Single cell type - USP12 - 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.	USP12
Gene descriptionⁱ Full gene name according to HGNC.	Ubiquitin specific peptidase 12
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.	3

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	Macrophages - Immune response (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 (Langerhans 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 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 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 (Langerhans 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

USP12 is part of cluster 41 Macrophages - Immune response with confidenceⁱ 0.99
307 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
NFKB1	Nuclear factor kappa B subunit 1	0.6522	41
PPP1R15B	Protein phosphatase 1 regulatory subunit 15B	0.6232	41
AGO2	Argonaute RISC catalytic component 2	0.6046	44
ATP13A3	ATPase 13A3	0.5967	41
TNFRSF10B	TNF receptor superfamily member 10b	0.5900	44
JMJD1C	Jumonji domain containing 1C	0.5882	44
TP53BP2	Tumor protein p53 binding protein 2	0.5844	41
NUP153	Nucleoporin 153	0.5785	44
RIPK2	Receptor interacting serine/threonine kinase 2	0.5781	41
SERPINB9	Serpin family B member 9	0.5718	41
TSC22D2	TSC22 domain family member 2	0.5707	44
CLEC20A	C-type lectin domain containing 20A	0.5579	44
CHD2	Chromodomain helicase DNA binding protein 2	0.5556	44
KDM6B	Lysine demethylase 6B	0.5544	41
NFAT5	Nuclear factor of activated T cells 5	0.5504	44

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	54.2 nTPM
Adipose tissue	70.5 nTPM
Breast	37.8 nTPM

Alveolar cells type 1	28.9 nTPM
Lung	28.9 nTPM

Alveolar cells type 2	29.9 nTPM
Lung	29.9 nTPM

Astrocytes	19.6 nTPM
Brain	19.6 nTPM

B-cells	42.1 nTPM
Adipose tissue	136.9 nTPM
Colon	51.1 nTPM
Breast	46.8 nTPM
Lymph node	46.4 nTPM
Stomach	36.3 nTPM
Spleen	29.0 nTPM
Bone marrow	22.9 nTPM
Kidney	19.0 nTPM
PBMC	17.1 nTPM
Liver	15.2 nTPM

Dendritic cells	26.5 nTPM
Adipose tissue	46.4 nTPM
Breast	25.2 nTPM
PBMC	8.0 nTPM

Endothelial cells	42.0 nTPM
Prostate	114.8 nTPM
Skin	87.5 nTPM
Endometrium	55.0 nTPM
Skeletal muscle	49.9 nTPM
Eye	45.3 nTPM
Esophagus	41.3 nTPM
Breast	39.7 nTPM
Heart muscle	35.9 nTPM
Ovary	35.4 nTPM
Lung	24.9 nTPM
Placenta	17.0 nTPM
Liver	15.6 nTPM
Testis	14.2 nTPM
Pancreas	11.6 nTPM

Fibroblasts	34.2 nTPM
Prostate	70.9 nTPM
Skin	60.3 nTPM
Skeletal muscle	43.3 nTPM
Heart muscle	41.7 nTPM
Stomach	41.6 nTPM
Adipose tissue	34.6 nTPM
Lung	23.4 nTPM
Breast	20.6 nTPM
Esophagus	19.2 nTPM
Ovary	10.4 nTPM
Placenta	9.6 nTPM

Intestinal goblet cells	27.5 nTPM
Colon	27.9 nTPM
Rectum	27.6 nTPM
Small intestine	27.1 nTPM

Macrophages	47.8 nTPM
Adipose tissue	133.5 nTPM
Endometrium	123.7 nTPM
Prostate	86.0 nTPM
PBMC	81.8 nTPM
Skeletal muscle	56.7 nTPM
Esophagus	40.9 nTPM
Breast	40.5 nTPM
Stomach	26.4 nTPM
Lung	24.6 nTPM
Pancreas	20.4 nTPM
Spleen	19.7 nTPM
Testis	17.4 nTPM
Ovary	16.9 nTPM
Bone marrow	15.0 nTPM
Kidney	13.7 nTPM

Paneth cells	37.4 nTPM
Colon	72.5 nTPM
Rectum	28.5 nTPM
Small intestine	11.3 nTPM

Plasma cells	37.1 nTPM
Adipose tissue	67.7 nTPM
Esophagus	49.4 nTPM
Stomach	40.8 nTPM
Spleen	20.8 nTPM
Bone marrow	6.6 nTPM

Respiratory ciliated cells	12.2 nTPM
Lung	17.5 nTPM
Bronchus	6.8 nTPM

Smooth muscle cells	42.8 nTPM
Prostate	91.6 nTPM
Skin	88.3 nTPM
Esophagus	46.5 nTPM
Adipose tissue	45.5 nTPM
Skeletal muscle	40.9 nTPM
Breast	37.9 nTPM
Endometrium	35.9 nTPM
Heart muscle	34.4 nTPM
Ovary	27.6 nTPM
Pancreas	11.8 nTPM
Bronchus	10.4 nTPM

T-cells	27.2 nTPM
Adipose tissue	62.1 nTPM
Endometrium	57.9 nTPM
Skin	40.1 nTPM
Breast	36.5 nTPM
Skeletal muscle	33.9 nTPM
Prostate	33.1 nTPM
Colon	31.8 nTPM
Stomach	28.5 nTPM
Lymph node	26.8 nTPM
Spleen	22.0 nTPM
Ovary	17.8 nTPM
Esophagus	13.1 nTPM
Liver	13.0 nTPM
PBMC	12.8 nTPM
Kidney	12.3 nTPM
Bone marrow	12.3 nTPM
Lung	9.1 nTPM

Basal prostatic cells	29.4 nTPM
Prostate	29.4 nTPM

Basal respiratory cells	7.0 nTPM
Bronchus	7.0 nTPM

Basal squamous epithelial cells	34.7 nTPM
Esophagus	34.7 nTPM

Cholangiocytes	17.2 nTPM
Liver	17.2 nTPM

Undifferentiated cells	24.1 nTPM
Rectum	29.8 nTPM
Colon	21.3 nTPM
Small intestine	21.3 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