Single cell type - SC5D - 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.	SC5D
Gene descriptionⁱ Full gene name according to HGNC.	Sterol-C5-desaturase
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Enzymes Human disease related genes Metabolic proteins Potential drug targets
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.	4

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, Hepatic stellate 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	Low cell line specificity
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, Hepatic stellate 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

SC5D 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	Serum amyloid A2	0.7615	15
SAA1	Serum amyloid A1	0.7570	15
SAA2-SAA4	SAA2-SAA4 readthrough	0.7268	15
ANGPTL8	Angiopoietin like 8	0.7164	15
ITIH3	Inter-alpha-trypsin inhibitor heavy chain 3	0.7053	15
CFHR1	Complement factor H related 1	0.7035	15
FGG	Fibrinogen gamma chain	0.7007	15
CRP	C-reactive protein	0.6995	15
APOC4	Apolipoprotein C4	0.6991	15
LBP	Lipopolysaccharide binding protein	0.6981	15
CFHR3	Complement factor H related 3	0.6952	15
CFHR4	Complement factor H related 4	0.6929	15
FGL1	Fibrinogen like 1	0.6894	15
MSMO1	Methylsterol monooxygenase 1	0.6848	15
EBP	EBP cholestenol delta-isomerase	0.6843	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	10.4 nTPM
Adipose tissue	10.7 nTPM
Breast	10.2 nTPM

Alveolar cells type 1	19.2 nTPM
Lung	19.2 nTPM

Alveolar cells type 2	31.9 nTPM
Lung	31.9 nTPM

Astrocytes	23.8 nTPM
Brain	23.8 nTPM

B-cells	62.6 nTPM
Adipose tissue	165.4 nTPM
Stomach	139.0 nTPM
Colon	103.8 nTPM
Spleen	72.0 nTPM
Lymph node	32.6 nTPM
Breast	32.1 nTPM
Liver	23.1 nTPM
Bone marrow	22.1 nTPM
Kidney	19.0 nTPM
PBMC	17.1 nTPM

Dendritic cells	47.5 nTPM
Adipose tissue	78.0 nTPM
Breast	36.8 nTPM
PBMC	27.9 nTPM

Endothelial cells	15.7 nTPM
Liver	82.6 nTPM
Pancreas	19.3 nTPM
Placenta	17.6 nTPM
Eye	17.0 nTPM
Ovary	12.8 nTPM
Breast	11.9 nTPM
Esophagus	9.8 nTPM
Prostate	8.9 nTPM
Skin	8.8 nTPM
Skeletal muscle	8.8 nTPM
Endometrium	8.3 nTPM
Heart muscle	7.3 nTPM
Testis	6.8 nTPM
Lung	0.0 nTPM

Fibroblasts	16.3 nTPM
Prostate	22.5 nTPM
Placenta	21.6 nTPM
Heart muscle	19.7 nTPM
Skin	18.0 nTPM
Adipose tissue	18.0 nTPM
Breast	16.5 nTPM
Esophagus	16.2 nTPM
Stomach	14.9 nTPM
Skeletal muscle	13.5 nTPM
Ovary	13.2 nTPM
Lung	5.6 nTPM

Intestinal goblet cells	15.3 nTPM
Rectum	18.3 nTPM
Colon	17.9 nTPM
Small intestine	9.6 nTPM

Macrophages	17.6 nTPM
Ovary	42.4 nTPM
Breast	29.4 nTPM
Stomach	26.4 nTPM
Adipose tissue	24.6 nTPM
Lung	18.9 nTPM
Esophagus	18.9 nTPM
Prostate	17.2 nTPM
Pancreas	15.3 nTPM
Skeletal muscle	14.4 nTPM
Bone marrow	12.5 nTPM
Kidney	12.0 nTPM
Testis	11.1 nTPM
Spleen	10.4 nTPM
Endometrium	9.9 nTPM
PBMC	0.0 nTPM

Paneth cells	18.8 nTPM
Colon	36.2 nTPM
Rectum	12.6 nTPM
Small intestine	7.5 nTPM

Plasma cells	20.9 nTPM
Adipose tissue	75.5 nTPM
Stomach	13.1 nTPM
Bone marrow	8.2 nTPM
Spleen	7.8 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	18.7 nTPM
Bronchus	21.4 nTPM
Lung	16.0 nTPM

Smooth muscle cells	14.7 nTPM
Bronchus	25.3 nTPM
Pancreas	21.3 nTPM
Prostate	19.4 nTPM
Heart muscle	18.4 nTPM
Ovary	17.4 nTPM
Breast	14.1 nTPM
Esophagus	14.0 nTPM
Skin	10.4 nTPM
Adipose tissue	8.9 nTPM
Skeletal muscle	6.4 nTPM
Endometrium	5.9 nTPM

T-cells	56.5 nTPM
Adipose tissue	239.2 nTPM
Breast	92.8 nTPM
Esophagus	85.2 nTPM
Stomach	75.5 nTPM
Spleen	75.2 nTPM
Lymph node	63.0 nTPM
Prostate	56.8 nTPM
Skeletal muscle	46.3 nTPM
Colon	45.1 nTPM
Skin	44.7 nTPM
Ovary	28.9 nTPM
Kidney	23.3 nTPM
Liver	21.2 nTPM
PBMC	19.2 nTPM
Bone marrow	18.2 nTPM
Endometrium	16.0 nTPM
Lung	10.6 nTPM

Basal keratinocytes	9.7 nTPM
Skin	9.7 nTPM

Basal prostatic cells	49.9 nTPM
Prostate	49.9 nTPM

Basal respiratory cells	48.9 nTPM
Bronchus	48.9 nTPM

Basal squamous epithelial cells	14.8 nTPM
Esophagus	14.8 nTPM

Undifferentiated cells	13.3 nTPM
Colon	15.4 nTPM
Small intestine	12.5 nTPM
Rectum	11.9 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