Single cell type - OTUD1 - The Human Protein Atlas

OTUD1

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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).	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.	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.	Monocytes - Innate 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.	Cell type enhanced (Skeletal myocytes, Monocytes, Langerhans cells, Macrophages)
Tau specificity scoreⁱ Tau specificity score is a numerical indicator of the specificity of the gene expression across cells or tissues. The value ranges from 0 and 1, where 0 indicates identical expression across all cells/tissue types, while 1 indicates expression in a single cell/tissue type.	0.57
Brain cluster specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell cluster types based on snRNA-seq data from brain samples. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. "cell type" refer to one of the 34 cluster names used to summarize the 2.5 million cells included in the brain cell representation.	Cell type enhanced (Central nervous system macrophage)
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.	Low immune cell specificity
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); neXtProt protein existence (neXtProt evidence);and a Human Protein Atlas antibody- or RNA based score (HPA evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable.	Evidence at protein level

ASSAYSⁱ

SINGLE CELL TYPESⁱ A summary of normalized 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 RNA single cell type specificity: Cell type enhanced (Skeletal myocytes, Monocytes, Langerhans cells, Macrophages)

TISSUE CELL TYPEⁱ The tissue cell type section provides a cell type specificity prediction for all protein coding genes. More information on the data available can be found here and a description of the analysis here.
	Core cell typesⁱ The core cell type table displays data for a panel of eight cell types that are found in many tissues. Colored dots indicate that the selected gene has core cell type specificity in the indicated tissue. Grey dots indicate that cell type is present within that tissue, but the selected gene is not predicted to be enriched there. Category Alphabetical Enrichment Tissue specific cell typesⁱ This plot shows the enrichment score of the selected gene in all non-core cell types found within the profiled tissues, allowing comparisons between different cell types within different tissues. An enlarged symbol indicates classification of the gene as cell type enriched in the corresponding cell type.

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Cell type enhanced (Central nervous system macrophage)

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
HPA datasetⁱ The resulting transcript expression values calculated as nTPM, resulting from the internal normalization pipeline for 18 immune cell types and total peripheral blood mononuclear cells (PBMC). Lineage Expression Alphabetical Immune cell type specificity: Low immune cell specificity
Monaco datasetⁱ The transcript expression values (nTPM) resulting from the internal normalization pipeline are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SINGLE CELL TYPE

OTUD1 is part of cluster 29 Monocytes - Innate immune response with confidenceⁱ 0.95
447 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
VENTX	VENT homeobox	0.7230	29
IL10	Interleukin 10	0.6901	29
OR2B11	Olfactory receptor family 2 subfamily B member 11	0.6844	29
NLRP3	NLR family pyrin domain containing 3	0.6817	29
FGL2	Fibrinogen like 2	0.6703	29
IL1B	Interleukin 1 beta	0.6373	29
VEGFA	Vascular endothelial growth factor A	0.6332	29
CCRL2	C-C motif chemokine receptor like 2	0.6311	29
IL1A	Interleukin 1 alpha	0.6299	29
EREG	Epiregulin	0.6190	29
ZFAND5	Zinc finger AN1-type containing 5	0.6160	29
RASGEF1B	RasGEF domain family member 1B	0.6110	29
C5AR2	Complement C5a receptor 2	0.6041	29
IER5	Immediate early response 5	0.6011	80
FCGR2C	Fc gamma receptor IIc (gene/pseudogene)	0.5950	58

