Single cell type - SKIC8 - The Human Protein Atlas

SKIC8

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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.	SKIC8
Gene descriptionⁱ Full gene name according to HGNC.	SKI8 subunit of superkiller complex
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 - Mixed function (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.	0.21
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

SKIC8 is part of cluster 15 Non-specific - Mixed function with confidenceⁱ 1
295 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.
PSMB5	Proteasome 20S subunit beta 5	0.6756	15
HNRNPCL1	Heterogeneous nuclear ribonucleoprotein C like 1	0.6685	15
PSMB6	Proteasome 20S subunit beta 6	0.6603	15
CUEDC2	CUE domain containing 2	0.6576	15
DOLK	Dolichol kinase	0.6557	15
GNG5B	G protein subunit gamma 5B	0.6479	15
CCT4	Chaperonin containing TCP1 subunit 4	0.6396	15
UBE2NL	Ubiquitin conjugating enzyme E2 N like (gene/pseudogene)	0.6393	15
GSTA5	Glutathione S-transferase alpha 5	0.6333	15
DCAF8L2	DDB1 and CUL4 associated factor 8 like 2	0.6314	15
ANP32D	Acidic nuclear phosphoprotein 32 family member D	0.6286	15
TXNDC9	Thioredoxin domain containing 9	0.6274	15
COPS6	COP9 signalosome subunit 6	0.6252	15
H2AC25	H2A clustered histone 25	0.6212	15
UBE2V2	Ubiquitin conjugating enzyme E2 V2	0.6180	15

IMMUNE CELLS

SKIC8 is part of cluster 13 Non-specific - Mitochondria with confidenceⁱ 0.95
458 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.
NDUFS4	NADH:ubiquinone oxidoreductase subunit S4	1.0000	13
PCCB	Propionyl-CoA carboxylase subunit beta	1.0000	13
ALG3	ALG3 alpha-1,3- mannosyltransferase	0.9762	13
ATG4B	Autophagy related 4B cysteine peptidase	0.9762	13
ACOX3	Acyl-CoA oxidase 3, pristanoyl	0.9762	13
PIGF	Phosphatidylinositol glycan anchor biosynthesis class F	0.9762	13
SRSF7	Serine and arginine rich splicing factor 7	0.9762	13
ITPA	Inosine triphosphatase	0.9762	13
SUMF2	Sulfatase modifying factor 2	0.9762	13
TMTC4	Transmembrane O-mannosyltransferase targeting cadherins 4	0.9524	13
PCBD1	Pterin-4 alpha-carbinolamine dehydratase 1	0.9524	13
DUS3L	Dihydrouridine synthase 3 like	0.9524	13
SEM1	SEM1 26S proteasome subunit	0.9524	13
RPL26L1	Ribosomal protein L26 like 1	0.9524	13
NDRG1	N-myc downstream regulated 1	0.9524	13

Adipocytes	38.6 nTPM
Adipose tissue	39.9 nTPM
Breast	37.2 nTPM

Alveolar cells type 1	36.7 nTPM
Lung	36.7 nTPM

Alveolar cells type 2	42.3 nTPM
Lung	42.3 nTPM

Astrocytes	19.5 nTPM
Brain	19.5 nTPM

B-cells	25.5 nTPM
Skin	71.1 nTPM
PBMC	33.9 nTPM
Spleen	31.0 nTPM
Lung	25.5 nTPM
Thymus	24.5 nTPM
Stomach	22.8 nTPM
Bone marrow	21.5 nTPM
Lymph node	20.5 nTPM
Adipose tissue	20.2 nTPM
Liver	19.3 nTPM
Salivary gland	19.3 nTPM
Esophagus	11.8 nTPM
Kidney	10.4 nTPM

Ciliated cells	53.8 nTPM
Fallopian tube	66.6 nTPM
Bronchus	60.4 nTPM
Lung	51.6 nTPM
Endometrium	36.6 nTPM

Club cells	52.1 nTPM
Bronchus	81.4 nTPM
Lung	40.5 nTPM
Prostate	34.3 nTPM

Dendritic cells	29.3 nTPM
PBMC	36.0 nTPM
Adipose tissue	22.7 nTPM

Endothelial cells	38.4 nTPM
Placenta	73.2 nTPM
Heart muscle	53.7 nTPM
Breast	52.7 nTPM
Skin	46.3 nTPM
Ovary	45.7 nTPM
Skeletal muscle	45.3 nTPM
Fallopian tube	41.8 nTPM
Testis	40.6 nTPM
Pancreas	38.8 nTPM
Liver	34.0 nTPM
Lung	32.9 nTPM
Tongue	32.9 nTPM
Thymus	31.7 nTPM
Endometrium	28.5 nTPM
Esophagus	28.5 nTPM
Vascular	24.9 nTPM
Prostate	21.5 nTPM
Salivary gland	19.0 nTPM

