Single cell type - USP16 - 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.	USP16
Gene descriptionⁱ Full gene name according to HGNC.	Ubiquitin specific peptidase 16
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Enzymes Metabolic proteins Plasma proteins Potential drug targets
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.	4

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	Early spermatids - Spermatogenesis (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 (Early spermatids)
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 (Early spermatids)

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

USP16 is part of cluster 29 Early spermatids - Spermatogenesis with confidenceⁱ 1
337 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
DHX36	DEAH-box helicase 36	0.6714	29
SENP2	SUMO specific peptidase 2	0.6329	29
C16orf92	Chromosome 16 open reading frame 92	0.6142	23
CCDC27	Coiled-coil domain containing 27	0.5955	29
C9orf131	Chromosome 9 open reading frame 131	0.5920	23
RNF148	Ring finger protein 148	0.5893	29
UBXN4	UBX domain protein 4	0.5874	29
ACRV1	Acrosomal vesicle protein 1	0.5799	29
C2orf74	Chromosome 2 open reading frame 74	0.5789	29
ZC3H18	Zinc finger CCCH-type containing 18	0.5776	52
PDILT	Protein disulfide isomerase like, testis expressed	0.5752	29
KIAA1143	KIAA1143	0.5746	23
FAM186A	Family with sequence similarity 186 member A	0.5702	29
C1orf185	Chromosome 1 open reading frame 185	0.5700	23
LRRC52	Leucine rich repeat containing 52	0.5699	23

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	60.3 nTPM
Adipose tissue	68.0 nTPM
Breast	52.6 nTPM

Alveolar cells type 1	86.6 nTPM
Lung	86.6 nTPM

Alveolar cells type 2	91.9 nTPM
Lung	91.9 nTPM

Astrocytes	27.4 nTPM
Brain	27.4 nTPM

B-cells	114.4 nTPM
Adipose tissue	183.4 nTPM
Colon	134.2 nTPM
Lymph node	126.0 nTPM
Stomach	121.7 nTPM
Liver	114.9 nTPM
Spleen	103.1 nTPM
Kidney	95.3 nTPM
Breast	93.5 nTPM
Bone marrow	90.8 nTPM
PBMC	81.4 nTPM

Dendritic cells	108.2 nTPM
Adipose tissue	159.2 nTPM
Breast	89.7 nTPM
PBMC	75.7 nTPM

Endothelial cells	55.0 nTPM
Skeletal muscle	85.8 nTPM
Prostate	79.9 nTPM
Eye	74.4 nTPM
Endometrium	62.5 nTPM
Testis	59.8 nTPM
Placenta	59.1 nTPM
Ovary	56.0 nTPM
Breast	56.0 nTPM
Pancreas	42.5 nTPM
Liver	41.2 nTPM
Skin	41.2 nTPM
Esophagus	37.6 nTPM
Lung	37.4 nTPM
Heart muscle	36.3 nTPM

Fibroblasts	68.3 nTPM
Skeletal muscle	91.4 nTPM
Lung	81.5 nTPM
Placenta	77.5 nTPM
Adipose tissue	76.6 nTPM
Heart muscle	75.5 nTPM
Prostate	70.5 nTPM
Ovary	64.0 nTPM
Breast	61.5 nTPM
Skin	52.6 nTPM
Stomach	52.0 nTPM
Esophagus	48.0 nTPM

Intestinal goblet cells	100.4 nTPM
Colon	159.4 nTPM
Small intestine	77.1 nTPM
Rectum	64.8 nTPM

Macrophages	69.4 nTPM
Adipose tissue	115.0 nTPM
Skeletal muscle	102.5 nTPM
Endometrium	92.3 nTPM
Testis	82.5 nTPM
Lung	78.5 nTPM
Spleen	76.7 nTPM
Kidney	74.2 nTPM
Bone marrow	65.0 nTPM
Stomach	64.5 nTPM
Prostate	59.6 nTPM
Breast	56.8 nTPM
Ovary	55.8 nTPM
PBMC	40.9 nTPM
Pancreas	40.8 nTPM
Esophagus	36.2 nTPM

Paneth cells	99.2 nTPM
Colon	135.1 nTPM
Rectum	83.7 nTPM
Small intestine	78.9 nTPM

Plasma cells	106.8 nTPM
Spleen	136.9 nTPM
Stomach	132.4 nTPM
Adipose tissue	130.3 nTPM
Bone marrow	79.1 nTPM
Esophagus	55.5 nTPM

Respiratory ciliated cells	94.1 nTPM
Lung	122.4 nTPM
Bronchus	65.8 nTPM

Smooth muscle cells	83.2 nTPM
Skeletal muscle	127.7 nTPM
Prostate	100.6 nTPM
Heart muscle	99.5 nTPM
Bronchus	89.7 nTPM
Pancreas	82.3 nTPM
Esophagus	80.6 nTPM
Endometrium	74.7 nTPM
Adipose tissue	71.6 nTPM
Ovary	70.2 nTPM
Breast	64.9 nTPM
Skin	53.3 nTPM

T-cells	105.3 nTPM
Adipose tissue	166.3 nTPM
Colon	151.1 nTPM
Skeletal muscle	137.1 nTPM
Prostate	127.8 nTPM
Endometrium	125.0 nTPM
PBMC	124.8 nTPM
Lymph node	119.6 nTPM
Lung	118.5 nTPM
Breast	92.3 nTPM
Kidney	91.8 nTPM
Esophagus	85.2 nTPM
Bone marrow	81.3 nTPM
Spleen	81.2 nTPM
Liver	77.2 nTPM
Stomach	76.0 nTPM
Skin	73.2 nTPM
Ovary	62.3 nTPM

Basal keratinocytes	57.2 nTPM
Skin	57.2 nTPM

Basal prostatic cells	132.5 nTPM
Prostate	132.5 nTPM

Basal respiratory cells	68.9 nTPM
Bronchus	68.9 nTPM

Basal squamous epithelial cells	55.2 nTPM
Esophagus	55.2 nTPM

Undifferentiated cells	90.6 nTPM
Colon	118.4 nTPM
Small intestine	77.2 nTPM
Rectum	76.3 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