Single cell type - TNFRSF25 - 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.	TNFRSF25
Gene descriptionⁱ Full gene name according to HGNC.	TNF receptor superfamily member 25
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	Membrane,Secreted
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	NK-cells & T-cells - Immune response (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 (T-cells, Excitatory neurons, Distal enterocytes)
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	Group enriched (T-reg, MAIT T-cell, naive CD4 T-cell, memory CD4 T-cell, memory 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 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	Cell line enhanced (HDLM-2, RPMI-8226)
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 many
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: Cell type enhanced (T-cells, Excitatory neurons, Distal enterocytes)

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

TNFRSF25 is part of cluster 63 NK-cells & T-cells - Immune response with confidenceⁱ 0.86
362 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
CD2	CD2 molecule	0.6753	24
TRBC2	T cell receptor beta constant 2	0.6684	7
TRAC	T cell receptor alpha constant	0.6631	63
HELB	DNA helicase B	0.6490	24
CD3G	CD3g molecule	0.6287	63
KRTAP12-3	Keratin associated protein 12-3	0.6259	63
CD3D	CD3d molecule	0.6185	63
TRAV40	T cell receptor alpha variable 40	0.6179	63
TRBC1	T cell receptor beta constant 1	0.6178	63
PPP1R2C	PPP1R2C family member C	0.5967	7
THEMIS	Thymocyte selection associated	0.5857	58
FXYD7	FXYD domain containing ion transport regulator 7	0.5769	21
CD40LG	CD40 ligand	0.5745	24
BCL11B	BAF chromatin remodeling complex subunit BCL11B	0.5692	24
SPOCK2	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 2	0.5600	24

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	19.0 nTPM
Adipose tissue	20.3 nTPM
Breast	17.8 nTPM

Alveolar cells type 1	3.2 nTPM
Lung	3.2 nTPM

Alveolar cells type 2	5.0 nTPM
Lung	5.0 nTPM

Astrocytes	3.9 nTPM
Brain	3.9 nTPM

B-cells	2.5 nTPM
Breast	9.4 nTPM
PBMC	5.7 nTPM
Adipose tissue	4.0 nTPM
Colon	3.2 nTPM
Lymph node	2.1 nTPM
Liver	0.9 nTPM
Kidney	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Dendritic cells	12.8 nTPM
Breast	21.8 nTPM
Adipose tissue	16.6 nTPM
PBMC	0.0 nTPM

Endothelial cells	11.5 nTPM
Ovary	41.1 nTPM
Lung	18.7 nTPM
Skeletal muscle	17.0 nTPM
Placenta	16.5 nTPM
Endometrium	15.2 nTPM
Testis	11.6 nTPM
Breast	8.4 nTPM
Esophagus	6.8 nTPM
Heart muscle	6.1 nTPM
Skin	6.0 nTPM
Prostate	4.8 nTPM
Pancreas	3.9 nTPM
Eye	2.4 nTPM
Liver	1.8 nTPM

Fibroblasts	2.3 nTPM
Skin	6.2 nTPM
Breast	4.9 nTPM
Placenta	3.8 nTPM
Ovary	3.3 nTPM
Lung	2.2 nTPM
Esophagus	1.4 nTPM
Skeletal muscle	1.3 nTPM
Prostate	0.9 nTPM
Heart muscle	0.6 nTPM
Adipose tissue	0.2 nTPM
Stomach	0.0 nTPM

Intestinal goblet cells	20.3 nTPM
Rectum	23.3 nTPM
Small intestine	19.8 nTPM
Colon	17.9 nTPM

Macrophages	4.0 nTPM
Breast	19.3 nTPM
Adipose tissue	11.8 nTPM
Esophagus	7.9 nTPM
Endometrium	5.1 nTPM
Skeletal muscle	4.5 nTPM
Testis	2.9 nTPM
Stomach	2.9 nTPM
Lung	2.8 nTPM
Kidney	1.5 nTPM
Bone marrow	1.2 nTPM
Ovary	0.5 nTPM
Prostate	0.0 nTPM
PBMC	0.0 nTPM
Pancreas	0.0 nTPM
Spleen	0.0 nTPM

Paneth cells	16.0 nTPM
Rectum	31.1 nTPM
Colon	13.2 nTPM
Small intestine	3.7 nTPM

Plasma cells	3.2 nTPM
Adipose tissue	15.5 nTPM
Spleen	0.6 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM

Respiratory ciliated cells	4.8 nTPM
Bronchus	6.7 nTPM
Lung	2.9 nTPM

Smooth muscle cells	2.6 nTPM
Ovary	5.7 nTPM
Endometrium	5.3 nTPM
Bronchus	4.6 nTPM
Breast	3.6 nTPM
Esophagus	3.1 nTPM
Skin	2.1 nTPM
Skeletal muscle	1.0 nTPM
Prostate	0.9 nTPM
Heart muscle	0.8 nTPM
Adipose tissue	0.7 nTPM
Pancreas	0.3 nTPM

T-cells	41.4 nTPM
Breast	80.0 nTPM
Skin	74.1 nTPM
PBMC	59.5 nTPM
Adipose tissue	54.1 nTPM
Lymph node	53.5 nTPM
Colon	53.2 nTPM
Kidney	50.0 nTPM
Lung	47.1 nTPM
Ovary	40.0 nTPM
Spleen	35.4 nTPM
Endometrium	35.1 nTPM
Liver	29.4 nTPM
Skeletal muscle	27.3 nTPM
Stomach	25.3 nTPM
Bone marrow	24.4 nTPM
Prostate	9.5 nTPM
Esophagus	6.6 nTPM

Basal keratinocytes	24.6 nTPM
Skin	24.6 nTPM

Basal respiratory cells	5.6 nTPM
Bronchus	5.6 nTPM

Basal squamous epithelial cells	11.4 nTPM
Esophagus	11.4 nTPM

Endometrial stromal cells	11.2 nTPM
Endometrium	11.2 nTPM

Undifferentiated cells	25.0 nTPM
Rectum	38.0 nTPM
Colon	24.6 nTPM
Small intestine	12.4 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