IMMUNE CELLS

OTUD1 is part of cluster 20 Non-specific - DNA binding with confidenceⁱ 1
266 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
PREX1	Phosphatidylinositol-3,4,5-trisphosphate dependent Rac exchange factor 1	0.9762	28
MRPL44	Mitochondrial ribosomal protein L44	0.9524	40
BLOC1S2	Biogenesis of lysosomal organelles complex 1 subunit 2	0.9048	20
FAS	Fas cell surface death receptor	0.9048	35
IFIH1	Interferon induced with helicase C domain 1	0.8810	40
TANK	TRAF family member associated NFKB activator	0.8810	28
NT5C3A	5'-nucleotidase, cytosolic IIIA	0.8571	20
ARSG	Arylsulfatase G	0.8571	35
LRP8	LDL receptor related protein 8	0.8571	20
RSPRY1	Ring finger and SPRY domain containing 1	0.8571	35
BNIP3L	BCL2 interacting protein 3 like	0.8571	35
HMGB1P1	High mobility group box 1 pseudogene 1	0.8333	35
PTK2B	Protein tyrosine kinase 2 beta	0.8333	2
OR7C1	Olfactory receptor family 7 subfamily C member 1	0.8333	20
VPS13B	Vacuolar protein sorting 13 homolog B	0.8333	2

Adipocytes	16.0 nTPM
Adipose tissue	17.6 nTPM
Breast	14.4 nTPM

Alveolar cells type 1	66.1 nTPM
Lung	66.1 nTPM

Alveolar cells type 2	16.4 nTPM
Lung	16.4 nTPM

Astrocytes	3.1 nTPM
Brain	3.1 nTPM

B-cells	79.2 nTPM
Adipose tissue	196.7 nTPM
Thymus	186.8 nTPM
Skin	128.7 nTPM
Salivary gland	121.5 nTPM
Lung	85.8 nTPM
Liver	53.1 nTPM
Stomach	52.7 nTPM
Spleen	50.7 nTPM
Lymph node	42.7 nTPM
Kidney	41.6 nTPM
Esophagus	41.3 nTPM
Bone marrow	14.6 nTPM
PBMC	13.9 nTPM

Ciliated cells	22.9 nTPM
Endometrium	34.5 nTPM
Fallopian tube	29.1 nTPM
Lung	19.2 nTPM
Bronchus	8.9 nTPM

Club cells	10.6 nTPM
Lung	15.9 nTPM
Prostate	11.1 nTPM
Bronchus	4.9 nTPM

Endothelial cells	17.9 nTPM
Lung	36.0 nTPM
Heart muscle	32.0 nTPM
Skeletal muscle	27.9 nTPM
Endometrium	25.7 nTPM
Salivary gland	22.4 nTPM
Esophagus	22.0 nTPM
Breast	22.0 nTPM
Skin	19.3 nTPM
Tongue	16.2 nTPM
Prostate	15.9 nTPM
Vascular	15.4 nTPM
Liver	15.1 nTPM
Thymus	14.2 nTPM
Placenta	11.4 nTPM
Fallopian tube	8.7 nTPM
Testis	7.9 nTPM
Ovary	7.0 nTPM
Pancreas	2.6 nTPM

Enteroendocrine cells	31.6 nTPM
Colon	81.1 nTPM
Small intestine	10.3 nTPM
Rectum	3.4 nTPM

Fibroblasts	21.9 nTPM
Heart muscle	39.8 nTPM
Adipose tissue	30.3 nTPM
Skin	29.3 nTPM
Fallopian tube	28.5 nTPM
Esophagus	28.1 nTPM
Thymus	25.8 nTPM
Vascular	25.8 nTPM
Stomach	21.6 nTPM
Liver	20.2 nTPM
Skeletal muscle	20.1 nTPM
Salivary gland	19.9 nTPM
Prostate	19.8 nTPM
Lung	17.2 nTPM
Breast	12.3 nTPM
Placenta	8.5 nTPM
Pancreas	2.5 nTPM

Granulocytes	13.2 nTPM
Lung	21.7 nTPM
Tongue	9.7 nTPM
Fallopian tube	8.3 nTPM

Intestinal goblet cells	73.0 nTPM
Colon	168.1 nTPM
Rectum	27.8 nTPM
Small intestine	23.2 nTPM

