Single cell type - ZBED1 - 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.	ZBED1
Gene descriptionⁱ Full gene name according to HGNC.	Zinc finger BED-type containing 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Transcription factors
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.	5

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	Bipolar cells - Visual perception (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 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 (BEWO)
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 many
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

ZBED1 is part of cluster 56 Bipolar cells - Visual perception with confidenceⁱ 1
199 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
TMEM94	Transmembrane protein 94	0.6041	40
SLC1A7	Solute carrier family 1 member 7	0.5566	56
SHF	Src homology 2 domain containing F	0.5511	40
TIGD5	Tigger transposable element derived 5	0.5270	7
SPRR2B	Small proline rich protein 2B	0.5265	40
NFIC	Nuclear factor I C	0.5222	2
KLHDC8A	Kelch domain containing 8A	0.5204	40
KIRREL2	Kirre like nephrin family adhesion molecule 2	0.5123	56
PLXDC1	Plexin domain containing 1	0.5050	56
KCNG4	Potassium voltage-gated channel modifier subfamily G member 4	0.4911	56
MC4R	Melanocortin 4 receptor	0.4897	56
CABP2	Calcium binding protein 2	0.4893	56
VSX1	Visual system homeobox 1	0.4885	56
IGSF1	Immunoglobulin superfamily member 1	0.4857	56
NEUROD4	Neuronal differentiation 4	0.4848	56

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	12.9 nTPM
Adipose tissue	14.7 nTPM
Breast	11.2 nTPM

Alveolar cells type 1	12.8 nTPM
Lung	12.8 nTPM

Alveolar cells type 2	11.7 nTPM
Lung	11.7 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	20.7 nTPM
PBMC	58.6 nTPM
Colon	33.5 nTPM
Bone marrow	22.9 nTPM
Spleen	22.2 nTPM
Lymph node	16.2 nTPM
Stomach	13.6 nTPM
Liver	13.1 nTPM
Adipose tissue	13.0 nTPM
Kidney	9.5 nTPM
Breast	4.0 nTPM

Dendritic cells	18.7 nTPM
PBMC	31.8 nTPM
Adipose tissue	14.6 nTPM
Breast	9.5 nTPM

Endothelial cells	17.5 nTPM
Ovary	27.8 nTPM
Prostate	25.7 nTPM
Skin	24.5 nTPM
Eye	23.5 nTPM
Skeletal muscle	20.3 nTPM
Testis	19.6 nTPM
Pancreas	19.3 nTPM
Liver	16.5 nTPM
Esophagus	15.4 nTPM
Endometrium	15.2 nTPM
Heart muscle	13.8 nTPM
Breast	10.9 nTPM
Placenta	9.7 nTPM
Lung	3.1 nTPM

Fibroblasts	22.6 nTPM
Prostate	40.7 nTPM
Adipose tissue	29.8 nTPM
Skeletal muscle	29.7 nTPM
Stomach	26.7 nTPM
Heart muscle	24.0 nTPM
Ovary	23.2 nTPM
Esophagus	21.3 nTPM
Skin	20.1 nTPM
Breast	13.9 nTPM
Placenta	9.7 nTPM
Lung	8.9 nTPM

Intestinal goblet cells	19.4 nTPM
Rectum	23.8 nTPM
Small intestine	19.5 nTPM
Colon	15.0 nTPM

Macrophages	19.5 nTPM
Ovary	40.3 nTPM
Stomach	32.2 nTPM
Skeletal muscle	27.9 nTPM
Adipose tissue	24.1 nTPM
Prostate	22.9 nTPM
Esophagus	22.0 nTPM
Lung	20.1 nTPM
Spleen	19.7 nTPM
Endometrium	17.7 nTPM
Bone marrow	16.3 nTPM
Breast	14.6 nTPM
Kidney	12.9 nTPM
Testis	12.2 nTPM
Pancreas	10.2 nTPM
PBMC	0.0 nTPM

Paneth cells	17.3 nTPM
Rectum	21.0 nTPM
Colon	19.7 nTPM
Small intestine	11.3 nTPM

Plasma cells	8.8 nTPM
Bone marrow	16.5 nTPM
Spleen	11.7 nTPM
Stomach	8.7 nTPM
Adipose tissue	7.0 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	15.8 nTPM
Lung	16.0 nTPM
Bronchus	15.5 nTPM

Smooth muscle cells	19.2 nTPM
Ovary	46.2 nTPM
Heart muscle	25.3 nTPM
Skeletal muscle	22.8 nTPM
Esophagus	20.1 nTPM
Adipose tissue	18.5 nTPM
Endometrium	18.1 nTPM
Prostate	16.2 nTPM
Pancreas	15.5 nTPM
Skin	11.8 nTPM
Breast	11.5 nTPM
Bronchus	4.8 nTPM

T-cells	14.4 nTPM
Liver	21.2 nTPM
PBMC	20.5 nTPM
Skeletal muscle	20.1 nTPM
Esophagus	19.7 nTPM
Stomach	17.4 nTPM
Colon	15.7 nTPM
Bone marrow	14.7 nTPM
Skin	13.8 nTPM
Lymph node	13.0 nTPM
Spleen	12.9 nTPM
Lung	12.2 nTPM
Kidney	11.6 nTPM
Adipose tissue	11.4 nTPM
Ovary	11.1 nTPM
Endometrium	10.4 nTPM
Breast	10.1 nTPM
Prostate	9.5 nTPM

Basal prostatic cells	17.6 nTPM
Prostate	17.6 nTPM

Basal respiratory cells	14.1 nTPM
Bronchus	14.1 nTPM

Basal squamous epithelial cells	29.6 nTPM
Esophagus	29.6 nTPM

Cholangiocytes	40.0 nTPM
Liver	40.0 nTPM

Undifferentiated cells	23.2 nTPM
Small intestine	28.5 nTPM
Rectum	24.9 nTPM
Colon	16.4 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