Single cell type - HPS4 - 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.	HPS4
Gene descriptionⁱ Full gene name according to HGNC.	HPS4 biogenesis of lysosomal organelles complex 3 subunit 2
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Human disease related genes
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.	4

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 - Transcription (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 (Rod photoreceptor cells, Cone photoreceptor 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 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	Cell line enhanced (REH)
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 (Rod photoreceptor cells, Cone photoreceptor 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

HPS4 is part of cluster 52 Non-specific - Transcription with confidenceⁱ 1
611 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
TSEN2	TRNA splicing endonuclease subunit 2	0.6296	52
ZNF606	Zinc finger protein 606	0.6247	52
SHPRH	SNF2 histone linker PHD RING helicase	0.6209	52
ZNF16	Zinc finger protein 16	0.6125	52
TIGD1	Tigger transposable element derived 1	0.6039	52
DDX17	DEAD-box helicase 17	0.5969	52
ZFP14	ZFP14 zinc finger protein	0.5919	52
ANKS3	Ankyrin repeat and sterile alpha motif domain containing 3	0.5588	9
SLC2A11	Solute carrier family 2 member 11	0.5545	9
CARF	Calcium responsive transcription factor	0.5378	52
TYW5	TRNA-yW synthesizing protein 5	0.5377	9
ZNF502	Zinc finger protein 502	0.5357	20
IKBKB	Inhibitor of nuclear factor kappa B kinase subunit beta	0.5319	9
TRMT13	TRNA methyltransferase 13 homolog	0.5265	52
GGA2	Golgi associated, gamma adaptin ear containing, ARF binding protein 2	0.5214	57

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	16.6 nTPM
Adipose tissue	22.3 nTPM
Breast	11.0 nTPM

Alveolar cells type 1	12.8 nTPM
Lung	12.8 nTPM

Alveolar cells type 2	32.4 nTPM
Lung	32.4 nTPM

Astrocytes	28.7 nTPM
Brain	28.7 nTPM

B-cells	38.7 nTPM
Colon	60.7 nTPM
Adipose tissue	54.2 nTPM
PBMC	51.3 nTPM
Kidney	47.6 nTPM
Stomach	40.4 nTPM
Bone marrow	35.1 nTPM
Lymph node	31.2 nTPM
Spleen	30.4 nTPM
Liver	21.5 nTPM
Breast	14.7 nTPM

Dendritic cells	31.7 nTPM
PBMC	59.8 nTPM
Adipose tissue	22.0 nTPM
Breast	13.5 nTPM

Endothelial cells	18.6 nTPM
Testis	37.3 nTPM
Prostate	25.1 nTPM
Heart muscle	23.7 nTPM
Eye	23.5 nTPM
Lung	21.8 nTPM
Placenta	19.9 nTPM
Ovary	19.3 nTPM
Liver	18.3 nTPM
Skeletal muscle	16.7 nTPM
Endometrium	15.1 nTPM
Skin	12.4 nTPM
Esophagus	11.8 nTPM
Breast	11.8 nTPM
Pancreas	3.9 nTPM

Fibroblasts	14.1 nTPM
Adipose tissue	22.7 nTPM
Ovary	22.3 nTPM
Placenta	19.2 nTPM
Skeletal muscle	18.4 nTPM
Prostate	14.4 nTPM
Breast	13.7 nTPM
Esophagus	13.1 nTPM
Skin	11.4 nTPM
Stomach	7.4 nTPM
Lung	6.7 nTPM
Heart muscle	5.7 nTPM

Intestinal goblet cells	20.1 nTPM
Rectum	22.3 nTPM
Small intestine	20.8 nTPM
Colon	17.2 nTPM

Macrophages	19.1 nTPM
PBMC	40.9 nTPM
Ovary	35.5 nTPM
Lung	24.3 nTPM
Testis	22.6 nTPM
Prostate	19.5 nTPM
Breast	18.6 nTPM
Adipose tissue	17.7 nTPM
Esophagus	17.3 nTPM
Endometrium	16.7 nTPM
Skeletal muscle	16.1 nTPM
Stomach	14.7 nTPM
Bone marrow	12.5 nTPM
Kidney	12.0 nTPM
Spleen	10.4 nTPM
Pancreas	7.7 nTPM

Paneth cells	13.6 nTPM
Rectum	22.6 nTPM
Small intestine	15.0 nTPM
Colon	3.3 nTPM

Plasma cells	25.1 nTPM
Adipose tissue	32.8 nTPM
Stomach	31.7 nTPM
Bone marrow	23.0 nTPM
Spleen	19.5 nTPM
Esophagus	18.4 nTPM

Respiratory ciliated cells	28.1 nTPM
Bronchus	28.5 nTPM
Lung	27.7 nTPM

Smooth muscle cells	12.2 nTPM
Ovary	19.9 nTPM
Adipose tissue	19.1 nTPM
Skeletal muscle	15.9 nTPM
Breast	14.6 nTPM
Endometrium	13.1 nTPM
Prostate	10.6 nTPM
Pancreas	10.1 nTPM
Heart muscle	9.5 nTPM
Skin	9.5 nTPM
Bronchus	6.8 nTPM
Esophagus	4.6 nTPM

T-cells	20.6 nTPM
PBMC	45.0 nTPM
Lung	28.8 nTPM
Kidney	26.0 nTPM
Liver	25.0 nTPM
Lymph node	24.2 nTPM
Bone marrow	23.9 nTPM
Adipose tissue	21.9 nTPM
Spleen	21.1 nTPM
Stomach	19.9 nTPM
Colon	19.5 nTPM
Skeletal muscle	19.1 nTPM
Skin	18.0 nTPM
Ovary	17.8 nTPM
Breast	17.5 nTPM
Endometrium	16.7 nTPM
Esophagus	6.6 nTPM
Prostate	0.0 nTPM

Basal prostatic cells	28.3 nTPM
Prostate	28.3 nTPM

Basal respiratory cells	28.9 nTPM
Bronchus	28.9 nTPM

Basal squamous epithelial cells	17.1 nTPM
Esophagus	17.1 nTPM

Collecting duct cells	42.3 nTPM
Kidney	42.3 nTPM

Undifferentiated cells	21.4 nTPM
Small intestine	25.4 nTPM
Rectum	24.9 nTPM
Colon	14.0 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