Single cell type - CCL3L1 - The Human Protein Atlas

CCL3L1

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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.	CCL3L1
Gene descriptionⁱ Full gene name according to HGNC.	C-C motif chemokine ligand 3 like 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.	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.	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.	Cell type enhanced (Hofbauer cells, Macrophages, Langerhans cells, Monocytes, Kupffer cells)
Tau specificity scoreⁱ Tau specificity score is a numerical indicator of the specificity of the gene expression across cells or tissues. The value ranges from 0 and 1, where 0 indicates identical expression across all cells/tissue types, while 1 indicates expression in a single cell/tissue type.	0.83
Brain cluster specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell cluster types based on snRNA-seq data from brain samples. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. "cell type" refer to one of the 34 cluster names used to summarize the 2.5 million cells included in the brain cell representation.	Cell type enriched (Central nervous system macrophage)
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.	Group enriched (eosinophil, neutrophil)
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); neXtProt protein existence (neXtProt evidence);and a Human Protein Atlas antibody- or RNA based score (HPA evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable.	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.	Protein predicted to be secreted

ASSAYSⁱ

SINGLE CELL TYPESⁱ A summary of normalized 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 RNA single cell type specificity: Cell type enhanced (Hofbauer cells, Macrophages, Langerhans cells, Monocytes, Kupffer cells)

TISSUE CELL TYPEⁱ The tissue cell type section provides a cell type specificity prediction for all protein coding genes. More information on the data available can be found here and a description of the analysis here.
	Core cell typesⁱ The core cell type table displays data for a panel of eight cell types that are found in many tissues. Colored dots indicate that the selected gene has core cell type specificity in the indicated tissue. Grey dots indicate that cell type is present within that tissue, but the selected gene is not predicted to be enriched there. Category Alphabetical Enrichment Tissue specific cell typesⁱ This plot shows the enrichment score of the selected gene in all non-core cell types found within the profiled tissues, allowing comparisons between different cell types within different tissues. An enlarged symbol indicates classification of the gene as cell type enriched in the corresponding cell type.

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Cell type enriched (Central nervous system macrophage)

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
HPA datasetⁱ The resulting transcript expression values calculated as nTPM, resulting from the internal normalization pipeline for 18 immune cell types and total peripheral blood mononuclear cells (PBMC). Lineage Expression Alphabetical Immune cell type specificity: Group enriched (eosinophil, neutrophil)
Monaco datasetⁱ The transcript expression values (nTPM) resulting from the internal normalization pipeline are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SINGLE CELL TYPE

CCL3L1 is part of cluster 58 Macrophages - Innate immune response with confidenceⁱ 1
420 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
CCL3	C-C motif chemokine ligand 3	0.9383	58
TNF	Tumor necrosis factor	0.8239	80
IFNA14	Interferon alpha 14	0.8193	58
IFNB1	Interferon beta 1	0.8039	29
CCL4L2	C-C motif chemokine ligand 4 like 2	0.7938	58
FCGR2C	Fc gamma receptor IIc (gene/pseudogene)	0.7926	58
FGF20	Fibroblast growth factor 20	0.7679	58
OR4B1	Olfactory receptor family 4 subfamily B member 1	0.7534	58
MS4A4E	Membrane spanning 4-domains A4E	0.7370	58
IFNA2	Interferon alpha 2	0.7280	80
PLCB2	Phospholipase C beta 2	0.7122	29
TRMT1	TRNA methyltransferase 1	0.7111	29
CSF1R	Colony stimulating factor 1 receptor	0.7005	58
MILR1	Mast cell immunoglobulin like receptor 1	0.6977	58
GLA	Galactosidase alpha	0.6973	80