Lymphatic endothelial cells	13.0 nTPM
Fallopian tube	26.0 nTPM
Ovary	0.0 nTPM

Macrophages	157.8 nTPM
Fallopian tube	682.1 nTPM
Endometrium	290.9 nTPM
Adipose tissue	262.4 nTPM
Skin	255.2 nTPM
Vascular	210.4 nTPM
Salivary gland	205.0 nTPM
Breast	176.0 nTPM
Prostate	165.2 nTPM
Testis	112.8 nTPM
Skeletal muscle	112.1 nTPM
Spleen	101.3 nTPM
Lung	79.9 nTPM
Stomach	77.2 nTPM
Tongue	74.8 nTPM
Kidney	59.3 nTPM
Esophagus	57.8 nTPM
Thymus	40.0 nTPM
Bone marrow	21.3 nTPM
Pancreas	14.4 nTPM

Paneth cells	20.1 nTPM
Colon	39.8 nTPM
Rectum	20.4 nTPM
Small intestine	0.0 nTPM

Basal keratinocytes	23.7 nTPM
Skin	33.2 nTPM
Tongue	14.1 nTPM

Basal prostatic cells	12.7 nTPM
Prostate	12.7 nTPM

Basal respiratory cells	4.5 nTPM
Bronchus	4.5 nTPM

Basal squamous epithelial cells	21.1 nTPM
Esophagus	21.1 nTPM

Plasma cells	74.0 nTPM
Salivary gland	189.4 nTPM
Stomach	104.3 nTPM
Thymus	100.7 nTPM
Fallopian tube	50.5 nTPM
Liver	47.6 nTPM
Spleen	47.4 nTPM
Esophagus	41.6 nTPM
Bone marrow	10.6 nTPM

Schwann cells	82.2 nTPM
Adipose tissue	184.7 nTPM
Esophagus	47.9 nTPM
Vascular	14.1 nTPM

Serous glandular cells	9.9 nTPM
Salivary gland	15.3 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	17.8 nTPM
Skeletal muscle	26.1 nTPM
Endometrium	25.0 nTPM
Adipose tissue	24.7 nTPM
Fallopian tube	21.4 nTPM
Liver	20.8 nTPM
Breast	20.3 nTPM
Skin	18.9 nTPM
Esophagus	18.0 nTPM
Lung	16.5 nTPM
Tongue	16.5 nTPM
Thymus	15.2 nTPM
Salivary gland	14.6 nTPM
Prostate	14.0 nTPM
Vascular	13.3 nTPM
Ovary	12.4 nTPM
Placenta	7.9 nTPM

Suprabasal keratinocytes	20.1 nTPM
Skin	29.7 nTPM
Tongue	10.6 nTPM

T-cells	20.9 nTPM
Adipose tissue	40.3 nTPM
Thymus	39.4 nTPM
Salivary gland	34.4 nTPM
Tongue	31.3 nTPM
Vascular	29.3 nTPM
Prostate	26.4 nTPM
Skin	25.6 nTPM
Lung	24.9 nTPM
Fallopian tube	24.4 nTPM
Skeletal muscle	20.0 nTPM
Esophagus	19.5 nTPM
Breast	18.5 nTPM
Endometrium	17.6 nTPM
Colon	17.5 nTPM
Lymph node	14.0 nTPM
Kidney	12.4 nTPM
Stomach	10.5 nTPM
Liver	10.1 nTPM
Spleen	9.1 nTPM
PBMC	7.4 nTPM
Bone marrow	5.5 nTPM

Undifferentiated cells	14.7 nTPM
Colon	24.4 nTPM
Rectum	13.5 nTPM
Small intestine	6.2 nTPM

Amygdala excitatory	6.1 nTPM
Hippocampus	8.0 nTPM
Cerebral cortex	6.9 nTPM
Basal ganglia	6.2 nTPM
Hypothalamus	5.5 nTPM
Amygdala	5.3 nTPM
Thalamus	5.0 nTPM

