Single cell type - OTUD1 - 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.	OTUD1
Gene descriptionⁱ Full gene name according to HGNC.	OTU deubiquitinase 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes
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.	1

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	Myocytes - 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 (Langerhans cells, Cardiomyocytes, Macrophages)
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	Cell line enhanced (CAPAN-2, HaCaT, SiHa)
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 (Langerhans cells, Cardiomyocytes, Macrophages)

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

OTUD1 is part of cluster 37 Myocytes - Muscle contraction with confidenceⁱ 1
107 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
MYLPF	Myosin light chain, phosphorylatable, fast skeletal muscle	0.7262	37
MYH2	Myosin heavy chain 2	0.7260	37
ATP1B4	ATPase Na+/K+ transporting family member beta 4	0.7254	37
TNNI1	Troponin I1, slow skeletal type	0.7251	37
MYH1	Myosin heavy chain 1	0.7249	37
TNNI2	Troponin I2, fast skeletal type	0.7216	37
MYBPC2	Myosin binding protein C2	0.7216	37
MYL1	Myosin light chain 1	0.7212	37
NEB	Nebulin	0.7206	37
MYOZ1	Myozenin 1	0.7195	37
CACNG1	Calcium voltage-gated channel auxiliary subunit gamma 1	0.7182	37
PRKAG3	Protein kinase AMP-activated non-catalytic subunit gamma 3	0.7181	37
ATP2A1	ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1	0.7176	37
CALML6	Calmodulin like 6	0.7176	37
IDI2	Isopentenyl-diphosphate delta isomerase 2	0.7171	37

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	17.3 nTPM
Adipose tissue	19.7 nTPM
Breast	15.0 nTPM

Alveolar cells type 1	67.3 nTPM
Lung	67.3 nTPM

Alveolar cells type 2	11.5 nTPM
Lung	11.5 nTPM

Astrocytes	3.3 nTPM
Brain	3.3 nTPM

B-cells	55.9 nTPM
Adipose tissue	216.0 nTPM
Colon	67.1 nTPM
Breast	64.1 nTPM
Liver	57.7 nTPM
Kidney	47.6 nTPM
Stomach	28.6 nTPM
Spleen	27.6 nTPM
Lymph node	24.6 nTPM
PBMC	15.7 nTPM
Bone marrow	9.8 nTPM

Dendritic cells	9.6 nTPM
Adipose tissue	19.4 nTPM
Breast	9.5 nTPM
PBMC	0.0 nTPM

Endothelial cells	25.6 nTPM
Eye	130.2 nTPM
Heart muscle	35.2 nTPM
Skeletal muscle	34.8 nTPM
Endometrium	26.3 nTPM
Liver	23.8 nTPM
Skin	21.2 nTPM
Esophagus	17.6 nTPM
Breast	16.5 nTPM
Prostate	10.5 nTPM
Placenta	10.2 nTPM
Testis	9.5 nTPM
Ovary	9.4 nTPM
Lung	9.3 nTPM
Pancreas	3.9 nTPM

Fibroblasts	20.8 nTPM
Heart muscle	46.1 nTPM
Skin	34.0 nTPM
Adipose tissue	32.1 nTPM
Skeletal muscle	22.2 nTPM
Esophagus	21.9 nTPM
Stomach	20.8 nTPM
Prostate	18.2 nTPM
Breast	14.9 nTPM
Ovary	7.0 nTPM
Placenta	6.0 nTPM
Lung	5.6 nTPM

Intestinal goblet cells	77.9 nTPM
Colon	197.2 nTPM
Rectum	27.0 nTPM
Small intestine	9.4 nTPM

Macrophages	105.7 nTPM
Endometrium	302.4 nTPM
Adipose tissue	254.3 nTPM
Prostate	186.9 nTPM
Breast	156.0 nTPM
Testis	122.5 nTPM
Skeletal muscle	109.0 nTPM
Spleen	99.5 nTPM
Ovary	90.0 nTPM
Stomach	76.2 nTPM
Kidney	62.8 nTPM
Esophagus	53.5 nTPM
Lung	38.1 nTPM
Bone marrow	21.2 nTPM
Pancreas	12.8 nTPM
PBMC	0.0 nTPM

Paneth cells	16.3 nTPM
Rectum	21.1 nTPM
Colon	16.5 nTPM
Small intestine	11.3 nTPM

Plasma cells	50.0 nTPM
Stomach	94.5 nTPM
Adipose tissue	74.1 nTPM
Spleen	42.6 nTPM
Esophagus	30.7 nTPM
Bone marrow	8.2 nTPM

Respiratory ciliated cells	9.8 nTPM
Bronchus	11.0 nTPM
Lung	8.7 nTPM

Smooth muscle cells	19.4 nTPM
Heart muscle	32.1 nTPM
Skeletal muscle	29.6 nTPM
Endometrium	26.0 nTPM
Adipose tissue	24.3 nTPM
Breast	22.7 nTPM
Skin	22.0 nTPM
Prostate	21.3 nTPM
Ovary	18.2 nTPM
Esophagus	10.9 nTPM
Bronchus	3.8 nTPM
Pancreas	2.5 nTPM

T-cells	16.5 nTPM
Prostate	61.6 nTPM
Adipose tissue	41.8 nTPM
Skin	28.1 nTPM
Breast	20.5 nTPM
Ovary	20.1 nTPM
Endometrium	18.3 nTPM
Skeletal muscle	18.2 nTPM
Kidney	13.1 nTPM
Lung	10.6 nTPM
Colon	10.5 nTPM
Liver	10.0 nTPM
PBMC	7.8 nTPM
Lymph node	6.5 nTPM
Stomach	5.6 nTPM
Spleen	4.9 nTPM
Bone marrow	3.5 nTPM
Esophagus	0.0 nTPM

Basal keratinocytes	32.0 nTPM
Skin	32.0 nTPM

Basal prostatic cells	7.1 nTPM
Prostate	7.1 nTPM

Basal respiratory cells	5.0 nTPM
Bronchus	5.0 nTPM

Basal squamous epithelial cells	13.6 nTPM
Esophagus	13.6 nTPM

Undifferentiated cells	24.3 nTPM
Colon	50.6 nTPM
Rectum	14.6 nTPM
Small intestine	7.6 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