Enteroendocrine cells	40.7 nTPM
Colon	66.0 nTPM
Small intestine	34.3 nTPM
Rectum	21.8 nTPM

Fibroblasts	50.0 nTPM
Pancreas	76.8 nTPM
Heart muscle	76.1 nTPM
Skeletal muscle	61.3 nTPM
Adipose tissue	60.2 nTPM
Skin	56.9 nTPM
Lung	53.7 nTPM
Placenta	49.5 nTPM
Thymus	49.3 nTPM
Breast	48.7 nTPM
Fallopian tube	47.8 nTPM
Liver	46.3 nTPM
Esophagus	40.6 nTPM
Stomach	38.9 nTPM
Salivary gland	36.3 nTPM
Vascular	35.8 nTPM
Prostate	22.4 nTPM

Granulocytes	34.0 nTPM
Lung	43.4 nTPM
Fallopian tube	39.2 nTPM
Tongue	19.4 nTPM

Intestinal goblet cells	39.1 nTPM
Colon	48.2 nTPM
Rectum	42.0 nTPM
Small intestine	27.3 nTPM

Lymphatic endothelial cells	42.2 nTPM
Fallopian tube	46.1 nTPM
Ovary	38.2 nTPM

Macrophages	35.8 nTPM
Lung	60.6 nTPM
Pancreas	57.6 nTPM
Testis	49.6 nTPM
Kidney	45.1 nTPM
Bone marrow	41.6 nTPM
Stomach	41.2 nTPM
Adipose tissue	36.7 nTPM
Endometrium	36.3 nTPM
Tongue	34.6 nTPM
Fallopian tube	33.8 nTPM
Skeletal muscle	30.7 nTPM
Prostate	30.4 nTPM
Spleen	29.1 nTPM
Skin	29.0 nTPM
Thymus	28.2 nTPM
Breast	27.3 nTPM
Vascular	25.7 nTPM
Salivary gland	24.2 nTPM
Esophagus	18.0 nTPM

Basal keratinocytes	52.6 nTPM
Tongue	59.4 nTPM
Skin	45.8 nTPM

Basal prostatic cells	29.2 nTPM
Prostate	29.2 nTPM

Basal respiratory cells	101.7 nTPM
Bronchus	101.7 nTPM

Basal squamous epithelial cells	32.6 nTPM
Esophagus	32.6 nTPM

Paneth cells	27.1 nTPM
Rectum	42.5 nTPM
Small intestine	20.7 nTPM
Colon	18.1 nTPM

Plasma cells	43.4 nTPM
Bone marrow	60.4 nTPM
Liver	58.6 nTPM
Spleen	58.2 nTPM
Thymus	56.0 nTPM
Fallopian tube	44.7 nTPM
Stomach	41.0 nTPM
Salivary gland	23.3 nTPM
Esophagus	5.2 nTPM

Schwann cells	27.4 nTPM
Adipose tissue	44.5 nTPM
Vascular	37.6 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	40.8 nTPM
Salivary gland	41.9 nTPM
Tongue	39.8 nTPM

Smooth muscle cells	36.6 nTPM
Placenta	75.5 nTPM
Skeletal muscle	47.9 nTPM
Fallopian tube	43.0 nTPM
Ovary	41.5 nTPM
Thymus	39.9 nTPM
Esophagus	38.4 nTPM
Liver	38.2 nTPM
Skin	37.0 nTPM
Adipose tissue	35.4 nTPM
Vascular	32.3 nTPM
Endometrium	31.5 nTPM
Breast	28.6 nTPM
Tongue	27.2 nTPM
Prostate	26.2 nTPM
Lung	23.5 nTPM
Salivary gland	19.6 nTPM

