cerebral cortex	42.2 nTPM
Thalamus	40.8 nTPM
Basal ganglia	36.2 nTPM

Astrocyte	59.0 nTPM
Cerebellum	85.7 nTPM
Amygdala	73.9 nTPM
Thalamus	72.1 nTPM
Midbrain	67.5 nTPM
Pons	61.7 nTPM
Basal ganglia	58.4 nTPM
Medulla oblongata	51.1 nTPM
Hippocampus	48.2 nTPM
Hypothalamus	46.8 nTPM
Cerebral cortex	45.3 nTPM
Spinal cord	38.4 nTPM

Bergmann glia	37.3 nTPM
Cerebellum	44.0 nTPM
Medulla oblongata	36.2 nTPM
Pons	31.6 nTPM

Central nervous system macrophage	87.6 nTPM
Amygdala	108.6 nTPM
Cerebellum	100.3 nTPM
Midbrain	99.7 nTPM
Hypothalamus	97.0 nTPM
Pons	90.7 nTPM
Basal ganglia	84.3 nTPM
Thalamus	81.6 nTPM
Spinal cord	81.0 nTPM
Medulla oblongata	76.3 nTPM
Hippocampus	75.6 nTPM
Cerebral cortex	68.6 nTPM

Cerebellar inhibitory	82.5 nTPM
Spinal cord	90.7 nTPM
Cerebellum	89.0 nTPM
Medulla oblongata	87.6 nTPM
Midbrain	82.7 nTPM
Pons	62.4 nTPM

Cge interneuron	38.5 nTPM
Hypothalamus	46.1 nTPM
Amygdala	42.1 nTPM
Thalamus	38.6 nTPM
Midbrain	38.1 nTPM
Hippocampus	35.1 nTPM
Basal ganglia	35.0 nTPM
Cerebral cortex	34.6 nTPM

Choroid plexus epithelial cell	123.4 nTPM
Basal ganglia	203.4 nTPM
Medulla oblongata	113.8 nTPM
Thalamus	93.2 nTPM
Hippocampus	83.2 nTPM

Committed oligodendrocyte precursor	36.0 nTPM
Medulla oblongata	50.3 nTPM
Basal ganglia	46.0 nTPM
Thalamus	45.0 nTPM
Spinal cord	40.5 nTPM
Amygdala	39.5 nTPM
Midbrain	37.8 nTPM
Cerebellum	31.7 nTPM
Hypothalamus	30.7 nTPM
Hippocampus	30.5 nTPM
Cerebral cortex	24.1 nTPM
Pons	20.4 nTPM

Deep-layer corticothalamic and 6b	42.7 nTPM
Hypothalamus	50.2 nTPM
Cerebral cortex	45.8 nTPM
Amygdala	44.8 nTPM
Hippocampus	44.4 nTPM
Basal ganglia	35.5 nTPM
Midbrain	35.5 nTPM

Deep-layer intratelencephalic	44.5 nTPM
Hypothalamus	51.8 nTPM
Amygdala	47.4 nTPM
Hippocampus	44.0 nTPM
Cerebral cortex	41.1 nTPM
Basal ganglia	37.9 nTPM

Deep-layer near-projecting	37.2 nTPM
Hypothalamus	52.7 nTPM
Basal ganglia	34.5 nTPM
Amygdala	34.4 nTPM
Cerebral cortex	34.2 nTPM
Hippocampus	30.2 nTPM

Eccentric medium spiny neuron	42.3 nTPM
Thalamus	44.8 nTPM
Amygdala	44.1 nTPM
Hippocampus	43.9 nTPM
Hypothalamus	42.0 nTPM
Basal ganglia	39.4 nTPM
Cerebral cortex	39.4 nTPM

Endothelial cell	32.8 nTPM
Pons	41.2 nTPM
Hypothalamus	38.5 nTPM
Basal ganglia	37.3 nTPM
Cerebellum	34.8 nTPM
Hippocampus	34.0 nTPM
Midbrain	31.2 nTPM
Thalamus	31.1 nTPM
Spinal cord	29.3 nTPM
Amygdala	29.1 nTPM
Medulla oblongata	27.7 nTPM
Cerebral cortex	26.2 nTPM