Single cell type - UBE2D4 - 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.	UBE2D4
Gene descriptionⁱ Full gene name according to HGNC.	Ubiquitin conjugating enzyme E2 D4 (putative)
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes Metabolic 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.	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 - Mitochondria (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 (Distal tubular cells)
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 (SH-SY5Y)
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 (Distal tubular cells)

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

UBE2D4 is part of cluster 7 Non-specific - Mitochondria with confidenceⁱ 1
481 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
MISP3	MISP family member 3	0.6112	35
ATP5F1D	ATP synthase F1 subunit delta	0.5907	7
TSR3	TSR3 ribosome maturation factor	0.5693	67
SEPHS2	Selenophosphate synthetase 2	0.5692	7
ATP5MC3	ATP synthase membrane subunit c locus 3	0.5534	7
EEF1AKMT4	EEF1A lysine methyltransferase 4	0.5528	7
RWDD4	RWD domain containing 4	0.5494	67
CYP27B1	Cytochrome P450 family 27 subfamily B member 1	0.5477	67
GATD3B	Glutamine amidotransferase like class 1 domain containing 3B	0.5437	67
STUB1	STIP1 homology and U-box containing protein 1	0.5413	39
NDUFAF8	NADH:ubiquinone oxidoreductase complex assembly factor 8	0.5409	7
MOCS2	Molybdenum cofactor synthesis 2	0.5379	39
ATP5PO	ATP synthase peripheral stalk subunit OSCP	0.5328	7
MCCD1	Mitochondrial coiled-coil domain 1	0.5322	67
ATP5PF	ATP synthase peripheral stalk subunit F6	0.5274	7

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	14.9 nTPM
Breast	20.2 nTPM
Adipose tissue	9.6 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	6.5 nTPM
Lung	6.5 nTPM

Astrocytes	8.8 nTPM
Brain	8.8 nTPM

B-cells	10.4 nTPM
Colon	22.3 nTPM
Spleen	14.2 nTPM
Breast	12.1 nTPM
PBMC	11.5 nTPM
Kidney	9.5 nTPM
Liver	8.8 nTPM
Lymph node	7.3 nTPM
Stomach	6.8 nTPM
Adipose tissue	6.0 nTPM
Bone marrow	5.7 nTPM

Dendritic cells	11.9 nTPM
Breast	12.4 nTPM
PBMC	12.0 nTPM
Adipose tissue	11.3 nTPM

Endothelial cells	12.9 nTPM
Esophagus	29.3 nTPM
Breast	23.9 nTPM
Skin	20.4 nTPM
Placenta	15.9 nTPM
Eye	15.4 nTPM
Heart muscle	15.4 nTPM
Liver	14.7 nTPM
Skeletal muscle	11.6 nTPM
Prostate	10.8 nTPM
Endometrium	7.9 nTPM
Ovary	6.9 nTPM
Testis	4.7 nTPM
Pancreas	3.9 nTPM
Lung	0.0 nTPM

Fibroblasts	14.9 nTPM
Skin	24.3 nTPM
Heart muscle	19.2 nTPM
Esophagus	18.2 nTPM
Skeletal muscle	17.7 nTPM
Breast	17.4 nTPM
Adipose tissue	16.9 nTPM
Stomach	13.4 nTPM
Ovary	12.2 nTPM
Prostate	10.5 nTPM
Placenta	6.8 nTPM
Lung	6.7 nTPM

Intestinal goblet cells	8.0 nTPM
Rectum	8.9 nTPM
Small intestine	8.7 nTPM
Colon	6.5 nTPM

Macrophages	12.5 nTPM
Kidney	24.2 nTPM
Pancreas	23.0 nTPM
Ovary	22.7 nTPM
Prostate	17.2 nTPM
Breast	16.3 nTPM
Skeletal muscle	13.0 nTPM
Endometrium	10.6 nTPM
Lung	10.2 nTPM
Adipose tissue	9.7 nTPM
Esophagus	9.4 nTPM
Spleen	9.3 nTPM
Testis	9.2 nTPM
Bone marrow	6.2 nTPM
Stomach	5.9 nTPM
PBMC	0.0 nTPM

Paneth cells	7.6 nTPM
Rectum	12.6 nTPM
Colon	6.5 nTPM
Small intestine	3.7 nTPM

Plasma cells	11.2 nTPM
Bone marrow	14.8 nTPM
Spleen	12.6 nTPM
Esophagus	12.3 nTPM
Stomach	11.6 nTPM
Adipose tissue	4.5 nTPM

Respiratory ciliated cells	5.5 nTPM
Bronchus	8.2 nTPM
Lung	2.9 nTPM

Smooth muscle cells	10.5 nTPM
Breast	15.4 nTPM
Skin	14.6 nTPM
Heart muscle	14.4 nTPM
Pancreas	14.0 nTPM
Prostate	11.9 nTPM
Adipose tissue	9.1 nTPM
Skeletal muscle	7.9 nTPM
Esophagus	7.8 nTPM
Ovary	7.7 nTPM
Bronchus	6.6 nTPM
Endometrium	6.5 nTPM

T-cells	8.8 nTPM
Colon	15.2 nTPM
Skin	13.3 nTPM
Breast	11.6 nTPM
Spleen	11.2 nTPM
Ovary	11.1 nTPM
Adipose tissue	10.9 nTPM
PBMC	10.3 nTPM
Kidney	10.2 nTPM
Stomach	9.6 nTPM
Prostate	9.5 nTPM
Liver	8.4 nTPM
Skeletal muscle	8.0 nTPM
Lymph node	7.6 nTPM
Bone marrow	7.3 nTPM
Endometrium	4.8 nTPM
Lung	0.0 nTPM
Esophagus	0.0 nTPM

Basal squamous epithelial cells	4.0 nTPM
Esophagus	4.0 nTPM

Cholangiocytes	14.3 nTPM
Liver	14.3 nTPM

Collecting duct cells	16.5 nTPM
Kidney	16.5 nTPM

Cone photoreceptor cells	2.1 nTPM
Eye	2.1 nTPM

Undifferentiated cells	8.4 nTPM
Small intestine	12.5 nTPM
Rectum	8.8 nTPM
Colon	3.9 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