Single cell type - ITCH - 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.	ITCH
Gene descriptionⁱ Full gene name according to HGNC.	Itchy E3 ubiquitin protein ligase
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Enzymes Human disease related genes Metabolic 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.	10

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	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 (Oligodendrocytes, Late 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 (Oligodendrocytes, Late 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

ITCH is part of cluster 25 Spermatids - Spermatogenesis with confidenceⁱ 1
458 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
KPNA1	Karyopherin subunit alpha 1	0.5957	31
C1orf159	Chromosome 1 open reading frame 159	0.5205	31
PSME4	Proteasome activator subunit 4	0.5153	44
NRDC	Nardilysin convertase	0.5132	31
FAR1	Fatty acyl-CoA reductase 1	0.5062	25
TLK2	Tousled like kinase 2	0.5017	25
ALMS1	ALMS1 centrosome and basal body associated protein	0.5005	25
TRIP12	Thyroid hormone receptor interactor 12	0.4882	44
BMP8A	Bone morphogenetic protein 8a	0.4849	25
PAFAH1B1	Platelet activating factor acetylhydrolase 1b regulatory subunit 1	0.4673	25
ARAP2	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	0.4599	42
TBC1D23	TBC1 domain family member 23	0.4589	44
MEX3D	Mex-3 RNA binding family member D	0.4568	31
ZMYM2	Zinc finger MYM-type containing 2	0.4529	25
ZBTB26	Zinc finger and BTB domain containing 26	0.4500	25

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	26.1 nTPM
Adipose tissue	33.5 nTPM
Breast	18.6 nTPM

Alveolar cells type 1	12.8 nTPM
Lung	12.8 nTPM

Alveolar cells type 2	21.8 nTPM
Lung	21.8 nTPM

Astrocytes	56.5 nTPM
Brain	56.5 nTPM

B-cells	33.1 nTPM
Spleen	56.1 nTPM
Stomach	54.0 nTPM
Bone marrow	49.1 nTPM
Adipose tissue	41.6 nTPM
Lymph node	33.3 nTPM
Breast	29.4 nTPM
Colon	25.5 nTPM
Liver	19.7 nTPM
PBMC	12.9 nTPM
Kidney	9.5 nTPM

Dendritic cells	46.1 nTPM
Adipose tissue	69.1 nTPM
Breast	37.5 nTPM
PBMC	31.8 nTPM

Endothelial cells	20.7 nTPM
Lung	43.7 nTPM
Endometrium	24.8 nTPM
Skeletal muscle	24.8 nTPM
Heart muscle	24.3 nTPM
Ovary	21.2 nTPM
Eye	21.0 nTPM
Prostate	20.2 nTPM
Pancreas	19.3 nTPM
Liver	19.2 nTPM
Esophagus	16.5 nTPM
Skin	15.0 nTPM
Breast	13.8 nTPM
Testis	13.6 nTPM
Placenta	13.1 nTPM

Fibroblasts	24.2 nTPM
Lung	49.2 nTPM
Adipose tissue	36.8 nTPM
Heart muscle	29.3 nTPM
Skeletal muscle	23.8 nTPM
Stomach	23.7 nTPM
Breast	19.3 nTPM
Prostate	18.2 nTPM
Esophagus	18.1 nTPM
Skin	18.0 nTPM
Ovary	15.5 nTPM
Placenta	14.3 nTPM

Intestinal goblet cells	16.9 nTPM
Colon	21.5 nTPM
Rectum	15.7 nTPM
Small intestine	13.6 nTPM

Macrophages	31.4 nTPM
Adipose tissue	55.2 nTPM
Bone marrow	53.7 nTPM
Spleen	50.8 nTPM
Stomach	46.9 nTPM
Endometrium	35.6 nTPM
Lung	35.2 nTPM
Skeletal muscle	33.5 nTPM
Ovary	33.0 nTPM
Testis	30.3 nTPM
Esophagus	29.9 nTPM
Breast	18.2 nTPM
Kidney	18.1 nTPM
Pancreas	15.3 nTPM
Prostate	15.0 nTPM
PBMC	0.0 nTPM

Paneth cells	23.7 nTPM
Colon	29.6 nTPM
Small intestine	22.5 nTPM
Rectum	18.9 nTPM

Plasma cells	50.3 nTPM
Stomach	63.1 nTPM
Adipose tissue	62.5 nTPM
Spleen	58.2 nTPM
Bone marrow	49.4 nTPM
Esophagus	18.4 nTPM

Respiratory ciliated cells	23.5 nTPM
Lung	30.6 nTPM
Bronchus	16.5 nTPM

Smooth muscle cells	22.0 nTPM
Adipose tissue	40.5 nTPM
Heart muscle	27.9 nTPM
Skeletal muscle	26.5 nTPM
Endometrium	26.4 nTPM
Breast	20.3 nTPM
Prostate	20.0 nTPM
Skin	17.8 nTPM
Ovary	17.4 nTPM
Esophagus	17.0 nTPM
Pancreas	15.4 nTPM
Bronchus	13.3 nTPM

T-cells	30.8 nTPM
Adipose tissue	52.9 nTPM
Spleen	47.9 nTPM
Bone marrow	47.8 nTPM
Stomach	43.6 nTPM
Endometrium	41.6 nTPM
Skeletal muscle	39.8 nTPM
Liver	36.3 nTPM
PBMC	27.3 nTPM
Esophagus	26.2 nTPM
Lung	25.8 nTPM
Lymph node	25.3 nTPM
Breast	23.6 nTPM
Colon	22.3 nTPM
Skin	19.8 nTPM
Ovary	17.8 nTPM
Kidney	16.4 nTPM
Prostate	9.5 nTPM

Basal prostatic cells	23.9 nTPM
Prostate	23.9 nTPM

Basal respiratory cells	11.7 nTPM
Bronchus	11.7 nTPM

Basal squamous epithelial cells	25.6 nTPM
Esophagus	25.6 nTPM

Collecting duct cells	31.3 nTPM
Kidney	31.3 nTPM

Undifferentiated cells	11.9 nTPM
Rectum	14.7 nTPM
Colon	10.6 nTPM
Small intestine	10.4 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