Single cell type - HMGCS1 - 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.	HMGCS1
Gene descriptionⁱ Full gene name according to HGNC.	3-hydroxy-3-methylglutaryl-CoA synthase 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes Metabolic proteins 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. Read more	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	3

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)
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 all
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 (AF22, GAMG, HBEC3-KT)
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)

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

HMGCS1 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
MSMO1	Methylsterol monooxygenase 1	0.8552	15
SAA2-SAA4	SAA2-SAA4 readthrough	0.8208	15
ANGPTL8	Angiopoietin like 8	0.8169	15
LBP	Lipopolysaccharide binding protein	0.8072	15
FGG	Fibrinogen gamma chain	0.8059	15
ITIH3	Inter-alpha-trypsin inhibitor heavy chain 3	0.8022	15
FGL1	Fibrinogen like 1	0.7947	15
CRP	C-reactive protein	0.7943	15
SERPINA10	Serpin family A member 10	0.7935	15
GC	GC vitamin D binding protein	0.7871	15
CFHR1	Complement factor H related 1	0.7868	15
APOC4	Apolipoprotein C4	0.7850	15
CFHR4	Complement factor H related 4	0.7841	15
FGB	Fibrinogen beta chain	0.7792	15
SERPINA11	Serpin family A member 11	0.7788	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	27.8 nTPM
Adipose tissue	30.3 nTPM
Breast	25.3 nTPM

Alveolar cells type 1	67.3 nTPM
Lung	67.3 nTPM

Alveolar cells type 2	172.6 nTPM
Lung	172.6 nTPM

Astrocytes	70.5 nTPM
Brain	70.5 nTPM

B-cells	44.8 nTPM
Adipose tissue	120.8 nTPM
Lymph node	55.0 nTPM
Spleen	52.9 nTPM
Colon	52.7 nTPM
Breast	52.2 nTPM
Liver	39.1 nTPM
Stomach	36.8 nTPM
Bone marrow	18.0 nTPM
Kidney	14.3 nTPM
PBMC	5.7 nTPM

Dendritic cells	43.3 nTPM
Adipose tissue	61.2 nTPM
Breast	60.9 nTPM
PBMC	8.0 nTPM

Endothelial cells	31.3 nTPM
Placenta	97.2 nTPM
Ovary	64.3 nTPM
Prostate	62.3 nTPM
Pancreas	34.7 nTPM
Esophagus	24.0 nTPM
Endometrium	23.8 nTPM
Breast	23.6 nTPM
Skin	22.4 nTPM
Skeletal muscle	22.0 nTPM
Lung	21.8 nTPM
Eye	20.3 nTPM
Liver	9.2 nTPM
Testis	8.9 nTPM
Heart muscle	4.1 nTPM

Enteroendocrine cells	92.1 nTPM
Colon	106.6 nTPM
Rectum	77.7 nTPM

Fibroblasts	32.3 nTPM
Placenta	73.3 nTPM
Lung	45.8 nTPM
Prostate	44.1 nTPM
Adipose tissue	35.6 nTPM
Skin	33.7 nTPM
Esophagus	29.0 nTPM
Stomach	25.3 nTPM
Skeletal muscle	22.5 nTPM
Ovary	20.2 nTPM
Breast	19.1 nTPM
Heart muscle	6.7 nTPM

Intestinal goblet cells	101.9 nTPM
Colon	200.8 nTPM
Rectum	64.9 nTPM
Small intestine	39.9 nTPM

Macrophages	27.5 nTPM
Adipose tissue	64.3 nTPM
Breast	58.3 nTPM
Ovary	43.2 nTPM
Prostate	38.9 nTPM
Esophagus	33.1 nTPM
Stomach	32.2 nTPM
Endometrium	31.1 nTPM
Skeletal muscle	24.0 nTPM
Spleen	19.7 nTPM
Lung	19.3 nTPM
Bone marrow	16.3 nTPM
Kidney	15.8 nTPM
Testis	11.1 nTPM
Pancreas	5.1 nTPM
PBMC	0.0 nTPM

Paneth cells	132.3 nTPM
Colon	359.1 nTPM
Rectum	34.2 nTPM
Small intestine	3.7 nTPM

Plasma cells	38.1 nTPM
Adipose tissue	63.8 nTPM
Esophagus	43.0 nTPM
Stomach	41.9 nTPM
Spleen	23.4 nTPM
Bone marrow	18.2 nTPM

Respiratory ciliated cells	51.1 nTPM
Lung	52.5 nTPM
Bronchus	49.7 nTPM

Smooth muscle cells	32.8 nTPM
Ovary	61.9 nTPM
Bronchus	58.8 nTPM
Prostate	49.1 nTPM
Adipose tissue	41.9 nTPM
Pancreas	28.8 nTPM
Endometrium	28.2 nTPM
Skin	26.9 nTPM
Breast	22.3 nTPM
Skeletal muscle	20.9 nTPM
Esophagus	17.0 nTPM
Heart muscle	5.0 nTPM

Basal keratinocytes	108.3 nTPM
Skin	108.3 nTPM

Basal prostatic cells	42.3 nTPM
Prostate	42.3 nTPM

Basal respiratory cells	93.8 nTPM
Bronchus	93.8 nTPM

Basal squamous epithelial cells	68.3 nTPM
Esophagus	68.3 nTPM

T-cells	36.4 nTPM
Breast	73.4 nTPM
Endometrium	62.3 nTPM
Adipose tissue	61.5 nTPM
Esophagus	58.9 nTPM
Lymph node	47.2 nTPM
Stomach	44.7 nTPM
Skin	44.2 nTPM
Prostate	37.9 nTPM
Colon	35.1 nTPM
Skeletal muscle	34.0 nTPM
Spleen	28.8 nTPM
Liver	27.3 nTPM
Lung	21.3 nTPM
Bone marrow	11.9 nTPM
Ovary	11.1 nTPM
PBMC	10.1 nTPM
Kidney	9.6 nTPM

Undifferentiated cells	62.9 nTPM
Colon	120.9 nTPM
Rectum	38.5 nTPM
Small intestine	29.3 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