Single cell type - SCD - The Human Protein Atlas

SCD

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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.	SCD
Gene descriptionⁱ Full gene name according to HGNC.	Stearoyl-CoA desaturase
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Enzymes Metabolic 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.	Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	1

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.	Hepatocytes - Metabolism (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.	Group enriched (Hepatocytes, Kupffer cells, Alveolar cells type 2, Oligodendrocytes)
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.	0.58
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.	Group enriched (Oligodendrocyte, Committed oligodendrocyte precursor)
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: Group enriched (Hepatocytes, Kupffer cells, Alveolar cells type 2, Oligodendrocytes)

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: Group enriched (Oligodendrocyte, Committed oligodendrocyte precursor)

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

SCD is part of cluster 62 Hepatocytes - Metabolism with confidenceⁱ 1
159 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.
ITIH3	Inter-alpha-trypsin inhibitor heavy chain 3	0.9186	62
PCSK9	Proprotein convertase subtilisin/kexin type 9	0.8953	62
UROC1	Urocanate hydratase 1	0.8896	62
CFHR4	Complement factor H related 4	0.8867	62
SERPINF2	Serpin family F member 2	0.8863	62
DHCR24	24-dehydrocholesterol reductase	0.8837	62
CRP	C-reactive protein	0.8830	62
F9	Coagulation factor IX	0.8750	62
LSS	Lanosterol synthase	0.8740	62
ANGPTL8	Angiopoietin like 8	0.8732	62
AGT	Angiotensinogen	0.8657	62
FGG	Fibrinogen gamma chain	0.8626	62
SPRN	Shadow of prion protein	0.8617	62
CP	Ceruloplasmin	0.8540	62
LBP	Lipopolysaccharide binding protein	0.8525	62

IMMUNE CELLS

SCD is part of cluster 30 Non-specific - DNA binding with confidenceⁱ 1
263 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.
ZNF491	Zinc finger protein 491	1.0000	30
ZFP41	ZFP41 zinc finger protein	0.9762	30
ANKRD17	Ankyrin repeat domain 17	0.9762	30
LSM2	LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated	0.9524	30
CDKL3	Cyclin dependent kinase like 3	0.9524	30
IPO4	Importin 4	0.9524	30
SLC4A5	Solute carrier family 4 member 5	0.9524	30
TRIM61	Tripartite motif containing 61	0.9524	30
ZNF135	Zinc finger protein 135	0.9524	30
CCDC102B	Coiled-coil domain containing 102B	0.9524	30
GCSH	Glycine cleavage system protein H	0.9524	30
KRI1	KRI1 homolog	0.9524	30
TENT4A	Terminal nucleotidyltransferase 4A	0.9524	30
MAGOHB	Mago homolog B, exon junction complex subunit	0.9524	30
MROH8	Maestro heat like repeat family member 8	0.9524	30

Adipocytes	3.0 nTPM
Breast	4.4 nTPM
Adipose tissue	1.6 nTPM

Alveolar cells type 1	65.0 nTPM
Lung	65.0 nTPM

Alveolar cells type 2	499.0 nTPM
Lung	499.0 nTPM

Astrocytes	32.2 nTPM
Brain	32.2 nTPM

B-cells	5.0 nTPM
Liver	33.8 nTPM
Lung	8.0 nTPM
Esophagus	5.9 nTPM
Salivary gland	4.3 nTPM
Skin	3.4 nTPM
Adipose tissue	2.9 nTPM
Thymus	2.4 nTPM
Spleen	1.9 nTPM
Lymph node	1.2 nTPM
Stomach	0.4 nTPM
Bone marrow	0.2 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM

Ciliated cells	22.9 nTPM
Bronchus	48.3 nTPM
Lung	26.7 nTPM
Endometrium	12.9 nTPM
Fallopian tube	3.6 nTPM

Club cells	70.2 nTPM
Lung	102.1 nTPM
Bronchus	98.3 nTPM
Prostate	10.2 nTPM

Endothelial cells	81.4 nTPM
Liver	1271.0 nTPM
Placenta	59.6 nTPM
Tongue	50.3 nTPM
Lung	23.7 nTPM
Endometrium	11.0 nTPM
Heart muscle	6.7 nTPM
Breast	6.2 nTPM
Fallopian tube	5.8 nTPM
Salivary gland	5.3 nTPM
Pancreas	5.2 nTPM
Vascular	4.6 nTPM
Thymus	4.4 nTPM
Ovary	4.3 nTPM
Esophagus	1.8 nTPM
Skin	1.7 nTPM
Prostate	1.7 nTPM
Testis	1.2 nTPM
Skeletal muscle	1.2 nTPM

