Single cell type - APEX1 - 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.	APEX1
Gene descriptionⁱ Full gene name according to HGNC.	Apurinic/apyrimidinic endodeoxyribonuclease 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes 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.	13

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	Non-specific - Translation (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	Low cell type specificity
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: Low cell type specificity

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

APEX1 is part of cluster 32 Non-specific - Translation with confidenceⁱ 1
175 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
C1QBP	Complement C1q binding protein	0.6325	39
NPM1	Nucleophosmin 1	0.6295	32
EIF3L	Eukaryotic translation initiation factor 3 subunit L	0.5953	32
IMPDH2	Inosine monophosphate dehydrogenase 2	0.5773	10
RPS7	Ribosomal protein S7	0.5717	32
NACA	Nascent polypeptide associated complex subunit alpha	0.5598	32
NME1	NME/NM23 nucleoside diphosphate kinase 1	0.5530	10
SNRPF	Small nuclear ribonucleoprotein polypeptide F	0.5444	32
NLE1	Notchless homolog 1	0.5420	39
PHB2	Prohibitin 2	0.5345	32
RBMX	RNA binding motif protein X-linked	0.5300	32
TP53	Tumor protein p53	0.5287	32
RPS3A	Ribosomal protein S3A	0.5225	32
NOA1	Nitric oxide associated 1	0.5189	32
EIF3M	Eukaryotic translation initiation factor 3 subunit M	0.5180	10

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	63.8 nTPM
Breast	79.9 nTPM
Adipose tissue	47.6 nTPM

Alveolar cells type 1	64.1 nTPM
Lung	64.1 nTPM

Alveolar cells type 2	57.6 nTPM
Lung	57.6 nTPM

Astrocytes	11.8 nTPM
Brain	11.8 nTPM

B-cells	120.3 nTPM
PBMC	192.7 nTPM
Kidney	176.2 nTPM
Spleen	116.6 nTPM
Bone marrow	112.8 nTPM
Colon	111.8 nTPM
Breast	109.7 nTPM
Liver	108.2 nTPM
Adipose tissue	103.7 nTPM
Lymph node	91.8 nTPM
Stomach	79.1 nTPM

Basal squamous epithelial cells	136.1 nTPM
Esophagus	136.1 nTPM

Dendritic cells	114.1 nTPM
PBMC	187.3 nTPM
Breast	79.1 nTPM
Adipose tissue	75.8 nTPM

Endothelial cells	75.6 nTPM
Pancreas	127.4 nTPM
Placenta	125.0 nTPM
Ovary	113.6 nTPM
Endometrium	96.0 nTPM
Lung	87.4 nTPM
Breast	81.8 nTPM
Skin	81.4 nTPM
Esophagus	63.5 nTPM
Testis	62.5 nTPM
Liver	57.7 nTPM
Prostate	52.3 nTPM
Eye	47.7 nTPM
Skeletal muscle	40.8 nTPM
Heart muscle	21.5 nTPM

Enteroendocrine cells	120.0 nTPM
Colon	159.9 nTPM
Rectum	80.1 nTPM

Erythroid cells	135.6 nTPM
Bone marrow	174.8 nTPM
Liver	96.4 nTPM

Fibroblasts	88.7 nTPM
Ovary	195.1 nTPM
Lung	122.9 nTPM
Placenta	110.0 nTPM
Breast	99.8 nTPM
Adipose tissue	85.0 nTPM
Prostate	80.6 nTPM
Skin	70.1 nTPM
Heart muscle	63.4 nTPM
Esophagus	53.5 nTPM
Stomach	52.0 nTPM
Skeletal muscle	43.9 nTPM

Intestinal goblet cells	85.4 nTPM
Rectum	103.4 nTPM
Colon	82.9 nTPM
Small intestine	70.0 nTPM

Macrophages	95.2 nTPM
Endometrium	150.3 nTPM
Breast	146.0 nTPM
Pancreas	132.7 nTPM
Testis	129.6 nTPM
Prostate	128.4 nTPM
Adipose tissue	127.1 nTPM
Ovary	126.5 nTPM
Lung	107.2 nTPM
Kidney	90.8 nTPM
Esophagus	73.9 nTPM
Skeletal muscle	68.4 nTPM
Bone marrow	51.2 nTPM
Spleen	47.7 nTPM
Stomach	35.1 nTPM
PBMC	13.6 nTPM

Paneth cells	73.1 nTPM
Rectum	130.4 nTPM
Small intestine	78.9 nTPM
Colon	9.9 nTPM

Plasma cells	71.1 nTPM
Spleen	85.9 nTPM
Bone marrow	85.7 nTPM
Stomach	75.2 nTPM
Esophagus	61.7 nTPM
Adipose tissue	47.1 nTPM

Cholangiocytes	111.5 nTPM
Liver	111.5 nTPM

Collecting duct cells	68.0 nTPM
Kidney	68.0 nTPM

Cone photoreceptor cells	41.7 nTPM
Eye	41.7 nTPM

Cytotrophoblasts	200.1 nTPM
Placenta	200.1 nTPM

Respiratory ciliated cells	64.6 nTPM
Lung	78.7 nTPM
Bronchus	50.4 nTPM

Smooth muscle cells	174.2 nTPM
Bronchus	596.7 nTPM
Skin	247.4 nTPM
Prostate	210.1 nTPM
Ovary	199.3 nTPM
Pancreas	158.2 nTPM
Endometrium	117.4 nTPM
Breast	109.6 nTPM
Adipose tissue	97.3 nTPM
Esophagus	65.2 nTPM
Skeletal muscle	60.9 nTPM
Heart muscle	54.7 nTPM

T-cells	75.1 nTPM
PBMC	141.0 nTPM
Skin	102.2 nTPM
Lung	101.7 nTPM
Kidney	97.9 nTPM
Liver	93.5 nTPM
Lymph node	90.7 nTPM
Adipose tissue	87.2 nTPM
Breast	77.9 nTPM
Bone marrow	66.6 nTPM
Spleen	66.3 nTPM
Ovary	64.5 nTPM
Endometrium	64.1 nTPM
Stomach	54.5 nTPM
Colon	50.8 nTPM
Skeletal muscle	49.1 nTPM
Prostate	42.6 nTPM
Esophagus	26.2 nTPM

Undifferentiated cells	157.6 nTPM
Small intestine	184.8 nTPM
Colon	147.4 nTPM
Rectum	140.5 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