Single cell type - USP48 - 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.	USP48
Gene descriptionⁱ Full gene name according to HGNC.	Ubiquitin specific peptidase 48
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes Metabolic proteins 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.	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	Granulosa cells - Unknown function (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 (Granulosa 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	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 (Granulosa 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

USP48 is part of cluster 40 Granulosa cells - Unknown function with confidenceⁱ 1
316 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
HUWE1	HECT, UBA and WWE domain containing E3 ubiquitin protein ligase 1	0.6870	40
TLL2	Tolloid like 2	0.6593	40
SPRR2F	Small proline rich protein 2F	0.6213	40
LRAT	Lecithin retinol acyltransferase	0.6190	40
GREB1	Growth regulating estrogen receptor binding 1	0.6174	40
GRB14	Growth factor receptor bound protein 14	0.6137	40
NPAP1	Nuclear pore associated protein 1	0.6114	40
ME2	Malic enzyme 2	0.6111	40
CCKBR	Cholecystokinin B receptor	0.6109	40
MRAP	Melanocortin 2 receptor accessory protein	0.6103	40
LPIN2	Lipin 2	0.6004	40
PPHLN1	Periphilin 1	0.5977	40
KYAT1	Kynurenine aminotransferase 1	0.5898	40
TVP23A	Trans-golgi network vesicle protein 23 homolog A	0.5846	40
TMEM200A	Transmembrane protein 200A	0.5809	40

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	37.9 nTPM
Breast	40.3 nTPM
Adipose tissue	35.6 nTPM

Alveolar cells type 1	54.5 nTPM
Lung	54.5 nTPM

Alveolar cells type 2	42.1 nTPM
Lung	42.1 nTPM

Astrocytes	32.0 nTPM
Brain	32.0 nTPM

B-cells	55.4 nTPM
Liver	76.9 nTPM
Lymph node	66.2 nTPM
Stomach	65.4 nTPM
Adipose tissue	64.7 nTPM
Bone marrow	58.9 nTPM
Spleen	55.0 nTPM
Breast	54.9 nTPM
Colon	39.9 nTPM
PBMC	38.6 nTPM
Kidney	33.4 nTPM

Dendritic cells	48.3 nTPM
Adipose tissue	48.7 nTPM
Breast	48.5 nTPM
PBMC	47.8 nTPM

Endothelial cells	32.5 nTPM
Heart muscle	55.5 nTPM
Endometrium	50.8 nTPM
Ovary	42.0 nTPM
Lung	40.6 nTPM
Placenta	34.7 nTPM
Skeletal muscle	34.7 nTPM
Breast	34.5 nTPM
Testis	26.6 nTPM
Skin	26.5 nTPM
Esophagus	25.7 nTPM
Pancreas	23.1 nTPM
Eye	21.8 nTPM
Liver	19.2 nTPM
Prostate	18.9 nTPM

Fibroblasts	42.0 nTPM
Ovary	67.6 nTPM
Lung	62.6 nTPM
Heart muscle	51.1 nTPM
Skeletal muscle	46.2 nTPM
Breast	44.4 nTPM
Placenta	43.1 nTPM
Adipose tissue	40.9 nTPM
Esophagus	38.7 nTPM
Skin	28.3 nTPM
Stomach	25.3 nTPM
Prostate	13.5 nTPM

Intestinal goblet cells	31.3 nTPM
Small intestine	34.0 nTPM
Colon	30.7 nTPM
Rectum	29.3 nTPM

Macrophages	34.4 nTPM
Stomach	52.7 nTPM
Skeletal muscle	45.4 nTPM
Endometrium	44.1 nTPM
Ovary	43.9 nTPM
Bone marrow	40.0 nTPM
Adipose tissue	39.4 nTPM
Lung	37.0 nTPM
Breast	37.0 nTPM
Spleen	36.3 nTPM
Testis	30.8 nTPM
PBMC	27.3 nTPM
Pancreas	25.5 nTPM
Esophagus	23.6 nTPM
Kidney	21.1 nTPM
Prostate	12.6 nTPM

Paneth cells	16.4 nTPM
Rectum	23.7 nTPM
Small intestine	18.8 nTPM
Colon	6.5 nTPM

Plasma cells	150.1 nTPM
Stomach	200.1 nTPM
Spleen	174.5 nTPM
Esophagus	172.5 nTPM
Bone marrow	120.3 nTPM
Adipose tissue	83.2 nTPM

Respiratory ciliated cells	27.3 nTPM
Lung	35.0 nTPM
Bronchus	19.6 nTPM

Smooth muscle cells	39.8 nTPM
Ovary	58.4 nTPM
Heart muscle	57.9 nTPM
Endometrium	53.2 nTPM
Breast	42.7 nTPM
Esophagus	41.9 nTPM
Skeletal muscle	39.4 nTPM
Adipose tissue	38.8 nTPM
Pancreas	36.1 nTPM
Bronchus	26.5 nTPM
Skin	25.8 nTPM
Prostate	17.2 nTPM

T-cells	41.8 nTPM
Ovary	53.4 nTPM
Adipose tissue	51.9 nTPM
Breast	50.8 nTPM
Endometrium	48.9 nTPM
Skeletal muscle	48.8 nTPM
Lymph node	48.1 nTPM
Lung	47.1 nTPM
Skin	41.4 nTPM
Colon	41.3 nTPM
Bone marrow	40.8 nTPM
Kidney	39.7 nTPM
Spleen	38.2 nTPM
Stomach	37.2 nTPM
PBMC	35.7 nTPM
Esophagus	32.8 nTPM
Liver	30.3 nTPM
Prostate	23.6 nTPM

Basal keratinocytes	22.2 nTPM
Skin	22.2 nTPM

Basal prostatic cells	25.1 nTPM
Prostate	25.1 nTPM

Basal squamous epithelial cells	33.0 nTPM
Esophagus	33.0 nTPM

Cholangiocytes	21.5 nTPM
Liver	21.5 nTPM

Undifferentiated cells	31.6 nTPM
Small intestine	32.1 nTPM
Rectum	31.9 nTPM
Colon	30.6 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