Single cell type - GCSH - 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.	GCSH
Gene descriptionⁱ Full gene name according to HGNC.	Glycine cleavage system protein H
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Human disease related genes Metabolic proteins 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	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	7

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	Extravillous trophoblasts - Unknown function (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 (Extravillous trophoblasts, Proximal tubular cells, Cytotrophoblasts)
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 (Extravillous trophoblasts, Proximal tubular cells, Cytotrophoblasts)

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

GCSH is part of cluster 38 Extravillous trophoblasts - Unknown function with confidenceⁱ 1
176 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
ERVH48-1	Endogenous retrovirus group 48 member 1	0.8872	38
ISM2	Isthmin 2	0.8773	38
GJA5	Gap junction protein alpha 5	0.8593	38
EZHIP	EZH inhibitory protein	0.8513	38
DLX4	Distal-less homeobox 4	0.8480	38
CLDN6	Claudin 6	0.8472	38
XAGE2	X antigen family member 2	0.8440	38
ERVMER34-1	Endogenous retrovirus group MER34 member 1, envelope	0.8410	38
MACIR	Macrophage immunometabolism regulator	0.8371	38
PEDS1	Plasmanylethanolamine desaturase 1	0.8254	38
NLRP2	NLR family pyrin domain containing 2	0.8188	38
CDK7	Cyclin dependent kinase 7	0.8187	38
SKP2	S-phase kinase associated protein 2	0.8169	38
CCNE1	Cyclin E1	0.8160	38
CLDN19	Claudin 19	0.8116	38

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	31.1 nTPM
Breast	43.3 nTPM
Adipose tissue	19.0 nTPM

Alveolar cells type 1	3.2 nTPM
Lung	3.2 nTPM

Alveolar cells type 2	5.9 nTPM
Lung	5.9 nTPM

Astrocytes	16.3 nTPM
Brain	16.3 nTPM

B-cells	24.8 nTPM
Liver	102.8 nTPM
Kidney	38.1 nTPM
Breast	30.7 nTPM
Colon	28.7 nTPM
Spleen	14.2 nTPM
Bone marrow	9.8 nTPM
PBMC	8.5 nTPM
Lymph node	5.7 nTPM
Stomach	5.4 nTPM
Adipose tissue	3.5 nTPM

Dendritic cells	13.8 nTPM
Breast	17.8 nTPM
PBMC	16.0 nTPM
Adipose tissue	7.7 nTPM

Endothelial cells	31.9 nTPM
Placenta	83.0 nTPM
Pancreas	61.8 nTPM
Breast	36.8 nTPM
Liver	36.7 nTPM
Prostate	36.6 nTPM
Skin	33.6 nTPM
Endometrium	30.8 nTPM
Testis	29.0 nTPM
Ovary	26.8 nTPM
Esophagus	22.5 nTPM
Eye	21.8 nTPM
Skeletal muscle	18.3 nTPM
Lung	6.2 nTPM
Heart muscle	2.6 nTPM

Fibroblasts	61.6 nTPM
Ovary	129.9 nTPM
Placenta	107.1 nTPM
Breast	105.4 nTPM
Prostate	70.3 nTPM
Skin	67.7 nTPM
Adipose tissue	49.1 nTPM
Stomach	43.0 nTPM
Skeletal muscle	35.9 nTPM
Esophagus	34.4 nTPM
Lung	32.4 nTPM
Heart muscle	2.4 nTPM

Intestinal goblet cells	34.3 nTPM
Rectum	48.6 nTPM
Small intestine	30.2 nTPM
Colon	24.3 nTPM

Macrophages	18.8 nTPM
Kidney	62.8 nTPM
Prostate	33.2 nTPM
Ovary	26.7 nTPM
Pancreas	25.5 nTPM
Endometrium	22.2 nTPM
Esophagus	20.4 nTPM
Breast	20.1 nTPM
Testis	16.3 nTPM
Lung	13.0 nTPM
Spleen	11.4 nTPM
Skeletal muscle	11.3 nTPM
Bone marrow	10.0 nTPM
Adipose tissue	8.8 nTPM
PBMC	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	17.8 nTPM
Rectum	31.8 nTPM
Small intestine	15.0 nTPM
Colon	6.5 nTPM

Plasma cells	51.7 nTPM
Spleen	100.4 nTPM
Bone marrow	57.7 nTPM
Esophagus	49.4 nTPM
Stomach	38.9 nTPM
Adipose tissue	12.2 nTPM

Respiratory ciliated cells	20.0 nTPM
Lung	21.9 nTPM
Bronchus	18.2 nTPM

Smooth muscle cells	50.2 nTPM
Pancreas	109.9 nTPM
Breast	76.9 nTPM
Skin	67.3 nTPM
Ovary	52.6 nTPM
Skeletal muscle	50.6 nTPM
Adipose tissue	49.6 nTPM
Prostate	48.7 nTPM
Endometrium	42.2 nTPM
Esophagus	40.3 nTPM
Bronchus	10.4 nTPM
Heart muscle	3.7 nTPM

T-cells	16.3 nTPM
Kidney	47.2 nTPM
Liver	29.3 nTPM
Endometrium	27.8 nTPM
Skin	25.7 nTPM
Colon	22.8 nTPM
PBMC	20.2 nTPM
Breast	14.6 nTPM
Lymph node	11.6 nTPM
Stomach	11.6 nTPM
Skeletal muscle	11.4 nTPM
Spleen	11.1 nTPM
Bone marrow	9.7 nTPM
Prostate	9.5 nTPM
Adipose tissue	6.9 nTPM
Ovary	6.7 nTPM
Esophagus	6.6 nTPM
Lung	4.5 nTPM

Basal keratinocytes	29.1 nTPM
Skin	29.1 nTPM

Basal prostatic cells	94.6 nTPM
Prostate	94.6 nTPM

Basal respiratory cells	73.6 nTPM
Bronchus	73.6 nTPM

Basal squamous epithelial cells	52.3 nTPM
Esophagus	52.3 nTPM

Undifferentiated cells	49.4 nTPM
Rectum	55.6 nTPM
Small intestine	53.0 nTPM
Colon	39.6 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