Astrocyte	5.0 nTPM
Spinal cord	7.1 nTPM
Basal ganglia	6.4 nTPM
Cerebellum	5.4 nTPM
Cerebral cortex	5.4 nTPM
Pons	5.0 nTPM
Hypothalamus	4.9 nTPM
Midbrain	4.7 nTPM
Thalamus	4.5 nTPM
Medulla oblongata	4.2 nTPM
Hippocampus	4.0 nTPM
Amygdala	3.7 nTPM

Bergmann glia	5.5 nTPM
Medulla oblongata	6.4 nTPM
Cerebellum	5.7 nTPM
Pons	4.3 nTPM

Central nervous system macrophage	34.7 nTPM
Basal ganglia	53.4 nTPM
Cerebellum	45.4 nTPM
Cerebral cortex	43.6 nTPM
Spinal cord	41.2 nTPM
Medulla oblongata	31.7 nTPM
Hypothalamus	31.0 nTPM
Midbrain	31.0 nTPM
Hippocampus	30.3 nTPM
Pons	29.6 nTPM
Thalamus	26.2 nTPM
Amygdala	18.7 nTPM

Cerebellar inhibitory	8.4 nTPM
Spinal cord	16.5 nTPM
Pons	6.9 nTPM
Cerebellum	6.5 nTPM
Medulla oblongata	6.3 nTPM
Midbrain	5.6 nTPM

Cge interneuron	7.5 nTPM
Cerebral cortex	8.5 nTPM
Basal ganglia	7.9 nTPM
Hippocampus	7.9 nTPM
Thalamus	7.5 nTPM
Amygdala	7.2 nTPM
Hypothalamus	6.9 nTPM
Midbrain	6.8 nTPM

Choroid plexus epithelial cell	3.4 nTPM
Medulla oblongata	5.0 nTPM
Basal ganglia	2.9 nTPM
Hippocampus	2.8 nTPM
Thalamus	2.7 nTPM

Committed oligodendrocyte precursor	4.8 nTPM
Medulla oblongata	9.0 nTPM
Spinal cord	7.4 nTPM
Amygdala	7.3 nTPM
Hypothalamus	6.8 nTPM
Basal ganglia	5.5 nTPM
Hippocampus	4.4 nTPM
Thalamus	4.1 nTPM
Pons	3.5 nTPM
Cerebral cortex	2.5 nTPM
Midbrain	2.5 nTPM
Cerebellum	0.0 nTPM

Deep-layer corticothalamic and 6b	6.8 nTPM
Hypothalamus	8.5 nTPM
Basal ganglia	7.5 nTPM
Cerebral cortex	7.2 nTPM
Amygdala	7.1 nTPM
Hippocampus	6.0 nTPM
Midbrain	4.4 nTPM

Deep-layer intratelencephalic	6.0 nTPM
Hypothalamus	6.9 nTPM
Cerebral cortex	6.1 nTPM
Hippocampus	6.1 nTPM
Amygdala	5.5 nTPM
Basal ganglia	5.3 nTPM

Deep-layer near-projecting	6.3 nTPM
Hippocampus	8.1 nTPM
Basal ganglia	6.7 nTPM
Cerebral cortex	6.4 nTPM
Hypothalamus	6.4 nTPM
Amygdala	3.9 nTPM

Eccentric medium spiny neuron	8.0 nTPM
Thalamus	9.1 nTPM
Hippocampus	8.3 nTPM
Hypothalamus	8.3 nTPM
Amygdala	7.5 nTPM
Basal ganglia	7.5 nTPM
Cerebral cortex	7.2 nTPM

Endothelial cell	11.2 nTPM
Hypothalamus	23.6 nTPM
Pons	18.7 nTPM
Medulla oblongata	16.4 nTPM
Amygdala	14.5 nTPM
Cerebellum	10.1 nTPM
Basal ganglia	9.3 nTPM
Hippocampus	9.0 nTPM
Thalamus	9.0 nTPM
Cerebral cortex	5.8 nTPM
Midbrain	3.8 nTPM
Spinal cord	3.5 nTPM