Single cell type - CXCR4 - 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.	CXCR4
Gene descriptionⁱ Full gene name according to HGNC.	C-X-C motif chemokine receptor 4
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes CD markers Disease related genes FDA approved drug targets G-protein coupled receptors 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	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	Cell type enhanced (B-cells, T-cells, dendritic cells, Plasma cells, Macrophages, 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	Low immune cell specificity
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	Cell line enhanced (Daudi, JURKAT, Karpas-707, MOLT-4, REH, U-266/70, U-698)
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

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 (B-cells, T-cells, dendritic cells, Plasma cells, Macrophages, 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

CXCR4 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
ZC3H12D	Zinc finger CCCH-type containing 12D	0.7876	24
STK17B	Serine/threonine kinase 17b	0.7672	24
STK4	Serine/threonine kinase 4	0.7566	24
SMCHD1	Structural maintenance of chromosomes flexible hinge domain containing 1	0.7531	24
CNOT6L	CCR4-NOT transcription complex subunit 6 like	0.7345	24
H2AC15	H2A clustered histone 15	0.7322	24
BICDL1	BICD family like cargo adaptor 1	0.7316	24
CRYBG1	Crystallin beta-gamma domain containing 1	0.7275	24
MARCHF9	Membrane associated ring-CH-type finger 9	0.7195	24
SEPTIN6	Septin 6	0.7180	24
CCR6	C-C motif chemokine receptor 6	0.7143	24
SMAP2	Small ArfGAP2	0.7061	24
SEPTIN1	Septin 1	0.7059	24
RGPD2	RANBP2 like and GRIP domain containing 2	0.7006	24
RESF1	Retroelement silencing factor 1	0.6968	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	32.0 nTPM
Breast	41.7 nTPM
Adipose tissue	22.2 nTPM

Alveolar cells type 1	16.0 nTPM
Lung	16.0 nTPM

Alveolar cells type 2	42.2 nTPM
Lung	42.2 nTPM

Astrocytes	8.5 nTPM
Brain	8.5 nTPM

Basal keratinocytes	41.0 nTPM
Skin	41.0 nTPM

B-cells	1446.9 nTPM
Adipose tissue	3474.9 nTPM
Lymph node	2841.6 nTPM
Stomach	2382.0 nTPM
Kidney	1299.8 nTPM
Spleen	1179.8 nTPM
Colon	950.5 nTPM
PBMC	686.7 nTPM
Breast	666.0 nTPM
Bone marrow	501.1 nTPM
Liver	487.2 nTPM

Dendritic cells	1015.1 nTPM
Adipose tissue	2469.9 nTPM
Breast	499.6 nTPM
PBMC	75.7 nTPM

Endothelial cells	67.6 nTPM
Pancreas	301.1 nTPM
Ovary	243.1 nTPM
Eye	139.2 nTPM
Skin	60.2 nTPM
Breast	41.2 nTPM
Prostate	38.1 nTPM
Liver	29.3 nTPM
Esophagus	23.8 nTPM
Placenta	20.5 nTPM
Skeletal muscle	15.4 nTPM
Endometrium	13.2 nTPM
Lung	12.5 nTPM
Heart muscle	4.8 nTPM
Testis	3.8 nTPM

Fibroblasts	28.9 nTPM
Stomach	112.9 nTPM
Prostate	56.2 nTPM
Skin	38.2 nTPM
Lung	34.7 nTPM
Breast	27.5 nTPM
Esophagus	15.6 nTPM
Placenta	9.9 nTPM
Heart muscle	7.8 nTPM
Skeletal muscle	5.8 nTPM
Adipose tissue	5.4 nTPM
Ovary	3.7 nTPM

Intestinal goblet cells	2.0 nTPM
Colon	5.8 nTPM
Rectum	0.4 nTPM
Small intestine	0.0 nTPM

Macrophages	513.6 nTPM
Adipose tissue	2313.7 nTPM
Testis	770.9 nTPM
Prostate	710.7 nTPM
Breast	632.6 nTPM
Esophagus	552.3 nTPM
Ovary	545.9 nTPM
Skeletal muscle	470.6 nTPM
Stomach	448.4 nTPM
Spleen	412.7 nTPM
Endometrium	282.2 nTPM
Kidney	229.9 nTPM
Lung	196.4 nTPM
Bone marrow	111.2 nTPM
PBMC	13.6 nTPM
Pancreas	12.8 nTPM

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

Plasma cells	534.2 nTPM
Adipose tissue	2223.5 nTPM
Stomach	168.0 nTPM
Spleen	135.0 nTPM
Esophagus	98.5 nTPM
Bone marrow	46.2 nTPM

Respiratory ciliated cells	2.4 nTPM
Lung	4.4 nTPM
Bronchus	0.4 nTPM

Smooth muscle cells	23.1 nTPM
Breast	67.1 nTPM
Esophagus	43.4 nTPM
Skin	35.5 nTPM
Adipose tissue	26.3 nTPM
Ovary	23.6 nTPM
Heart muscle	17.9 nTPM
Skeletal muscle	14.7 nTPM
Endometrium	12.9 nTPM
Prostate	10.3 nTPM
Pancreas	1.9 nTPM
Bronchus	0.0 nTPM

Cholangiocytes	11.5 nTPM
Liver	11.5 nTPM

Cytotrophoblasts	1.5 nTPM
Placenta	1.5 nTPM

Distal tubular cells	13.7 nTPM
Kidney	13.7 nTPM

Early spermatids	1.2 nTPM
Testis	1.2 nTPM

T-cells	1436.5 nTPM
Adipose tissue	5595.4 nTPM
Prostate	2196.5 nTPM
Lymph node	2118.3 nTPM
Ovary	1975.3 nTPM
Breast	1922.1 nTPM
Skeletal muscle	1584.1 nTPM
Stomach	1436.4 nTPM
Skin	1273.8 nTPM
Spleen	1221.2 nTPM
Esophagus	1198.8 nTPM
Liver	1087.0 nTPM
Kidney	631.8 nTPM
Colon	577.3 nTPM
Lung	537.7 nTPM
Bone marrow	449.6 nTPM
Endometrium	333.6 nTPM
PBMC	281.7 nTPM

Undifferentiated cells	1.8 nTPM
Colon	4.7 nTPM
Small intestine	0.3 nTPM
Rectum	0.2 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