Single cell type - SCD - The Human Protein Atlas

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). Read more	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. Read more	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. Read more	Hepatocytes - Hemostasis (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. Read more	Cell type enhanced (Hepatocytes, Oligodendrocytes, Alveolar cells type 2, Granulosa cells)
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. Read more	Low immune cell specificity
Immune cell distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in many
Cell line specificityⁱ RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines. Read more	Cell line enhanced (ASC diff, CAPAN-2)
Cell line distributionⁱ RNA distribution category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into five different categories (detected in all, detected in many, detected in some, detected in single and not detected) according to their pattern of detected RNA expression across the panel of cell lines. Read more	Detected in all
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); a Human Protein Atlas antibody- or RNA based score (HPA evidence); and evidence based on PeptideAtlas (MS evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable. Read more	Evidence at protein level

SINGLE CELL TYPESⁱ A summary of 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 Group Expression Alphabetical RNA single cell type specificity: Cell type enhanced (Hepatocytes, Oligodendrocytes, Alveolar cells type 2, Granulosa cells)

SINGLE CELL TISSUES OVERVIEWⁱ An overview of all tissues where single cell type expression has been analyzed. Each tissue name and corresponding UMAP plot is clickable and redirects to the selected tissue.
Adipose tissue Bone marrow Brain Breast Bronchus Colon Endometrium Esophagus Eye Heart muscle Kidney Liver Lung Lymph node Ovary Pancreas Placenta Prostate Rectum Skeletal muscle Skin Small intestine Spleen Stomach Testis

EXPRESSION CLUSTERING & CORRELATIONⁱ

SCD is part of cluster 15 Hepatocytes - Hemostasis with confidenceⁱ 1
129 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell type 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. Read more	Clusterⁱ ID of the expression cluster of the neighboring gene. Read more
SAA2-SAA4	SAA2-SAA4 readthrough	0.8343	15
SAA2	Serum amyloid A2	0.8201	15
PCSK9	Proprotein convertase subtilisin/kexin type 9	0.8129	15
C4BPA	Complement component 4 binding protein alpha	0.8052	15
LSS	Lanosterol synthase	0.7999	15
SAA1	Serum amyloid A1	0.7995	15
CFHR1	Complement factor H related 1	0.7954	15
ANGPTL8	Angiopoietin like 8	0.7912	15
MSMO1	Methylsterol monooxygenase 1	0.7910	15
CRP	C-reactive protein	0.7857	15
LBP	Lipopolysaccharide binding protein	0.7809	15
ITIH3	Inter-alpha-trypsin inhibitor heavy chain 3	0.7803	15
DHCR24	24-dehydrocholesterol reductase	0.7781	15
CFHR3	Complement factor H related 3	0.7732	15
CFHR4	Complement factor H related 4	0.7694	15

SINGLE CELL TISSUESⁱ Single cell RNA levels of annotated cell type clusters are shown separately for each analyzed tissue. For easier navigation across tissues, use the above Single cell tissue overview, where each tissue name and UMAP plot is clickable and redirects to the selected tissue, alternatively the grey browser on the left side of the window. Barchart shows nTPM levels in each annotated cluster of single cells. To the left, a UMAP plot illustrates the RNA expression profile. The tissue name and plots are clickable and redirect to a more detailed interactive page. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. Please note that the same cell type may be found in several clusters.
Cluster Expression Alphabetical Adipose tissue
Cluster Expression Alphabetical Bone marrow
Cluster Expression Alphabetical Brain
Cluster Expression Alphabetical Breast
Cluster Expression Alphabetical Bronchus
Cluster Expression Alphabetical Colon
Cluster Expression Alphabetical Endometrium
Cluster Expression Alphabetical Esophagus
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Lymph node
Cluster Expression Alphabetical Ovary
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skeletal muscle
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Spleen
Cluster Expression Alphabetical Stomach
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ

Organ

Expression

Alphabetical

Adipocytes	3.8 nTPM
Breast	5.0 nTPM
Adipose tissue	2.6 nTPM

Alveolar cells type 1	54.5 nTPM
Lung	54.5 nTPM

Astrocytes	34.0 nTPM
Brain	34.0 nTPM

B-cells	15.7 nTPM
Liver	134.2 nTPM
Colon	14.4 nTPM
Adipose tissue	3.5 nTPM
Spleen	1.7 nTPM
Breast	1.3 nTPM
Lymph node	1.1 nTPM
Stomach	0.9 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Bone marrow	0.0 nTPM

