Single cell type - XCL1 - 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.	XCL1
Gene descriptionⁱ Full gene name according to HGNC.	X-C motif chemokine ligand 1
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	Secreted
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	1

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	NK-cells & T-cells - 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	Group enriched (T-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	Immune cell enriched (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 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	Cell line enhanced (CACO-2, Hep G2, SCLC-21H, SuSa, U-266/70, U-266/84)
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
Extracellular locationⁱ A possible secretion of the protein was predicted based on N-terminal signal sequence (signal peptide) predictions and transmembrane region predictions, and subsequently annotated for its local or systemic secretion based on literature, function, and protein and RNA expression data. Read more	Protein predicted to be secreted

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)

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

XCL1 is part of cluster 63 NK-cells & T-cells - Immune response with confidenceⁱ 1
362 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
XCL2	X-C motif chemokine ligand 2	0.9326	63
CCL4	C-C motif chemokine ligand 4	0.8788	63
IL18RAP	Interleukin 18 receptor accessory protein	0.8677	63
CRTAM	Cytotoxic and regulatory T cell molecule	0.8664	24
CCL5	C-C motif chemokine ligand 5	0.8457	63
KLRC1	Killer cell lectin like receptor C1	0.8356	63
TBX21	T-box transcription factor 21	0.8298	63
SYTL3	Synaptotagmin like 3	0.8242	24
MYBL1	MYB proto-oncogene like 1	0.8237	24
SH2D2A	SH2 domain containing 2A	0.8235	63
KLRC2	Killer cell lectin like receptor C2	0.8226	63
PTPN22	Protein tyrosine phosphatase non-receptor type 22	0.8221	24
TNFSF14	TNF superfamily member 14	0.8213	63
FASLG	Fas ligand	0.8193	63
KIR3DL3	Killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3	0.8169	63

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	2.3 nTPM
Breast	3.6 nTPM
Adipose tissue	0.9 nTPM

Alveolar cells type 1	3.2 nTPM
Lung	3.2 nTPM

Alveolar cells type 2	5.5 nTPM
Lung	5.5 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	1.5 nTPM
Liver	5.5 nTPM
Adipose tissue	5.5 nTPM
Stomach	1.4 nTPM
Breast	1.3 nTPM
Bone marrow	0.8 nTPM
Lymph node	0.4 nTPM
Spleen	0.3 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM

Dendritic cells	185.3 nTPM
Adipose tissue	386.9 nTPM
Breast	165.1 nTPM
PBMC	4.0 nTPM

Endothelial cells	1.9 nTPM
Skin	10.9 nTPM
Esophagus	5.2 nTPM
Breast	2.8 nTPM
Endometrium	2.5 nTPM
Heart muscle	2.1 nTPM
Liver	1.8 nTPM
Placenta	1.1 nTPM
Prostate	0.5 nTPM
Skeletal muscle	0.2 nTPM
Eye	0.0 nTPM
Lung	0.0 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Ovary	0.0 nTPM

Fibroblasts	1.9 nTPM
Placenta	8.3 nTPM
Skin	6.0 nTPM
Breast	2.6 nTPM
Stomach	1.5 nTPM
Adipose tissue	0.7 nTPM
Esophagus	0.6 nTPM
Prostate	0.4 nTPM
Skeletal muscle	0.3 nTPM
Heart muscle	0.1 nTPM
Lung	0.0 nTPM
Ovary	0.0 nTPM

Intestinal goblet cells	0.8 nTPM
Colon	2.2 nTPM
Rectum	0.3 nTPM
Small intestine	0.0 nTPM

Macrophages	3.1 nTPM
Breast	26.9 nTPM
Adipose tissue	7.0 nTPM
Spleen	4.2 nTPM
Endometrium	3.0 nTPM
Stomach	2.9 nTPM
Lung	2.1 nTPM
Skeletal muscle	0.4 nTPM
Ovary	0.1 nTPM
Kidney	0.0 nTPM
Prostate	0.0 nTPM
PBMC	0.0 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

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

Plasma cells	7.6 nTPM
Adipose tissue	27.7 nTPM
Spleen	3.7 nTPM
Stomach	3.4 nTPM
Bone marrow	3.3 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	0.0 nTPM
Lung	0.0 nTPM
Bronchus	0.0 nTPM

Smooth muscle cells	1.7 nTPM
Breast	8.6 nTPM
Esophagus	4.6 nTPM
Skin	2.4 nTPM
Endometrium	1.1 nTPM
Adipose tissue	0.7 nTPM
Heart muscle	0.5 nTPM
Prostate	0.4 nTPM
Skeletal muscle	0.2 nTPM
Pancreas	0.0 nTPM
Bronchus	0.0 nTPM
Ovary	0.0 nTPM

T-cells	213.4 nTPM
Endometrium	874.2 nTPM
Esophagus	478.2 nTPM
Skin	449.0 nTPM
Spleen	265.6 nTPM
Breast	226.7 nTPM
Liver	178.5 nTPM
Prostate	175.1 nTPM
Stomach	173.2 nTPM
Colon	156.4 nTPM
Adipose tissue	148.1 nTPM
Lung	120.0 nTPM
Skeletal muscle	110.4 nTPM
Lymph node	83.7 nTPM
Ovary	82.3 nTPM
Bone marrow	71.0 nTPM
Kidney	25.3 nTPM
PBMC	10.8 nTPM

Undifferentiated cells	0.4 nTPM
Rectum	0.5 nTPM
Colon	0.4 nTPM
Small intestine	0.4 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