Suprabasal keratinocytes	79.0 nTPM
Tongue	98.2 nTPM
Skin	59.8 nTPM

T-cells	29.2 nTPM
PBMC	46.5 nTPM
Kidney	44.3 nTPM
Colon	40.9 nTPM
Liver	39.3 nTPM
Bone marrow	33.4 nTPM
Stomach	33.2 nTPM
Fallopian tube	32.0 nTPM
Prostate	29.1 nTPM
Lymph node	28.1 nTPM
Thymus	27.7 nTPM
Skeletal muscle	27.6 nTPM
Skin	27.3 nTPM
Spleen	27.1 nTPM
Lung	26.6 nTPM
Vascular	25.7 nTPM
Tongue	25.0 nTPM
Endometrium	23.1 nTPM
Adipose tissue	21.6 nTPM
Salivary gland	21.3 nTPM
Breast	21.0 nTPM
Esophagus	12.2 nTPM

Undifferentiated cells	65.1 nTPM
Colon	79.8 nTPM
Rectum	58.0 nTPM
Small intestine	57.4 nTPM

Amygdala excitatory	56.3 nTPM
Cerebral cortex	64.5 nTPM
Hippocampus	64.4 nTPM
Thalamus	60.8 nTPM
Basal ganglia	56.3 nTPM
Amygdala	53.6 nTPM
Hypothalamus	38.5 nTPM

Astrocyte	45.6 nTPM
Cerebral cortex	50.4 nTPM
Basal ganglia	47.3 nTPM
Medulla oblongata	47.2 nTPM
Midbrain	47.2 nTPM
Hippocampus	46.4 nTPM
Pons	46.0 nTPM
Spinal cord	45.7 nTPM
Amygdala	44.8 nTPM
Thalamus	44.8 nTPM
Hypothalamus	43.0 nTPM
Cerebellum	38.6 nTPM

Bergmann glia	46.1 nTPM
Cerebellum	47.4 nTPM
Pons	46.0 nTPM
Medulla oblongata	44.8 nTPM

Central nervous system macrophage	39.9 nTPM
Hypothalamus	45.2 nTPM
Spinal cord	44.5 nTPM
Pons	42.7 nTPM
Cerebral cortex	42.5 nTPM
Midbrain	40.6 nTPM
Hippocampus	40.1 nTPM
Cerebellum	37.9 nTPM
Thalamus	37.9 nTPM
Medulla oblongata	37.7 nTPM
Amygdala	35.1 nTPM
Basal ganglia	34.8 nTPM

Cerebellar inhibitory	67.1 nTPM
Spinal cord	85.2 nTPM
Pons	64.9 nTPM
Medulla oblongata	64.4 nTPM
Cerebellum	60.7 nTPM
Midbrain	60.0 nTPM

Cge interneuron	53.7 nTPM
Hippocampus	59.3 nTPM
Cerebral cortex	58.8 nTPM
Basal ganglia	58.4 nTPM
Midbrain	54.7 nTPM
Thalamus	54.1 nTPM
Amygdala	51.7 nTPM
Hypothalamus	38.7 nTPM

Choroid plexus epithelial cell	35.9 nTPM
Hippocampus	49.9 nTPM
Medulla oblongata	37.0 nTPM
Thalamus	30.1 nTPM
Basal ganglia	26.4 nTPM

Committed oligodendrocyte precursor	41.6 nTPM
Thalamus	52.2 nTPM
Basal ganglia	47.1 nTPM
Cerebral cortex	46.9 nTPM
Hypothalamus	45.1 nTPM
Hippocampus	41.9 nTPM
Midbrain	41.2 nTPM
Spinal cord	40.5 nTPM
Pons	39.8 nTPM
Medulla oblongata	36.1 nTPM
Cerebellum	34.9 nTPM
Amygdala	31.6 nTPM

Deep-layer corticothalamic and 6b	53.2 nTPM
Basal ganglia	65.5 nTPM
Hippocampus	62.3 nTPM
Cerebral cortex	58.7 nTPM
Amygdala	54.3 nTPM
Midbrain	46.6 nTPM
Hypothalamus	31.9 nTPM

Deep-layer intratelencephalic	54.2 nTPM
Basal ganglia	64.1 nTPM
Hippocampus	59.6 nTPM
Cerebral cortex	57.5 nTPM
Amygdala	54.3 nTPM
Hypothalamus	35.5 nTPM

Deep-layer near-projecting	54.5 nTPM
Cerebral cortex	63.0 nTPM
Basal ganglia	60.5 nTPM
Hippocampus	58.2 nTPM
Amygdala	57.6 nTPM
Hypothalamus	33.0 nTPM

Eccentric medium spiny neuron	59.0 nTPM
Hippocampus	63.4 nTPM
Cerebral cortex	60.8 nTPM
Hypothalamus	59.7 nTPM
Basal ganglia	59.5 nTPM
Amygdala	56.5 nTPM
Thalamus	54.1 nTPM