Basal keratinocytes	3.7 nTPM
Skin	3.7 nTPM

Dendritic cells	4.7 nTPM
Adipose tissue	9.3 nTPM
Breast	4.7 nTPM
PBMC	0.0 nTPM

Endothelial cells	12.5 nTPM
Placenta	62.0 nTPM
Ovary	21.1 nTPM
Lung	18.7 nTPM
Liver	14.7 nTPM
Endometrium	12.2 nTPM
Prostate	10.8 nTPM
Eye	10.5 nTPM
Pancreas	7.7 nTPM
Heart muscle	6.8 nTPM
Breast	4.4 nTPM
Skin	2.7 nTPM
Esophagus	2.1 nTPM
Testis	1.4 nTPM
Skeletal muscle	0.7 nTPM

Fibroblasts	15.9 nTPM
Placenta	57.2 nTPM
Ovary	49.6 nTPM
Heart muscle	32.3 nTPM
Prostate	10.3 nTPM
Lung	10.1 nTPM
Stomach	4.4 nTPM
Esophagus	4.1 nTPM
Skin	3.3 nTPM
Breast	1.5 nTPM
Adipose tissue	1.2 nTPM
Skeletal muscle	0.7 nTPM

Intestinal goblet cells	16.4 nTPM
Colon	20.1 nTPM
Rectum	16.7 nTPM
Small intestine	12.4 nTPM

Macrophages	21.2 nTPM
Lung	130.8 nTPM
Ovary	53.4 nTPM
Esophagus	20.4 nTPM
Spleen	19.7 nTPM
Kidney	13.7 nTPM
Breast	13.7 nTPM
Endometrium	13.3 nTPM
Prostate	12.6 nTPM
Stomach	11.7 nTPM
Adipose tissue	7.2 nTPM
Bone marrow	6.2 nTPM
Testis	5.2 nTPM
Pancreas	5.1 nTPM
Skeletal muscle	4.5 nTPM
PBMC	0.0 nTPM

Paneth cells	2.7 nTPM
Rectum	4.8 nTPM
Colon	3.3 nTPM
Small intestine	0.0 nTPM

Plasma cells	3.7 nTPM
Adipose tissue	9.7 nTPM
Bone marrow	5.0 nTPM
Spleen	3.7 nTPM
Esophagus	0.0 nTPM
Stomach	0.0 nTPM

Respiratory ciliated cells	31.0 nTPM
Bronchus	51.7 nTPM
Lung	10.2 nTPM

Smooth muscle cells	25.7 nTPM
Bronchus	140.9 nTPM
Pancreas	59.0 nTPM
Ovary	49.2 nTPM
Heart muscle	11.8 nTPM
Adipose tissue	5.6 nTPM
Prostate	5.0 nTPM
Esophagus	4.6 nTPM
Endometrium	4.2 nTPM
Skin	1.0 nTPM
Breast	0.7 nTPM
Skeletal muscle	0.2 nTPM

T-cells	6.6 nTPM
Lung	28.8 nTPM
Liver	19.9 nTPM
Endometrium	13.3 nTPM
Adipose tissue	9.8 nTPM
Esophagus	6.6 nTPM
Colon	5.7 nTPM
Spleen	5.5 nTPM
Skeletal muscle	3.8 nTPM
Breast	3.7 nTPM
Bone marrow	3.5 nTPM
Skin	3.3 nTPM
Lymph node	3.0 nTPM
PBMC	1.7 nTPM
Kidney	1.4 nTPM
Stomach	1.4 nTPM
Prostate	0.0 nTPM
Ovary	0.0 nTPM

Cholangiocytes	28.6 nTPM
Liver	28.6 nTPM

Early spermatids	52.6 nTPM
Testis	52.6 nTPM

Endometrial stromal cells	9.0 nTPM
Endometrium	9.0 nTPM

Exocrine glandular cells	67.9 nTPM
Pancreas	67.9 nTPM

Undifferentiated cells	38.9 nTPM
Colon	78.2 nTPM
Small intestine	20.2 nTPM
Rectum	18.1 nTPM

Adipose tissue

Bone marrow

Brain

Breast

Bronchus

Colon

Endometrium

Esophagus

Eye

Heart muscle

Kidney

Liver

Lung

Lymph node

Ovary

Pancreas

Placenta

Prostate

Rectum

Skeletal muscle

Skin

Small intestine

Spleen

Stomach

Testis

PBMC