Single cell type - CD4 - 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.	CD4
Gene descriptionⁱ Full gene name according to HGNC.	CD4 molecule
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	CD markers FDA approved drug targets 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	Intracellular,Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	3

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	Macrophages - Innate 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 (Hepatic stellate cells, Kupffer cells, Hofbauer cells, Macrophages, monocytes, Langerhans 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 (plasmacytoid DC, classical monocyte, intermediate monocyte, non-classical monocyte, myeloid DC, T-reg, memory CD4 T-cell, naive CD4 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	Group enriched (HEL, HL-60, NB-4, THP-1, U-937)
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 (Hepatic stellate cells, Kupffer cells, Hofbauer cells, Macrophages, monocytes, Langerhans 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

CD4 is part of cluster 4 Macrophages - Innate immune response with confidenceⁱ 1
228 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
MS4A6A	Membrane spanning 4-domains A6A	0.7293	4
TPP1	Tripeptidyl peptidase 1	0.6770	4
CD163	CD163 molecule	0.6607	4
C3AR1	Complement C3a receptor 1	0.6579	4
RNASE6	Ribonuclease A family member k6	0.6522	41
MPEG1	Macrophage expressed 1	0.6396	19
SH3TC1	SH3 domain and tetratricopeptide repeats 1	0.6156	41
LILRB4	Leukocyte immunoglobulin like receptor B4	0.6004	4
CD5L	CD5 molecule like	0.5982	4
MS4A4A	Membrane spanning 4-domains A4A	0.5889	4
STAB1	Stabilin 1	0.5889	4
GPR34	G protein-coupled receptor 34	0.5883	4
OTULINL	OTU deubiquitinase with linear linkage specificity like	0.5825	65
CSF1R	Colony stimulating factor 1 receptor	0.5819	4
CREBL2	CAMP responsive element binding protein like 2	0.5768	4

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	4.5 nTPM
Breast	7.7 nTPM
Adipose tissue	1.3 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	5.2 nTPM
Lung	5.2 nTPM

Astrocytes	1.6 nTPM
Brain	1.6 nTPM

B-cells	5.2 nTPM
Colon	17.6 nTPM
Liver	13.9 nTPM
PBMC	7.1 nTPM
Breast	5.3 nTPM
Adipose tissue	3.5 nTPM
Lymph node	2.9 nTPM
Bone marrow	0.8 nTPM
Stomach	0.5 nTPM
Kidney	0.0 nTPM
Spleen	0.0 nTPM

Dendritic cells	61.9 nTPM
PBMC	175.3 nTPM
Adipose tissue	7.9 nTPM
Breast	2.5 nTPM

Endothelial cells	9.6 nTPM
Liver	74.3 nTPM
Eye	31.6 nTPM
Skin	6.1 nTPM
Breast	4.8 nTPM
Heart muscle	4.0 nTPM
Placenta	4.0 nTPM
Esophagus	3.1 nTPM
Prostate	2.0 nTPM
Skeletal muscle	1.6 nTPM
Testis	1.1 nTPM
Endometrium	0.8 nTPM
Ovary	0.4 nTPM
Lung	0.0 nTPM
Pancreas	0.0 nTPM

Fibroblasts	3.7 nTPM
Placenta	11.7 nTPM
Lung	8.9 nTPM
Skin	4.9 nTPM
Stomach	4.4 nTPM
Breast	4.0 nTPM
Esophagus	3.7 nTPM
Skeletal muscle	1.6 nTPM
Ovary	0.6 nTPM
Heart muscle	0.5 nTPM
Adipose tissue	0.5 nTPM
Prostate	0.2 nTPM

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

Macrophages	109.0 nTPM
Ovary	272.5 nTPM
Adipose tissue	214.0 nTPM
Spleen	141.0 nTPM
Skeletal muscle	135.2 nTPM
Esophagus	119.6 nTPM
Kidney	119.5 nTPM
Endometrium	119.5 nTPM
Testis	101.1 nTPM
Breast	88.1 nTPM
Bone marrow	80.0 nTPM
Prostate	76.8 nTPM
Lung	74.3 nTPM
Stomach	70.3 nTPM
Pancreas	23.0 nTPM
PBMC	0.0 nTPM

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

Plasma cells	2.5 nTPM
Adipose tissue	11.6 nTPM
Spleen	0.7 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM

Respiratory ciliated cells	20.3 nTPM
Lung	29.1 nTPM
Bronchus	11.5 nTPM

Smooth muscle cells	13.5 nTPM
Adipose tissue	35.7 nTPM
Skin	24.0 nTPM
Breast	22.9 nTPM
Esophagus	18.6 nTPM
Endometrium	14.3 nTPM
Ovary	9.5 nTPM
Skeletal muscle	8.7 nTPM
Pancreas	4.8 nTPM
Prostate	4.7 nTPM
Bronchus	2.9 nTPM
Heart muscle	2.0 nTPM

T-cells	34.0 nTPM
Adipose tissue	90.7 nTPM
PBMC	51.9 nTPM
Lymph node	50.4 nTPM
Skeletal muscle	48.8 nTPM
Lung	47.1 nTPM
Breast	37.6 nTPM
Skin	36.4 nTPM
Spleen	34.3 nTPM
Kidney	32.2 nTPM
Bone marrow	31.8 nTPM
Colon	30.9 nTPM
Stomach	28.6 nTPM
Liver	24.1 nTPM
Esophagus	13.1 nTPM
Endometrium	13.0 nTPM
Prostate	4.7 nTPM
Ovary	2.2 nTPM

Basal keratinocytes	3.4 nTPM
Skin	3.4 nTPM

Basal prostatic cells	0.3 nTPM
Prostate	0.3 nTPM

Cholangiocytes	8.6 nTPM
Liver	8.6 nTPM

Cytotrophoblasts	0.9 nTPM
Placenta	0.9 nTPM

Undifferentiated cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	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