Single cell type - TOPBP1 - 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.	TOPBP1
Gene descriptionⁱ Full gene name according to HGNC.	DNA topoisomerase II binding protein 1
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.	2

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 - Cell cycle regulation (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 (Late spermatids, Spermatocytes)
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 (Late spermatids, Spermatocytes)

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

TOPBP1 is part of cluster 12 Non-specific - Cell cycle regulation with confidenceⁱ 1
294 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
NCAPG2	Non-SMC condensin II complex subunit G2	0.5811	12
ATAD5	ATPase family AAA domain containing 5	0.5261	12
RAD51AP1	RAD51 associated protein 1	0.5000	12
NEIL3	Nei like DNA glycosylase 3	0.4983	12
NCAPD2	Non-SMC condensin I complex subunit D2	0.4982	12
NCAPD3	Non-SMC condensin II complex subunit D3	0.4957	12
FOXM1	Forkhead box M1	0.4845	12
WDHD1	WD repeat and HMG-box DNA binding protein 1	0.4837	12
TMPO	Thymopoietin	0.4826	12
BUB1B	BUB1 mitotic checkpoint serine/threonine kinase B	0.4820	12
ORC1	Origin recognition complex subunit 1	0.4799	12
KIF11	Kinesin family member 11	0.4782	12
NCAPG	Non-SMC condensin I complex subunit G	0.4770	12
SKA3	Spindle and kinetochore associated complex subunit 3	0.4684	12
FBXO5	F-box protein 5	0.4671	12

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	17.1 nTPM
Breast	17.8 nTPM
Adipose tissue	16.4 nTPM

Alveolar cells type 1	22.4 nTPM
Lung	22.4 nTPM

Alveolar cells type 2	21.9 nTPM
Lung	21.9 nTPM

Astrocytes	10.7 nTPM
Brain	10.7 nTPM

B-cells	22.8 nTPM
Spleen	31.1 nTPM
Lymph node	30.1 nTPM
Bone marrow	28.6 nTPM
Stomach	28.6 nTPM
Adipose tissue	24.0 nTPM
Breast	22.8 nTPM
Liver	22.6 nTPM
Colon	20.8 nTPM
PBMC	9.9 nTPM
Kidney	9.5 nTPM

Dendritic cells	33.9 nTPM
PBMC	39.8 nTPM
Adipose tissue	36.5 nTPM
Breast	25.2 nTPM

Endothelial cells	16.0 nTPM
Lung	28.1 nTPM
Heart muscle	22.1 nTPM
Ovary	21.3 nTPM
Endometrium	21.2 nTPM
Pancreas	19.3 nTPM
Skeletal muscle	18.5 nTPM
Esophagus	15.4 nTPM
Breast	14.9 nTPM
Testis	14.5 nTPM
Placenta	14.2 nTPM
Liver	10.1 nTPM
Eye	9.7 nTPM
Prostate	8.5 nTPM
Skin	5.9 nTPM

Fibroblasts	14.9 nTPM
Ovary	23.4 nTPM
Skeletal muscle	20.1 nTPM
Heart muscle	19.3 nTPM
Adipose tissue	18.3 nTPM
Stomach	16.3 nTPM
Breast	14.8 nTPM
Esophagus	14.7 nTPM
Lung	12.3 nTPM
Placenta	10.1 nTPM
Skin	9.0 nTPM
Prostate	5.9 nTPM

Intestinal goblet cells	13.9 nTPM
Colon	15.7 nTPM
Small intestine	15.6 nTPM
Rectum	10.2 nTPM

Macrophages	18.2 nTPM
Lung	34.6 nTPM
Bone marrow	25.0 nTPM
Skeletal muscle	23.8 nTPM
Stomach	23.5 nTPM
Adipose tissue	20.9 nTPM
Spleen	19.7 nTPM
Ovary	19.5 nTPM
Breast	18.2 nTPM
Kidney	18.1 nTPM
Endometrium	17.5 nTPM
Esophagus	15.8 nTPM
Pancreas	15.3 nTPM
Testis	15.1 nTPM
Prostate	5.7 nTPM
PBMC	0.0 nTPM

Paneth cells	11.6 nTPM
Rectum	17.0 nTPM
Small intestine	11.3 nTPM
Colon	6.5 nTPM

Plasma cells	37.5 nTPM
Spleen	67.7 nTPM
Bone marrow	44.5 nTPM
Adipose tissue	32.2 nTPM
Esophagus	24.6 nTPM
Stomach	18.4 nTPM

Respiratory ciliated cells	8.7 nTPM
Lung	13.1 nTPM
Bronchus	4.2 nTPM

Smooth muscle cells	12.2 nTPM
Ovary	25.8 nTPM
Endometrium	22.9 nTPM
Pancreas	15.4 nTPM
Esophagus	12.4 nTPM
Heart muscle	11.3 nTPM
Breast	11.0 nTPM
Skeletal muscle	10.6 nTPM
Adipose tissue	10.6 nTPM
Prostate	4.7 nTPM
Bronchus	4.7 nTPM
Skin	4.6 nTPM

T-cells	23.3 nTPM
Lung	38.0 nTPM
Lymph node	30.5 nTPM
Skeletal muscle	29.8 nTPM
Endometrium	28.2 nTPM
Adipose tissue	27.8 nTPM
Bone marrow	27.6 nTPM
Spleen	27.4 nTPM
Colon	26.1 nTPM
Stomach	25.6 nTPM
Prostate	23.6 nTPM
Breast	21.1 nTPM
PBMC	20.1 nTPM
Ovary	20.1 nTPM
Liver	15.9 nTPM
Kidney	13.7 nTPM
Esophagus	13.1 nTPM
Skin	8.3 nTPM

Basal prostatic cells	8.8 nTPM
Prostate	8.8 nTPM

Basal respiratory cells	7.8 nTPM
Bronchus	7.8 nTPM

Basal squamous epithelial cells	20.5 nTPM
Esophagus	20.5 nTPM

Cholangiocytes	12.8 nTPM
Liver	12.8 nTPM

Undifferentiated cells	14.8 nTPM
Small intestine	18.1 nTPM
Rectum	16.0 nTPM
Colon	10.4 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