IMMUNE CELLS

CCL3L1 is part of cluster 21 Neutrophils - Unknown function with confidenceⁱ 1
492 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
CCNK	Cyclin K	0.9762	21
GNB2	G protein subunit beta 2	0.9762	21
PLEKHG3	Pleckstrin homology and RhoGEF domain containing G3	0.9762	21
CCDC146	Coiled-coil domain containing 146	0.9762	21
CCL4L2	C-C motif chemokine ligand 4 like 2	0.9524	45
SVIL	Supervillin	0.9524	21
B3GNT8	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 8	0.9524	21
ZFP36L2	ZFP36 ring finger protein like 2	0.9524	45
PNRC1	Proline rich nuclear receptor coactivator 1	0.9524	21
CTDSP1	CTD small phosphatase 1	0.9524	21
CABIN1	Calcineurin binding protein 1	0.9524	21
THRA	Thyroid hormone receptor alpha	0.9286	21
CAMK2G	Calcium/calmodulin dependent protein kinase II gamma	0.9286	21
RGS18	Regulator of G protein signaling 18	0.9286	21
RNF167	Ring finger protein 167	0.9286	45

Adipocytes	8.0 nTPM
Breast	15.9 nTPM
Adipose tissue	0.2 nTPM

Alveolar cells type 1	0.2 nTPM
Lung	0.2 nTPM

Alveolar cells type 2	0.2 nTPM
Lung	0.2 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	5.9 nTPM
Skin	40.7 nTPM
Liver	14.5 nTPM
Adipose tissue	11.5 nTPM
Stomach	3.4 nTPM
Lymph node	2.2 nTPM
Spleen	2.2 nTPM
Bone marrow	2.1 nTPM
Salivary gland	0.5 nTPM
Thymus	0.2 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM

Ciliated cells	1.6 nTPM
Fallopian tube	6.4 nTPM
Lung	0.2 nTPM
Endometrium	0.0 nTPM
Bronchus	0.0 nTPM

Club cells	0.2 nTPM
Prostate	0.4 nTPM
Lung	0.3 nTPM
Bronchus	0.0 nTPM

Endothelial cells	1.9 nTPM
Tongue	6.8 nTPM
Liver	5.0 nTPM
Salivary gland	4.8 nTPM
Placenta	4.5 nTPM
Vascular	3.1 nTPM
Skin	2.0 nTPM
Heart muscle	1.9 nTPM
Fallopian tube	1.3 nTPM
Prostate	1.2 nTPM
Breast	0.9 nTPM
Endometrium	0.6 nTPM
Esophagus	0.5 nTPM
Lung	0.5 nTPM
Skeletal muscle	0.3 nTPM
Ovary	0.2 nTPM
Thymus	0.1 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM

Enteroendocrine cells	0.8 nTPM
Colon	2.3 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Fibroblasts	2.2 nTPM
Liver	7.1 nTPM
Pancreas	6.9 nTPM
Vascular	3.6 nTPM
Breast	3.3 nTPM
Skin	2.8 nTPM
Skeletal muscle	2.6 nTPM
Salivary gland	2.0 nTPM
Heart muscle	1.5 nTPM
Placenta	1.5 nTPM
Fallopian tube	1.4 nTPM
Prostate	1.3 nTPM
Adipose tissue	0.4 nTPM
Esophagus	0.3 nTPM
Thymus	0.2 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM

Granulocytes	5.8 nTPM
Lung	9.6 nTPM
Fallopian tube	7.9 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	1.1 nTPM
Colon	3.4 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Lymphatic endothelial cells	0.2 nTPM
Fallopian tube	0.5 nTPM
Ovary	0.0 nTPM

Macrophages	500.2 nTPM
Breast	2315.4 nTPM
Fallopian tube	1066.1 nTPM
Endometrium	1011.6 nTPM
Spleen	602.5 nTPM
Esophagus	565.1 nTPM
Adipose tissue	564.9 nTPM
Stomach	547.9 nTPM
Salivary gland	484.5 nTPM
Pancreas	478.9 nTPM
Skin	392.2 nTPM
Testis	370.1 nTPM
Prostate	358.7 nTPM
Vascular	308.7 nTPM
Tongue	186.9 nTPM
Kidney	136.3 nTPM
Skeletal muscle	92.7 nTPM
Lung	12.2 nTPM
Thymus	6.2 nTPM
Bone marrow	3.0 nTPM

