Single cell type - USP40 - 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.	USP40
Gene descriptionⁱ Full gene name according to HGNC.	Ubiquitin specific peptidase 40
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	Astrocytes - Nervous system maintenance (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 (Oligodendrocytes, Astrocytes)
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 some
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 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: Cell type enhanced (Oligodendrocytes, Astrocytes)

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

USP40 is part of cluster 64 Astrocytes - Nervous system maintenance with confidenceⁱ 1
169 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
TRIM66	Tripartite motif containing 66	0.5421	64
PLEKHA7	Pleckstrin homology domain containing A7	0.5340	64
PIDD1	P53-induced death domain protein 1	0.5245	47
SLX4IP	SLX4 interacting protein	0.5127	42
PAN2	Poly(A) specific ribonuclease subunit PAN2	0.5066	52
ANO8	Anoctamin 8	0.5062	64
GRIN2C	Glutamate ionotropic receptor NMDA type subunit 2C	0.5061	64
FAN1	FANCD2 and FANCI associated nuclease 1	0.5027	42
ATXN2	Ataxin 2	0.5024	52
PLXNB3	Plexin B3	0.4933	64
TTC23	Tetratricopeptide repeat domain 23	0.4917	52
MEGF10	Multiple EGF like domains 10	0.4889	64
NRBP2	Nuclear receptor binding protein 2	0.4754	64
ATP13A4	ATPase 13A4	0.4730	64
GPC5	Glypican 5	0.4685	64

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	11.8 nTPM
Adipose tissue	12.8 nTPM
Breast	10.8 nTPM

Alveolar cells type 1	32.1 nTPM
Lung	32.1 nTPM

Alveolar cells type 2	35.5 nTPM
Lung	35.5 nTPM

B-cells	7.9 nTPM
Breast	12.1 nTPM
Lymph node	11.7 nTPM
Bone marrow	9.8 nTPM
Stomach	8.6 nTPM
Spleen	8.3 nTPM
Liver	8.0 nTPM
Adipose tissue	6.6 nTPM
PBMC	5.7 nTPM
Kidney	4.8 nTPM
Colon	3.2 nTPM

Basal keratinocytes	7.4 nTPM
Skin	7.4 nTPM

Dendritic cells	6.7 nTPM
PBMC	12.0 nTPM
Adipose tissue	4.5 nTPM
Breast	3.6 nTPM

Endothelial cells	11.1 nTPM
Heart muscle	23.0 nTPM
Esophagus	16.4 nTPM
Liver	15.6 nTPM
Endometrium	13.6 nTPM
Skeletal muscle	12.9 nTPM
Breast	12.3 nTPM
Ovary	11.3 nTPM
Eye	10.5 nTPM
Placenta	8.0 nTPM
Testis	8.0 nTPM
Pancreas	7.7 nTPM
Lung	6.2 nTPM
Prostate	5.6 nTPM
Skin	5.0 nTPM

Fibroblasts	11.9 nTPM
Lung	20.1 nTPM
Skeletal muscle	17.9 nTPM
Esophagus	17.4 nTPM
Breast	13.8 nTPM
Ovary	13.6 nTPM
Adipose tissue	12.6 nTPM
Stomach	8.9 nTPM
Placenta	8.7 nTPM
Heart muscle	8.0 nTPM
Skin	4.9 nTPM
Prostate	4.6 nTPM

Intestinal goblet cells	10.9 nTPM
Small intestine	12.9 nTPM
Colon	10.0 nTPM
Rectum	10.0 nTPM

Macrophages	9.1 nTPM
Ovary	17.4 nTPM
Lung	12.7 nTPM
Esophagus	12.6 nTPM
Skeletal muscle	12.5 nTPM
Bone marrow	10.0 nTPM
Testis	9.8 nTPM
Adipose tissue	8.9 nTPM
Stomach	8.8 nTPM
Breast	8.0 nTPM
Endometrium	7.9 nTPM
Pancreas	7.7 nTPM
Spleen	7.2 nTPM
Prostate	6.9 nTPM
Kidney	6.1 nTPM
PBMC	0.0 nTPM

Paneth cells	12.6 nTPM
Small intestine	18.8 nTPM
Colon	9.9 nTPM
Rectum	9.2 nTPM

Plasma cells	10.9 nTPM
Bone marrow	14.8 nTPM
Stomach	14.5 nTPM
Spleen	11.1 nTPM
Adipose tissue	7.8 nTPM
Esophagus	6.1 nTPM

Respiratory ciliated cells	21.0 nTPM
Lung	26.2 nTPM
Bronchus	15.9 nTPM

Smooth muscle cells	10.6 nTPM
Skeletal muscle	16.2 nTPM
Adipose tissue	15.4 nTPM
Esophagus	14.0 nTPM
Endometrium	12.3 nTPM
Heart muscle	11.3 nTPM
Pancreas	9.6 nTPM
Skin	8.7 nTPM
Ovary	8.5 nTPM
Breast	8.1 nTPM
Prostate	7.5 nTPM
Bronchus	4.7 nTPM

T-cells	5.5 nTPM
Esophagus	13.1 nTPM
Lung	12.2 nTPM
Lymph node	9.0 nTPM
Stomach	6.3 nTPM
Spleen	6.0 nTPM
Kidney	5.5 nTPM
Endometrium	5.3 nTPM
Bone marrow	5.2 nTPM
Prostate	4.7 nTPM
Skeletal muscle	4.4 nTPM
PBMC	4.1 nTPM
Adipose tissue	4.1 nTPM
Breast	3.9 nTPM
Liver	3.5 nTPM
Colon	3.3 nTPM
Ovary	2.2 nTPM
Skin	1.4 nTPM

Collecting duct cells	16.5 nTPM
Kidney	16.5 nTPM

Cone photoreceptor cells	25.0 nTPM
Eye	25.0 nTPM

Cytotrophoblasts	21.2 nTPM
Placenta	21.2 nTPM

Early spermatids	8.4 nTPM
Testis	8.4 nTPM

Undifferentiated cells	12.1 nTPM
Small intestine	14.1 nTPM
Rectum	12.7 nTPM
Colon	9.5 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