Single cell type - USP28 - 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.	USP28
Gene descriptionⁱ Full gene name according to HGNC.	Ubiquitin specific peptidase 28
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.	9

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	Cardiomyocytes - Muscle contraction (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 (Cardiomyocytes, NK-cells, Excitatory neurons)
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 (Cardiomyocytes, NK-cells, Excitatory neurons)

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

USP28 is part of cluster 54 Cardiomyocytes - Muscle contraction with confidenceⁱ 1
250 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
MYOM2	Myomesin 2	0.7621	54
ACTN2	Actinin alpha 2	0.5933	54
CSRP3	Cysteine and glycine rich protein 3	0.5842	54
SMYD1	SET and MYND domain containing 1	0.5836	54
KLHL31	Kelch like family member 31	0.5833	54
SAMD3	Sterile alpha motif domain containing 3	0.5814	63
FSD2	Fibronectin type III and SPRY domain containing 2	0.5810	54
NEXN	Nexilin F-actin binding protein	0.5780	54
ZNF106	Zinc finger protein 106	0.5777	54
TRDC	T cell receptor delta constant	0.5745	63
AGK	Acylglycerol kinase	0.5739	63
SYNPO2L	Synaptopodin 2 like	0.5715	54
SH2D1B	SH2 domain containing 1B	0.5714	63
FGFBP2	Fibroblast growth factor binding protein 2	0.5713	63
CKMT2	Creatine kinase, mitochondrial 2	0.5690	54

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	7.3 nTPM
Breast	9.9 nTPM
Adipose tissue	4.7 nTPM

Alveolar cells type 1	9.6 nTPM
Lung	9.6 nTPM

Alveolar cells type 2	8.8 nTPM
Lung	8.8 nTPM

Astrocytes	18.3 nTPM
Brain	18.3 nTPM

B-cells	17.8 nTPM
Adipose tissue	35.1 nTPM
PBMC	34.3 nTPM
Bone marrow	18.8 nTPM
Liver	17.3 nTPM
Stomach	16.8 nTPM
Lymph node	16.6 nTPM
Spleen	14.2 nTPM
Breast	12.1 nTPM
Colon	8.0 nTPM
Kidney	4.8 nTPM

Dendritic cells	32.1 nTPM
Adipose tissue	53.1 nTPM
Breast	35.3 nTPM
PBMC	8.0 nTPM

Endothelial cells	7.9 nTPM
Heart muscle	25.0 nTPM
Ovary	15.1 nTPM
Endometrium	13.7 nTPM
Placenta	9.7 nTPM
Eye	8.1 nTPM
Testis	8.0 nTPM
Breast	7.5 nTPM
Skeletal muscle	6.8 nTPM
Prostate	4.9 nTPM
Liver	4.6 nTPM
Esophagus	4.2 nTPM
Skin	3.5 nTPM
Lung	0.0 nTPM
Pancreas	0.0 nTPM

Fibroblasts	12.2 nTPM
Heart muscle	54.5 nTPM
Ovary	14.6 nTPM
Skeletal muscle	10.4 nTPM
Adipose tissue	9.9 nTPM
Breast	9.5 nTPM
Esophagus	7.4 nTPM
Prostate	6.5 nTPM
Placenta	6.4 nTPM
Stomach	6.0 nTPM
Lung	4.5 nTPM
Skin	4.2 nTPM

Intestinal goblet cells	9.6 nTPM
Small intestine	13.1 nTPM
Rectum	10.5 nTPM
Colon	5.0 nTPM

Macrophages	7.4 nTPM
Spleen	13.5 nTPM
Prostate	10.3 nTPM
Endometrium	10.3 nTPM
Ovary	10.2 nTPM
Breast	9.0 nTPM
Lung	8.6 nTPM
Kidney	8.3 nTPM
Esophagus	7.9 nTPM
Adipose tissue	7.5 nTPM
Skeletal muscle	7.4 nTPM
Testis	6.9 nTPM
Bone marrow	6.2 nTPM
Stomach	2.9 nTPM
Pancreas	2.5 nTPM
PBMC	0.0 nTPM

Paneth cells	5.3 nTPM
Rectum	8.8 nTPM
Small intestine	3.7 nTPM
Colon	3.3 nTPM

Plasma cells	21.7 nTPM
Adipose tissue	30.3 nTPM
Bone marrow	29.7 nTPM
Spleen	23.2 nTPM
Stomach	13.0 nTPM
Esophagus	12.3 nTPM

Respiratory ciliated cells	14.6 nTPM
Lung	16.0 nTPM
Bronchus	13.0 nTPM

Smooth muscle cells	11.0 nTPM
Heart muscle	26.1 nTPM
Esophagus	15.5 nTPM
Ovary	12.7 nTPM
Endometrium	12.1 nTPM
Breast	10.4 nTPM
Adipose tissue	10.0 nTPM
Skeletal muscle	9.8 nTPM
Prostate	9.1 nTPM
Pancreas	5.7 nTPM
Skin	5.6 nTPM
Bronchus	3.7 nTPM

T-cells	18.6 nTPM
Liver	44.2 nTPM
Bone marrow	38.6 nTPM
Skeletal muscle	31.9 nTPM
Ovary	31.1 nTPM
Endometrium	26.7 nTPM
Lung	25.8 nTPM
Spleen	23.6 nTPM
Kidney	21.2 nTPM
Adipose tissue	18.4 nTPM
Breast	15.1 nTPM
PBMC	14.5 nTPM
Colon	8.5 nTPM
Stomach	6.7 nTPM
Skin	5.5 nTPM
Lymph node	3.9 nTPM
Prostate	0.0 nTPM
Esophagus	0.0 nTPM

Basal keratinocytes	1.7 nTPM
Skin	1.7 nTPM

Basal squamous epithelial cells	13.6 nTPM
Esophagus	13.6 nTPM

Cytotrophoblasts	4.4 nTPM
Placenta	4.4 nTPM

Distal tubular cells	5.9 nTPM
Kidney	5.9 nTPM

Undifferentiated cells	8.9 nTPM
Small intestine	11.3 nTPM
Rectum	10.3 nTPM
Colon	5.2 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