Enteroendocrine cells	13.1 nTPM
Rectum	20.1 nTPM
Colon	19.0 nTPM
Small intestine	0.0 nTPM

Erythroid cells	124.1 nTPM
Liver	237.7 nTPM
Bone marrow	10.5 nTPM

Fibroblasts	13.0 nTPM
Pancreas	53.9 nTPM
Thymus	33.0 nTPM
Lung	28.0 nTPM
Heart muscle	24.8 nTPM
Vascular	21.3 nTPM
Liver	14.2 nTPM
Placenta	7.6 nTPM
Salivary gland	5.2 nTPM
Stomach	4.3 nTPM
Prostate	4.0 nTPM
Esophagus	3.5 nTPM
Skin	3.2 nTPM
Fallopian tube	3.0 nTPM
Adipose tissue	1.3 nTPM
Breast	0.8 nTPM
Skeletal muscle	0.6 nTPM

Granulocytes	19.0 nTPM
Tongue	34.0 nTPM
Lung	18.2 nTPM
Fallopian tube	5.0 nTPM

Intestinal goblet cells	9.5 nTPM
Rectum	14.6 nTPM
Colon	10.6 nTPM
Small intestine	3.4 nTPM

Lymphatic endothelial cells	9.9 nTPM
Ovary	16.4 nTPM
Fallopian tube	3.3 nTPM

Macrophages	29.5 nTPM
Lung	187.3 nTPM
Prostate	97.2 nTPM
Tongue	48.0 nTPM
Vascular	31.6 nTPM
Thymus	25.9 nTPM
Esophagus	20.6 nTPM
Salivary gland	18.7 nTPM
Spleen	18.0 nTPM
Skin	17.8 nTPM
Kidney	15.0 nTPM
Breast	14.5 nTPM
Endometrium	11.1 nTPM
Stomach	10.3 nTPM
Fallopian tube	10.0 nTPM
Pancreas	8.2 nTPM
Bone marrow	8.1 nTPM
Adipose tissue	7.7 nTPM
Skeletal muscle	5.2 nTPM
Testis	5.0 nTPM

Basal keratinocytes	44.5 nTPM
Tongue	85.3 nTPM
Skin	3.7 nTPM

Basal respiratory cells	116.9 nTPM
Bronchus	116.9 nTPM

Bipolar cells	8.6 nTPM
Eye	8.6 nTPM

Cholangiocytes	85.9 nTPM
Liver	85.9 nTPM

Paneth cells	3.7 nTPM
Rectum	3.9 nTPM
Colon	3.6 nTPM
Small intestine	3.5 nTPM

Plasma cells	64.4 nTPM
Liver	489.7 nTPM
Thymus	12.8 nTPM
Bone marrow	4.5 nTPM
Spleen	3.6 nTPM
Salivary gland	3.6 nTPM
Stomach	0.4 nTPM
Fallopian tube	0.3 nTPM
Esophagus	0.0 nTPM

Schwann cells	131.8 nTPM
Vascular	211.0 nTPM
Esophagus	179.7 nTPM
Adipose tissue	4.7 nTPM

Serous glandular cells	50.0 nTPM
Tongue	88.4 nTPM
Salivary gland	11.5 nTPM

Smooth muscle cells	12.6 nTPM
Tongue	97.9 nTPM
Placenta	45.1 nTPM
Liver	20.4 nTPM
Thymus	7.2 nTPM
Lung	5.9 nTPM
Salivary gland	4.8 nTPM
Vascular	4.6 nTPM
Esophagus	3.6 nTPM
Endometrium	3.3 nTPM
Ovary	3.1 nTPM
Skin	1.9 nTPM
Breast	1.4 nTPM
Fallopian tube	1.4 nTPM
Adipose tissue	0.9 nTPM
Skeletal muscle	0.4 nTPM
Prostate	0.0 nTPM

Suprabasal keratinocytes	142.7 nTPM
Tongue	283.1 nTPM
Skin	2.4 nTPM

T-cells	6.6 nTPM
Liver	26.5 nTPM
Tongue	23.6 nTPM
Lung	12.1 nTPM
Endometrium	10.1 nTPM
Vascular	10.1 nTPM
Adipose tissue	9.5 nTPM
Spleen	5.5 nTPM
Salivary gland	5.4 nTPM
Prostate	4.6 nTPM
Fallopian tube	4.4 nTPM
Skeletal muscle	4.2 nTPM
Thymus	4.0 nTPM
Breast	3.6 nTPM
Skin	3.5 nTPM
Lymph node	2.8 nTPM
Bone marrow	2.7 nTPM
Colon	1.9 nTPM
Kidney	1.8 nTPM
Stomach	1.5 nTPM
PBMC	1.4 nTPM
Esophagus	0.0 nTPM

