Single cell type - TRAF4 - 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.	TRAF4
Gene descriptionⁱ Full gene name according to HGNC.	TNF receptor associated factor 4
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-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	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	Epithelial cell types - Mixed 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 (Urothelial 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	Immune cell enriched (plasmacytoid DC)
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	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 (Urothelial 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

TRAF4 is part of cluster 22 Epithelial cell types - Mixed function with confidenceⁱ 1
298 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
CLDN4	Claudin 4	0.7579	22
ATG101	Autophagy related 101	0.6802	22
UGCG	UDP-glucose ceramide glucosyltransferase	0.6569	22
UPK3A	Uroplakin 3A	0.6444	35
TM4SF1	Transmembrane 4 L six family member 1	0.6438	22
TMEM30B	Transmembrane protein 30B	0.6422	22
ARHGEF35	Rho guanine nucleotide exchange factor 35	0.6270	22
HEBP2	Heme binding protein 2	0.6259	22
TNFRSF21	TNF receptor superfamily member 21	0.6239	22
EDDM3B	Epididymal protein 3B	0.6168	35
SH3BP4	SH3 domain binding protein 4	0.6155	35
SHB	SH2 domain containing adaptor protein B	0.6152	22
OCLN	Occludin	0.6058	22
ERRFI1	ERBB receptor feedback inhibitor 1	0.6048	22
C3orf52	Chromosome 3 open reading frame 52	0.6029	22

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	9.3 nTPM
Breast	9.7 nTPM
Adipose tissue	8.9 nTPM

Alveolar cells type 1	22.4 nTPM
Lung	22.4 nTPM

Alveolar cells type 2	28.3 nTPM
Lung	28.3 nTPM

Astrocytes	28.4 nTPM
Brain	28.4 nTPM

B-cells	59.2 nTPM
Adipose tissue	111.2 nTPM
Colon	87.9 nTPM
Spleen	82.0 nTPM
Lymph node	79.4 nTPM
Breast	57.5 nTPM
Stomach	49.9 nTPM
Bone marrow	43.4 nTPM
Kidney	33.4 nTPM
PBMC	29.9 nTPM
Liver	17.3 nTPM

Basal squamous epithelial cells	122.3 nTPM
Esophagus	122.3 nTPM

Dendritic cells	88.3 nTPM
PBMC	183.3 nTPM
Adipose tissue	45.6 nTPM
Breast	36.1 nTPM

Endothelial cells	20.7 nTPM
Prostate	59.1 nTPM
Skin	43.1 nTPM
Ovary	36.1 nTPM
Pancreas	34.7 nTPM
Breast	31.0 nTPM
Endometrium	22.1 nTPM
Placenta	17.0 nTPM
Esophagus	15.5 nTPM
Testis	12.2 nTPM
Skeletal muscle	7.4 nTPM
Eye	4.8 nTPM
Lung	3.1 nTPM
Liver	2.7 nTPM
Heart muscle	0.5 nTPM

Enteroendocrine cells	84.1 nTPM
Colon	117.2 nTPM
Rectum	51.0 nTPM

Fibroblasts	20.4 nTPM
Prostate	85.9 nTPM
Skin	36.1 nTPM
Placenta	22.8 nTPM
Ovary	19.0 nTPM
Lung	15.7 nTPM
Breast	14.9 nTPM
Stomach	10.4 nTPM
Skeletal muscle	8.4 nTPM
Adipose tissue	5.5 nTPM
Esophagus	5.1 nTPM
Heart muscle	0.4 nTPM

Intestinal goblet cells	81.6 nTPM
Colon	119.4 nTPM
Small intestine	65.4 nTPM
Rectum	60.1 nTPM

Macrophages	16.0 nTPM
Adipose tissue	60.5 nTPM
Endometrium	46.8 nTPM
Prostate	36.7 nTPM
Breast	22.6 nTPM
Esophagus	18.9 nTPM
Skeletal muscle	18.2 nTPM
Stomach	11.7 nTPM
Spleen	10.4 nTPM
Kidney	5.3 nTPM
Ovary	3.5 nTPM
Testis	2.9 nTPM
Lung	2.5 nTPM
PBMC	0.0 nTPM
Pancreas	0.0 nTPM
Bone marrow	0.0 nTPM

Paneth cells	125.7 nTPM
Colon	204.2 nTPM
Rectum	105.4 nTPM
Small intestine	67.5 nTPM

Plasma cells	36.6 nTPM
Stomach	56.7 nTPM
Adipose tissue	42.5 nTPM
Spleen	37.7 nTPM
Esophagus	24.6 nTPM
Bone marrow	21.4 nTPM

Respiratory ciliated cells	68.7 nTPM
Bronchus	105.4 nTPM
Lung	32.1 nTPM

Cholangiocytes	44.3 nTPM
Liver	44.3 nTPM

Collecting duct cells	20.2 nTPM
Kidney	20.2 nTPM

Cone photoreceptor cells	6.2 nTPM
Eye	6.2 nTPM

Cytotrophoblasts	107.9 nTPM
Placenta	107.9 nTPM

Smooth muscle cells	34.9 nTPM
Bronchus	106.5 nTPM
Ovary	91.1 nTPM
Prostate	45.9 nTPM
Skin	40.8 nTPM
Pancreas	36.3 nTPM
Endometrium	24.6 nTPM
Skeletal muscle	14.7 nTPM
Adipose tissue	8.9 nTPM
Breast	8.3 nTPM
Esophagus	4.6 nTPM
Heart muscle	1.9 nTPM

T-cells	31.5 nTPM
Prostate	75.7 nTPM
Colon	73.7 nTPM
Skin	67.7 nTPM
Adipose tissue	59.3 nTPM
Breast	47.1 nTPM
Esophagus	45.9 nTPM
Endometrium	43.7 nTPM
Spleen	28.7 nTPM
Lymph node	23.1 nTPM
Skeletal muscle	15.7 nTPM
Ovary	15.6 nTPM
Stomach	15.0 nTPM
PBMC	5.2 nTPM
Liver	4.8 nTPM
Kidney	4.7 nTPM
Bone marrow	4.7 nTPM
Lung	4.5 nTPM

Undifferentiated cells	93.5 nTPM
Colon	146.5 nTPM
Rectum	70.7 nTPM
Small intestine	63.4 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