Single cell type - CD3E - 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.	CD3E
Gene descriptionⁱ Full gene name according to HGNC.	CD3e molecule
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	CD markers Disease related genes FDA approved drug targets Human disease related genes Transporters
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
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	2

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	T-cells - T-cell receptor (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 (T-cells, dendritic cells, NK-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	Group enriched (naive CD8 T-cell, naive CD4 T-cell, gdT-cell, memory CD8 T-cell, T-reg, MAIT T-cell, memory CD4 T-cell, NK-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 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	Group enriched (JURKAT, MOLT-4)
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: Group enriched (T-cells, dendritic cells, NK-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

CD3E is part of cluster 58 T-cells - T-cell receptor with confidenceⁱ 1
180 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
TRAV4	T cell receptor alpha variable 4	0.9462	58
CD5	CD5 molecule	0.9375	58
TRBV14	T cell receptor beta variable 14	0.9296	58
CD6	CD6 molecule	0.9292	58
UBASH3A	Ubiquitin associated and SH3 domain containing A	0.9191	58
TRAV13-2	T cell receptor alpha variable 13-2	0.9150	58
TRAV17	T cell receptor alpha variable 17	0.9145	58
TRAV36DV7	T cell receptor alpha variable 36/delta variable 7	0.9144	58
TRBJ1-2	T cell receptor beta joining 1-2	0.9023	58
TRBV18	T cell receptor beta variable 18	0.8965	58
TRAV41	T cell receptor alpha variable 41	0.8959	58
TRAV8-3	T cell receptor alpha variable 8-3	0.8958	58
TRAV19	T cell receptor alpha variable 19	0.8953	58
TRBV2	T cell receptor beta variable 2	0.8944	58
TRBV15	T cell receptor beta variable 15	0.8942	58

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	4.9 nTPM
Breast	8.9 nTPM
Adipose tissue	0.9 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	8.6 nTPM
Lung	8.6 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	12.9 nTPM
PBMC	27.1 nTPM
Adipose tissue	24.6 nTPM
Lymph node	21.2 nTPM
Breast	16.0 nTPM
Spleen	8.3 nTPM
Stomach	8.1 nTPM
Bone marrow	7.4 nTPM
Liver	6.4 nTPM
Colon	4.8 nTPM
Kidney	4.8 nTPM

Dendritic cells	213.6 nTPM
Breast	365.6 nTPM
Adipose tissue	259.2 nTPM
PBMC	16.0 nTPM

Endothelial cells	2.5 nTPM
Skin	8.8 nTPM
Liver	8.2 nTPM
Lung	6.2 nTPM
Breast	5.2 nTPM
Esophagus	3.7 nTPM
Skeletal muscle	1.5 nTPM
Endometrium	1.1 nTPM
Heart muscle	0.3 nTPM
Eye	0.0 nTPM
Placenta	0.0 nTPM
Prostate	0.0 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Ovary	0.0 nTPM

Fibroblasts	5.3 nTPM
Stomach	35.6 nTPM
Breast	8.4 nTPM
Skin	7.0 nTPM
Esophagus	2.8 nTPM
Placenta	1.9 nTPM
Lung	1.2 nTPM
Skeletal muscle	0.9 nTPM
Adipose tissue	0.2 nTPM
Heart muscle	0.1 nTPM
Prostate	0.0 nTPM
Ovary	0.0 nTPM

Intestinal goblet cells	0.0 nTPM
Rectum	0.1 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Macrophages	12.6 nTPM
Breast	96.9 nTPM
Adipose tissue	23.1 nTPM
Stomach	20.5 nTPM
Bone marrow	20.0 nTPM
Spleen	11.4 nTPM
Endometrium	6.8 nTPM
Lung	5.7 nTPM
Kidney	3.0 nTPM
Ovary	1.2 nTPM
Skeletal muscle	0.8 nTPM
Prostate	0.0 nTPM
PBMC	0.0 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Esophagus	0.0 nTPM

Paneth cells	1.1 nTPM
Colon	3.3 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Plasma cells	41.4 nTPM
Adipose tissue	115.4 nTPM
Bone marrow	49.4 nTPM
Stomach	23.1 nTPM
Spleen	18.9 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	0.0 nTPM
Lung	0.0 nTPM
Bronchus	0.0 nTPM

Smooth muscle cells	2.7 nTPM
Breast	19.3 nTPM
Skin	5.6 nTPM
Skeletal muscle	2.1 nTPM
Esophagus	1.5 nTPM
Prostate	0.6 nTPM
Ovary	0.4 nTPM
Heart muscle	0.2 nTPM
Endometrium	0.1 nTPM
Pancreas	0.0 nTPM
Bronchus	0.0 nTPM
Adipose tissue	0.0 nTPM

T-cells	601.4 nTPM
Stomach	1346.2 nTPM
Spleen	1012.9 nTPM
Lymph node	986.4 nTPM
Bone marrow	921.4 nTPM
Kidney	761.2 nTPM
Adipose tissue	672.2 nTPM
Breast	618.8 nTPM
PBMC	597.4 nTPM
Colon	525.5 nTPM
Ovary	524.9 nTPM
Esophagus	504.4 nTPM
Liver	452.7 nTPM
Skin	417.3 nTPM
Skeletal muscle	387.4 nTPM
Endometrium	208.8 nTPM
Prostate	170.4 nTPM
Lung	115.4 nTPM

Collecting duct cells	1.8 nTPM
Kidney	1.8 nTPM

Undifferentiated cells	0.6 nTPM
Colon	1.4 nTPM
Rectum	0.3 nTPM
Small intestine	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