Undifferentiated cells	25.0 nTPM
Colon	46.4 nTPM
Small intestine	18.2 nTPM
Rectum	10.5 nTPM

Amygdala excitatory	8.8 nTPM
Basal ganglia	12.2 nTPM
Hypothalamus	12.1 nTPM
Amygdala	10.0 nTPM
Hippocampus	7.9 nTPM
Cerebral cortex	5.9 nTPM
Thalamus	5.0 nTPM

Astrocyte	76.0 nTPM
Spinal cord	236.7 nTPM
Hypothalamus	82.0 nTPM
Pons	77.8 nTPM
Medulla oblongata	77.7 nTPM
Hippocampus	67.5 nTPM
Cerebellum	58.4 nTPM
Midbrain	58.2 nTPM
Cerebral cortex	55.1 nTPM
Thalamus	49.4 nTPM
Amygdala	42.5 nTPM
Basal ganglia	31.1 nTPM

Bergmann glia	81.0 nTPM
Medulla oblongata	85.2 nTPM
Cerebellum	80.1 nTPM
Pons	77.7 nTPM

Central nervous system macrophage	27.6 nTPM
Spinal cord	44.5 nTPM
Pons	34.5 nTPM
Midbrain	34.3 nTPM
Hippocampus	32.1 nTPM
Cerebellum	26.2 nTPM
Hypothalamus	25.5 nTPM
Thalamus	24.3 nTPM
Medulla oblongata	24.2 nTPM
Cerebral cortex	21.4 nTPM
Amygdala	20.1 nTPM
Basal ganglia	16.4 nTPM

Cerebellar inhibitory	6.3 nTPM
Pons	11.4 nTPM
Spinal cord	8.2 nTPM
Medulla oblongata	5.9 nTPM
Midbrain	3.4 nTPM
Cerebellum	2.7 nTPM

Cge interneuron	8.4 nTPM
Thalamus	10.8 nTPM
Amygdala	10.1 nTPM
Hippocampus	9.4 nTPM
Midbrain	8.1 nTPM
Basal ganglia	8.0 nTPM
Cerebral cortex	7.0 nTPM
Hypothalamus	5.6 nTPM

Choroid plexus epithelial cell	22.3 nTPM
Thalamus	76.7 nTPM
Medulla oblongata	8.3 nTPM
Basal ganglia	4.2 nTPM
Hippocampus	0.0 nTPM

Committed oligodendrocyte precursor	205.0 nTPM
Hypothalamus	373.5 nTPM
Thalamus	345.3 nTPM
Amygdala	290.4 nTPM
Basal ganglia	214.1 nTPM
Pons	205.4 nTPM
Hippocampus	164.5 nTPM
Midbrain	152.0 nTPM
Cerebral cortex	150.7 nTPM
Cerebellum	141.1 nTPM
Spinal cord	136.1 nTPM
Medulla oblongata	81.3 nTPM

Deep-layer corticothalamic and 6b	6.5 nTPM
Hippocampus	14.3 nTPM
Amygdala	6.7 nTPM
Basal ganglia	5.4 nTPM
Hypothalamus	4.5 nTPM
Midbrain	4.4 nTPM
Cerebral cortex	3.6 nTPM

Deep-layer intratelencephalic	14.1 nTPM
Hippocampus	17.8 nTPM
Amygdala	14.9 nTPM
Basal ganglia	14.6 nTPM
Hypothalamus	12.0 nTPM
Cerebral cortex	11.0 nTPM

Deep-layer near-projecting	15.9 nTPM
Hypothalamus	18.4 nTPM
Amygdala	17.0 nTPM
Cerebral cortex	15.8 nTPM
Basal ganglia	15.2 nTPM
Hippocampus	13.3 nTPM

Eccentric medium spiny neuron	3.6 nTPM
Amygdala	5.8 nTPM
Cerebral cortex	5.8 nTPM
Thalamus	3.6 nTPM
Hippocampus	2.9 nTPM
Hypothalamus	1.8 nTPM
Basal ganglia	1.6 nTPM