Paneth cells	1.3 nTPM
Colon	3.6 nTPM
Rectum	0.2 nTPM
Small intestine	0.0 nTPM

Plasma cells	4.5 nTPM
Salivary gland	17.5 nTPM
Liver	9.5 nTPM
Spleen	4.6 nTPM
Stomach	2.9 nTPM
Fallopian tube	1.3 nTPM
Thymus	0.6 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

Schwann cells	2.0 nTPM
Adipose tissue	3.9 nTPM
Vascular	2.1 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	10.4 nTPM
Salivary gland	20.8 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	2.6 nTPM
Liver	9.3 nTPM
Breast	6.4 nTPM
Salivary gland	6.2 nTPM
Placenta	4.2 nTPM
Endometrium	3.1 nTPM
Skin	2.6 nTPM
Prostate	2.4 nTPM
Vascular	2.2 nTPM
Esophagus	1.2 nTPM
Fallopian tube	1.0 nTPM
Tongue	0.9 nTPM
Ovary	0.7 nTPM
Skeletal muscle	0.6 nTPM
Adipose tissue	0.2 nTPM
Thymus	0.1 nTPM
Lung	0.0 nTPM

T-cells	48.7 nTPM
Liver	282.6 nTPM
Colon	169.6 nTPM
Endometrium	87.0 nTPM
Skin	57.1 nTPM
Spleen	49.7 nTPM
Esophagus	46.2 nTPM
Vascular	44.2 nTPM
Adipose tissue	40.0 nTPM
Stomach	36.9 nTPM
Bone marrow	34.0 nTPM
Breast	31.0 nTPM
Lung	28.4 nTPM
Prostate	25.5 nTPM
Tongue	19.2 nTPM
Kidney	17.7 nTPM
Fallopian tube	13.2 nTPM
Lymph node	12.6 nTPM
Skeletal muscle	9.8 nTPM
PBMC	7.2 nTPM
Salivary gland	6.1 nTPM
Thymus	4.2 nTPM

Undifferentiated cells	1.4 nTPM
Colon	4.0 nTPM
Rectum	0.1 nTPM
Small intestine	0.0 nTPM

Amygdala excitatory	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Thalamus	0.0 nTPM

Astrocyte	0.0 nTPM
Cerebellum	0.2 nTPM
Basal ganglia	0.1 nTPM
Hypothalamus	0.1 nTPM
Pons	0.1 nTPM
Amygdala	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Spinal cord	0.0 nTPM
Thalamus	0.0 nTPM

Bergmann glia	0.0 nTPM
Cerebellum	0.0 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	8.1 nTPM
Cerebellum	24.7 nTPM
Basal ganglia	17.7 nTPM
Hippocampus	8.1 nTPM
Pons	7.8 nTPM
Midbrain	6.9 nTPM
Spinal cord	6.8 nTPM
Cerebral cortex	5.0 nTPM
Thalamus	4.4 nTPM
Medulla oblongata	3.0 nTPM
Hypothalamus	2.6 nTPM
Amygdala	2.4 nTPM

Cerebellar inhibitory	0.0 nTPM
Pons	0.1 nTPM
Cerebellum	0.0 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM
Thalamus	0.0 nTPM

Choroid plexus epithelial cell	0.0 nTPM
Thalamus	0.0 nTPM
Basal ganglia	0.0 nTPM
Hippocampus	0.0 nTPM
Medulla oblongata	0.0 nTPM

Committed oligodendrocyte precursor	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebellum	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM
Thalamus	0.0 nTPM

Deep-layer corticothalamic and 6b	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	0.2 nTPM
Basal ganglia	0.8 nTPM
Amygdala	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM

Deep-layer near-projecting	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM

Eccentric medium spiny neuron	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Thalamus	0.0 nTPM

Endothelial cell	0.1 nTPM
Basal ganglia	0.9 nTPM
Amygdala	0.0 nTPM
Cerebellum	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM
Thalamus	0.0 nTPM

Ependymal cell	0.0 nTPM
Thalamus	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM