Single cell type - GPC3 - 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.	GPC3
Gene descriptionⁱ Full gene name according to HGNC.	Glypican 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes 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,Membrane
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	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	Cell type enhanced (Fibroblasts, Syncytiotrophoblasts, Muller glia cells, Cytotrophoblasts, Extravillous trophoblasts)
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 enhanced (naive CD4 T-cell, naive CD8 T-cell)
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 some
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	Group enriched (HAP1, Hep G2)
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

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 (Fibroblasts, Syncytiotrophoblasts, Muller glia cells, Cytotrophoblasts, Extravillous trophoblasts)

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

GPC3 is part of cluster 33 Fibroblasts - ECM organization with confidenceⁱ 1
171 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
ISM1	Isthmin 1	0.9021	50
LBHD2	LBH domain containing 2	0.8919	33
LUM	Lumican	0.8667	33
SRPX	Sushi repeat containing protein X-linked	0.8548	33
OLFML3	Olfactomedin like 3	0.8444	33
OGN	Osteoglycin	0.8394	33
CIBAR1	CBY1 interacting BAR domain containing 1	0.8334	33
CCN2	Cellular communication network factor 2	0.8185	50
COL6A2	Collagen type VI alpha 2 chain	0.8125	33
CCN1	Cellular communication network factor 1	0.7976	50
DENND2B	DENN domain containing 2B	0.7917	50
COL6A1	Collagen type VI alpha 1 chain	0.7848	33
CTHRC1	Collagen triple helix repeat containing 1	0.7570	33
POGLUT3	Protein O-glucosyltransferase 3	0.7368	50
ECM1	Extracellular matrix protein 1	0.7358	50

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	28.5 nTPM
Adipose tissue	43.6 nTPM
Breast	13.3 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	1.7 nTPM
Lung	1.7 nTPM

Astrocytes	0.3 nTPM
Brain	0.3 nTPM

B-cells	1.0 nTPM
Kidney	9.5 nTPM
Colon	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Breast	0.0 nTPM

Dendritic cells	0.8 nTPM
Breast	1.8 nTPM
Adipose tissue	0.6 nTPM
PBMC	0.0 nTPM

Endothelial cells	1.8 nTPM
Placenta	12.5 nTPM
Skin	3.2 nTPM
Lung	3.1 nTPM
Breast	2.3 nTPM
Skeletal muscle	1.3 nTPM
Prostate	1.1 nTPM
Esophagus	0.6 nTPM
Heart muscle	0.5 nTPM
Endometrium	0.2 nTPM
Ovary	0.1 nTPM
Eye	0.0 nTPM
Liver	0.0 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM

Fibroblasts	404.2 nTPM
Placenta	1765.0 nTPM
Adipose tissue	1729.8 nTPM
Breast	551.1 nTPM
Skeletal muscle	120.5 nTPM
Skin	92.4 nTPM
Ovary	74.9 nTPM
Lung	36.9 nTPM
Prostate	31.4 nTPM
Esophagus	23.2 nTPM
Stomach	11.9 nTPM
Heart muscle	9.3 nTPM

Intestinal goblet cells	3.1 nTPM
Small intestine	5.0 nTPM
Rectum	3.0 nTPM
Colon	1.4 nTPM

Macrophages	1.0 nTPM
Skeletal muscle	4.7 nTPM
Breast	3.5 nTPM
Kidney	3.0 nTPM
Adipose tissue	1.6 nTPM
Lung	1.2 nTPM
Testis	0.6 nTPM
Endometrium	0.4 nTPM
Prostate	0.0 nTPM
PBMC	0.0 nTPM
Pancreas	0.0 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	2.6 nTPM
Small intestine	7.5 nTPM
Rectum	0.2 nTPM
Colon	0.0 nTPM

Plasma cells	0.4 nTPM
Adipose tissue	1.9 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Respiratory ciliated cells	24.3 nTPM
Lung	48.1 nTPM
Bronchus	0.6 nTPM

Smooth muscle cells	21.3 nTPM
Adipose tissue	162.1 nTPM
Skeletal muscle	22.6 nTPM
Breast	13.3 nTPM
Prostate	10.6 nTPM
Esophagus	7.8 nTPM
Heart muscle	5.5 nTPM
Skin	4.2 nTPM
Endometrium	2.9 nTPM
Pancreas	2.6 nTPM
Ovary	1.6 nTPM
Bronchus	1.0 nTPM

T-cells	1.1 nTPM
Skin	9.7 nTPM
Skeletal muscle	3.8 nTPM
Kidney	2.0 nTPM
Lung	1.5 nTPM
Breast	1.4 nTPM
Adipose tissue	0.2 nTPM
Colon	0.0 nTPM
Liver	0.0 nTPM
Prostate	0.0 nTPM
PBMC	0.0 nTPM
Endometrium	0.0 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Basal keratinocytes	10.5 nTPM
Skin	10.5 nTPM

Basal prostatic cells	4.8 nTPM
Prostate	4.8 nTPM

Basal respiratory cells	17.0 nTPM
Bronchus	17.0 nTPM

Cytotrophoblasts	65.1 nTPM
Placenta	65.1 nTPM

Undifferentiated cells	4.1 nTPM
Small intestine	9.1 nTPM
Rectum	1.8 nTPM
Colon	1.3 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