Single cell type - GPATCH4 - 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.	GPATCH4
Gene descriptionⁱ Full gene name according to HGNC.	G-patch domain containing 4
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	Non-specific - Basic cellular processes (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	Low cell type specificity
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	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: Low cell type specificity

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

GPATCH4 is part of cluster 39 Non-specific - Basic cellular processes with confidenceⁱ 0.99
586 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
PUS1	Pseudouridine synthase 1	0.8105	39
PPAN	Peter pan homolog	0.7204	39
MRTO4	MRT4 homolog, ribosome maturation factor	0.7057	39
BYSL	Bystin like	0.7000	39
NOP16	NOP16 nucleolar protein	0.6923	39
TOMM40	Translocase of outer mitochondrial membrane 40	0.6869	39
NOM1	Nucleolar protein with MIF4G domain 1	0.6821	39
NOC2L	NOC2 like nucleolar associated transcriptional repressor	0.6686	39
DKC1	Dyskerin pseudouridine synthase 1	0.6404	39
DPH2	Diphthamide biosynthesis 2	0.6383	39
GRWD1	Glutamate rich WD repeat containing 1	0.6353	39
NIFK	Nucleolar protein interacting with the FHA domain of MKI67	0.6151	39
RRP1	Ribosomal RNA processing 1	0.6130	39
DDX21	DExD-box helicase 21	0.6069	39
ZNF593	Zinc finger protein 593	0.6040	39

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	17.0 nTPM
Breast	21.1 nTPM
Adipose tissue	12.9 nTPM

Alveolar cells type 1	32.1 nTPM
Lung	32.1 nTPM

Alveolar cells type 2	38.3 nTPM
Lung	38.3 nTPM

Astrocytes	5.2 nTPM
Brain	5.2 nTPM

B-cells	36.0 nTPM
Liver	57.1 nTPM
Colon	49.5 nTPM
Spleen	46.8 nTPM
Kidney	38.1 nTPM
Adipose tissue	35.6 nTPM
Stomach	34.9 nTPM
PBMC	32.9 nTPM
Breast	22.8 nTPM
Bone marrow	22.1 nTPM
Lymph node	20.4 nTPM

Dendritic cells	19.5 nTPM
Adipose tissue	23.5 nTPM
Breast	22.9 nTPM
PBMC	12.0 nTPM

Endothelial cells	32.5 nTPM
Lung	62.4 nTPM
Prostate	51.6 nTPM
Pancreas	46.4 nTPM
Skin	37.6 nTPM
Placenta	37.5 nTPM
Testis	32.9 nTPM
Endometrium	31.8 nTPM
Esophagus	28.4 nTPM
Breast	28.2 nTPM
Ovary	25.9 nTPM
Skeletal muscle	20.8 nTPM
Heart muscle	18.7 nTPM
Eye	17.0 nTPM
Liver	16.5 nTPM

Fibroblasts	29.0 nTPM
Lung	59.2 nTPM
Prostate	55.7 nTPM
Ovary	43.1 nTPM
Skin	28.8 nTPM
Skeletal muscle	27.2 nTPM
Placenta	23.0 nTPM
Stomach	20.8 nTPM
Adipose tissue	20.6 nTPM
Heart muscle	18.7 nTPM
Breast	11.4 nTPM
Esophagus	10.3 nTPM

Intestinal goblet cells	26.1 nTPM
Colon	37.1 nTPM
Small intestine	23.3 nTPM
Rectum	17.9 nTPM

Macrophages	19.0 nTPM
Lung	42.5 nTPM
Endometrium	32.2 nTPM
Pancreas	25.5 nTPM
Testis	25.0 nTPM
Prostate	21.8 nTPM
Ovary	20.2 nTPM
Breast	19.7 nTPM
Kidney	19.6 nTPM
Skeletal muscle	18.0 nTPM
Spleen	17.6 nTPM
Adipose tissue	12.6 nTPM
Esophagus	12.6 nTPM
Stomach	8.8 nTPM
Bone marrow	8.7 nTPM
PBMC	0.0 nTPM

Paneth cells	17.5 nTPM
Rectum	24.5 nTPM
Small intestine	15.0 nTPM
Colon	13.2 nTPM

Plasma cells	23.8 nTPM
Spleen	48.4 nTPM
Bone marrow	36.2 nTPM
Stomach	14.7 nTPM
Adipose tissue	13.6 nTPM
Esophagus	6.1 nTPM

Respiratory ciliated cells	14.9 nTPM
Lung	17.5 nTPM
Bronchus	12.3 nTPM

Smooth muscle cells	45.4 nTPM
Prostate	82.2 nTPM
Pancreas	73.1 nTPM
Skin	56.2 nTPM
Bronchus	48.3 nTPM
Skeletal muscle	45.5 nTPM
Ovary	36.0 nTPM
Breast	35.3 nTPM
Endometrium	33.9 nTPM
Adipose tissue	33.8 nTPM
Esophagus	31.0 nTPM
Heart muscle	24.6 nTPM

T-cells	26.3 nTPM
Lung	50.1 nTPM
PBMC	39.0 nTPM
Kidney	32.9 nTPM
Colon	32.3 nTPM
Stomach	29.0 nTPM
Liver	28.4 nTPM
Endometrium	28.3 nTPM
Bone marrow	26.5 nTPM
Spleen	25.4 nTPM
Lymph node	23.9 nTPM
Adipose tissue	23.8 nTPM
Skin	22.6 nTPM
Esophagus	19.7 nTPM
Skeletal muscle	18.7 nTPM
Breast	17.5 nTPM
Ovary	15.6 nTPM
Prostate	14.2 nTPM

Basal keratinocytes	73.7 nTPM
Skin	73.7 nTPM

Basal prostatic cells	65.9 nTPM
Prostate	65.9 nTPM

Basal squamous epithelial cells	26.2 nTPM
Esophagus	26.2 nTPM

Cholangiocytes	25.8 nTPM
Liver	25.8 nTPM

Undifferentiated cells	43.6 nTPM
Colon	69.3 nTPM
Small intestine	35.7 nTPM
Rectum	25.8 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