Single cell type - CD2 - 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.	CD2
Gene descriptionⁱ Full gene name according to HGNC.	CD2 molecule
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	CD markers FDA approved drug targets
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.	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	Non-specific - Transcription regulation (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, NK-cells, dendritic 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 (NK-cell, memory CD8 T-cell, T-reg, memory CD4 T-cell, naive CD8 T-cell, gdT-cell, MAIT 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 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 (HDLM-2, 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, NK-cells, dendritic 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

CD2 is part of cluster 24 Non-specific - Transcription regulation with confidenceⁱ 1
415 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
CD3G	CD3g molecule	0.9428	63
CD3D	CD3d molecule	0.8908	63
TRBC2	T cell receptor beta constant 2	0.8700	7
CD40LG	CD40 ligand	0.8619	24
CD6	CD6 molecule	0.8451	58
TRAT1	T cell receptor associated transmembrane adaptor 1	0.8183	24
ICOS	Inducible T cell costimulator	0.8091	24
TRBC1	T cell receptor beta constant 1	0.8077	63
CXCR6	C-X-C motif chemokine receptor 6	0.8019	24
FOXP3	Forkhead box P3	0.7986	24
TRAC	T cell receptor alpha constant	0.7968	63
PDCD1	Programmed cell death 1	0.7956	24
GPR171	G protein-coupled receptor 171	0.7952	24
TIGIT	T cell immunoreceptor with Ig and ITIM domains	0.7951	24
CD28	CD28 molecule	0.7876	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	5.0 nTPM
Breast	9.2 nTPM
Adipose tissue	0.9 nTPM

Alveolar cells type 1	3.2 nTPM
Lung	3.2 nTPM

Alveolar cells type 2	17.5 nTPM
Lung	17.5 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	12.3 nTPM
Adipose tissue	49.1 nTPM
PBMC	25.7 nTPM
Breast	21.3 nTPM
Lymph node	7.1 nTPM
Liver	6.6 nTPM
Bone marrow	4.1 nTPM
Stomach	4.1 nTPM
Colon	3.2 nTPM
Spleen	1.4 nTPM
Kidney	0.0 nTPM

Dendritic cells	158.3 nTPM
Breast	266.1 nTPM
Adipose tissue	192.8 nTPM
PBMC	16.0 nTPM

Endothelial cells	2.9 nTPM
Liver	10.1 nTPM
Skin	7.8 nTPM
Heart muscle	7.7 nTPM
Breast	4.0 nTPM
Esophagus	3.7 nTPM
Lung	3.1 nTPM
Skeletal muscle	1.8 nTPM
Endometrium	1.5 nTPM
Prostate	0.5 nTPM
Eye	0.0 nTPM
Placenta	0.0 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Ovary	0.0 nTPM

Fibroblasts	2.5 nTPM
Breast	8.6 nTPM
Stomach	7.4 nTPM
Skin	3.7 nTPM
Lung	2.2 nTPM
Heart muscle	1.7 nTPM
Placenta	1.0 nTPM
Skeletal muscle	0.9 nTPM
Esophagus	0.6 nTPM
Prostate	0.4 nTPM
Adipose tissue	0.3 nTPM
Ovary	0.0 nTPM

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

Macrophages	19.1 nTPM
Breast	108.0 nTPM
Adipose tissue	44.7 nTPM
Stomach	35.1 nTPM
Testis	20.9 nTPM
Endometrium	14.0 nTPM
Lung	10.9 nTPM
Skeletal muscle	10.7 nTPM
Kidney	10.6 nTPM
Bone marrow	10.0 nTPM
Spleen	8.3 nTPM
Esophagus	6.3 nTPM
Ovary	6.1 nTPM
Prostate	1.2 nTPM
PBMC	0.0 nTPM
Pancreas	0.0 nTPM

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

Plasma cells	42.3 nTPM
Adipose tissue	190.3 nTPM
Bone marrow	9.9 nTPM
Spleen	6.4 nTPM
Stomach	4.7 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	0.0 nTPM
Lung	0.0 nTPM
Bronchus	0.0 nTPM

Smooth muscle cells	4.1 nTPM
Breast	21.1 nTPM
Heart muscle	9.7 nTPM
Skin	5.9 nTPM
Esophagus	4.6 nTPM
Skeletal muscle	1.7 nTPM
Prostate	0.6 nTPM
Endometrium	0.5 nTPM
Ovary	0.3 nTPM
Adipose tissue	0.2 nTPM
Pancreas	0.0 nTPM
Bronchus	0.0 nTPM

T-cells	476.8 nTPM
Adipose tissue	906.8 nTPM
Ovary	700.7 nTPM
Breast	677.8 nTPM
Kidney	658.5 nTPM
Liver	526.0 nTPM
Stomach	522.2 nTPM
PBMC	511.8 nTPM
Lung	469.3 nTPM
Skeletal muscle	413.9 nTPM
Spleen	411.2 nTPM
Bone marrow	396.5 nTPM
Lymph node	374.3 nTPM
Colon	364.5 nTPM
Endometrium	332.8 nTPM
Skin	331.1 nTPM
Esophagus	294.8 nTPM
Prostate	213.0 nTPM

Cytotrophoblasts	0.1 nTPM
Placenta	0.1 nTPM

Early spermatids	23.5 nTPM
Testis	23.5 nTPM

Undifferentiated cells	0.5 nTPM
Colon	1.3 nTPM
Rectum	0.1 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