Single cell type - PRG4 - 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.	PRG4
Gene descriptionⁱ Full gene name according to HGNC.	Proteoglycan 4
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Human disease related genes Plasma proteins
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	Secreted
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	6

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	Fibroblasts - ECM organization (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	Group enriched (Hepatocytes, Fibroblasts)
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	Immune cell enriched (T-reg)
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 single
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 enriched (ASC diff)
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 some
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
Extracellular locationⁱ A possible secretion of the protein was predicted based on N-terminal signal sequence (signal peptide) predictions and transmembrane region predictions, and subsequently annotated for its local or systemic secretion based on literature, function, and protein and RNA expression data. Read more	Protein predicted to be secreted

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: Group enriched (Hepatocytes, Fibroblasts)

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

PRG4 is part of cluster 50 Fibroblasts - ECM organization with confidenceⁱ 1
441 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
PVALEF	Parvalbumin like EF-hand containing	0.6772	11
AC092143.1	Novel protein (MC1R-TUBB3 readthrough)	0.6766	11
F10	Coagulation factor X	0.6651	50
HAS1	Hyaluronan synthase 1	0.6471	50
AC131160.1	Presenilin associated rhomboid like	0.6460	11
C1R	Complement C1r	0.6368	50
CYP21A2	Cytochrome P450 family 21 subfamily A member 2	0.6332	15
CFH	Complement factor H	0.6307	50
ECM2	Extracellular matrix protein 2	0.6278	50
AL021546.1	Novel protein	0.6262	11
OGN	Osteoglycin	0.6228	33
MEDAG	Mesenteric estrogen dependent adipogenesis	0.6087	50
AC058822.1	Novel FIP1L1-PDGFRA fusion protein	0.6067	11
ELN	Elastin	0.6002	50
CXorf49	Chromosome X open reading frame 49	0.5925	11

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	5.1 nTPM
Adipose tissue	9.8 nTPM
Breast	0.4 nTPM

Alveolar cells type 1	22.4 nTPM
Lung	22.4 nTPM

Alveolar cells type 2	16.2 nTPM
Lung	16.2 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	1.3 nTPM
Liver	12.7 nTPM
Lymph node	0.2 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Breast	0.0 nTPM

Dendritic cells	0.1 nTPM
Adipose tissue	0.4 nTPM
PBMC	0.0 nTPM
Breast	0.0 nTPM

Endothelial cells	4.1 nTPM
Lung	37.4 nTPM
Heart muscle	6.3 nTPM
Skeletal muscle	5.7 nTPM
Liver	4.6 nTPM
Placenta	1.1 nTPM
Endometrium	0.9 nTPM
Skin	0.8 nTPM
Breast	0.4 nTPM
Eye	0.0 nTPM
Prostate	0.0 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM

Fibroblasts	320.6 nTPM
Lung	2842.9 nTPM
Adipose tissue	275.5 nTPM
Skeletal muscle	179.1 nTPM
Heart muscle	177.9 nTPM
Skin	23.2 nTPM
Breast	18.1 nTPM
Prostate	9.5 nTPM
Placenta	0.0 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM
Stomach	0.0 nTPM

Intestinal goblet cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Macrophages	2.8 nTPM
Lung	34.1 nTPM
Skeletal muscle	6.4 nTPM
Spleen	1.0 nTPM
Endometrium	0.4 nTPM
Breast	0.2 nTPM
Adipose tissue	0.1 nTPM
Kidney	0.0 nTPM
Prostate	0.0 nTPM
PBMC	0.0 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Plasma cells	0.1 nTPM
Adipose tissue	0.6 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Respiratory ciliated cells	10.9 nTPM
Lung	21.9 nTPM
Bronchus	0.0 nTPM

Smooth muscle cells	1.5 nTPM
Heart muscle	6.4 nTPM
Skeletal muscle	6.2 nTPM
Adipose tissue	2.1 nTPM
Skin	0.7 nTPM
Endometrium	0.7 nTPM
Pancreas	0.3 nTPM
Ovary	0.1 nTPM
Prostate	0.0 nTPM
Bronchus	0.0 nTPM
Esophagus	0.0 nTPM
Breast	0.0 nTPM

T-cells	2.3 nTPM
Lung	18.2 nTPM
Liver	7.2 nTPM
Skeletal muscle	7.2 nTPM
Lymph node	2.2 nTPM
Skin	0.9 nTPM
PBMC	0.8 nTPM
Bone marrow	0.7 nTPM
Spleen	0.7 nTPM
Colon	0.5 nTPM
Adipose tissue	0.4 nTPM
Endometrium	0.3 nTPM
Kidney	0.0 nTPM
Prostate	0.0 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM
Stomach	0.0 nTPM
Breast	0.0 nTPM

Cholangiocytes	10.0 nTPM
Liver	10.0 nTPM

Endometrial stromal cells	3.7 nTPM
Endometrium	3.7 nTPM

Undifferentiated cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 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