Single cell type - HMGCL - 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.	HMGCL
Gene descriptionⁱ Full gene name according to HGNC.	3-hydroxy-3-methylglutaryl-CoA lyase
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Enzymes Human disease related genes Metabolic proteins Plasma 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	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	Proximal tubular cells - Tubular reabsorption (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 (Proximal tubular cells, 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	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 (Proximal tubular cells, 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

HMGCL is part of cluster 67 Proximal tubular cells - Tubular reabsorption with confidenceⁱ 1
499 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
SDHC	Succinate dehydrogenase complex subunit C	0.7159	67
TRAPPC6A	Trafficking protein particle complex 6A	0.6882	67
GCDH	Glutaryl-CoA dehydrogenase	0.6668	67
DCXR	Dicarbonyl and L-xylulose reductase	0.6640	67
ALDH2	Aldehyde dehydrogenase 2 family member	0.6567	67
ECHS1	Enoyl-CoA hydratase, short chain 1	0.6471	67
HAO2	Hydroxyacid oxidase 2	0.6246	67
NIT2	Nitrilase family member 2	0.6236	67
GRHPR	Glyoxylate and hydroxypyruvate reductase	0.6197	67
MT1X	Metallothionein 1X	0.6186	67
LYG1	Lysozyme g1	0.6179	67
SUCLG1	Succinate-CoA ligase GDP/ADP-forming subunit alpha	0.6145	67
MT1G	Metallothionein 1G	0.6139	67
SLC2A9	Solute carrier family 2 member 9	0.6129	67
MAJIN	Membrane anchored junction protein	0.6126	67

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	19.9 nTPM
Breast	24.0 nTPM
Adipose tissue	15.7 nTPM

Alveolar cells type 1	12.8 nTPM
Lung	12.8 nTPM

Alveolar cells type 2	25.7 nTPM
Lung	25.7 nTPM

Astrocytes	14.0 nTPM
Brain	14.0 nTPM

B-cells	16.3 nTPM
Kidney	61.9 nTPM
Liver	22.8 nTPM
PBMC	20.0 nTPM
Bone marrow	13.1 nTPM
Stomach	9.6 nTPM
Lymph node	8.4 nTPM
Spleen	8.3 nTPM
Breast	6.6 nTPM
Colon	6.4 nTPM
Adipose tissue	6.0 nTPM

Dendritic cells	10.0 nTPM
Breast	15.7 nTPM
Adipose tissue	10.3 nTPM
PBMC	4.0 nTPM

Endothelial cells	22.5 nTPM
Placenta	37.5 nTPM
Testis	30.2 nTPM
Liver	28.4 nTPM
Pancreas	27.0 nTPM
Heart muscle	25.1 nTPM
Ovary	22.5 nTPM
Breast	21.2 nTPM
Eye	20.3 nTPM
Prostate	20.0 nTPM
Skeletal muscle	19.6 nTPM
Esophagus	16.0 nTPM
Skin	15.7 nTPM
Endometrium	15.7 nTPM
Lung	15.6 nTPM

Fibroblasts	20.8 nTPM
Placenta	27.7 nTPM
Ovary	27.6 nTPM
Adipose tissue	27.3 nTPM
Breast	23.0 nTPM
Skeletal muscle	22.5 nTPM
Esophagus	22.4 nTPM
Prostate	21.3 nTPM
Heart muscle	19.5 nTPM
Skin	15.3 nTPM
Stomach	13.4 nTPM
Lung	8.9 nTPM

Intestinal goblet cells	49.5 nTPM
Colon	56.5 nTPM
Rectum	49.5 nTPM
Small intestine	42.5 nTPM

Macrophages	23.5 nTPM
Kidney	45.3 nTPM
Ovary	42.2 nTPM
Pancreas	35.7 nTPM
Lung	28.8 nTPM
Bone marrow	25.0 nTPM
Prostate	22.9 nTPM
Esophagus	22.0 nTPM
Breast	21.6 nTPM
Testis	20.3 nTPM
Skeletal muscle	17.0 nTPM
Spleen	16.5 nTPM
Endometrium	14.7 nTPM
Stomach	14.7 nTPM
PBMC	13.6 nTPM
Adipose tissue	11.9 nTPM

Paneth cells	53.8 nTPM
Small intestine	67.5 nTPM
Rectum	54.3 nTPM
Colon	39.6 nTPM

Plasma cells	8.3 nTPM
Spleen	11.4 nTPM
Bone marrow	9.9 nTPM
Stomach	7.6 nTPM
Adipose tissue	6.4 nTPM
Esophagus	6.1 nTPM

Respiratory ciliated cells	31.5 nTPM
Bronchus	32.4 nTPM
Lung	30.6 nTPM

Smooth muscle cells	21.6 nTPM
Pancreas	35.3 nTPM
Heart muscle	27.4 nTPM
Ovary	23.8 nTPM
Skeletal muscle	22.3 nTPM
Breast	22.3 nTPM
Prostate	21.3 nTPM
Esophagus	20.1 nTPM
Adipose tissue	18.3 nTPM
Bronchus	17.7 nTPM
Skin	16.7 nTPM
Endometrium	12.1 nTPM

T-cells	15.2 nTPM
Kidney	43.8 nTPM
Liver	28.9 nTPM
Lung	19.7 nTPM
PBMC	18.8 nTPM
Bone marrow	16.8 nTPM
Skeletal muscle	16.7 nTPM
Ovary	13.4 nTPM
Esophagus	13.1 nTPM
Breast	11.9 nTPM
Colon	11.4 nTPM
Endometrium	11.3 nTPM
Spleen	10.1 nTPM
Adipose tissue	10.0 nTPM
Skin	9.7 nTPM
Stomach	9.3 nTPM
Lymph node	8.5 nTPM
Prostate	4.7 nTPM

Basal keratinocytes	5.9 nTPM
Skin	5.9 nTPM

Basal prostatic cells	29.9 nTPM
Prostate	29.9 nTPM

Cholangiocytes	41.5 nTPM
Liver	41.5 nTPM

Collecting duct cells	49.7 nTPM
Kidney	49.7 nTPM

Undifferentiated cells	48.9 nTPM
Colon	49.4 nTPM
Rectum	48.9 nTPM
Small intestine	48.4 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