Single cell type - LILRB4 - The Human Protein Atlas

LILRB4

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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.	LILRB4
Gene descriptionⁱ Full gene name according to HGNC.	Leukocyte immunoglobulin like receptor B4
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	CD markers
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.	Membrane, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	7

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 (Dendritic cells, Hofbauer cells, Kupffer cells, Macrophages, Plasma 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.	0.89
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.	Immune cell enhanced (plasmacytoid DC)
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

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 (Dendritic cells, Hofbauer cells, Kupffer cells, Macrophages, Plasma 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: Immune cell enhanced (plasmacytoid DC)
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

LILRB4 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.
MILR1	Mast cell immunoglobulin like receptor 1	0.8152	58
CCR2	C-C motif chemokine receptor 2	0.7817	29
MPEG1	Macrophage expressed 1	0.7486	29
SIGLEC9	Sialic acid binding Ig like lectin 9	0.7329	29
CRYBB1	Crystallin beta B1	0.7043	58
TLR7	Toll like receptor 7	0.7026	58
TBXAS1	Thromboxane A synthase 1	0.6823	58
CD14	CD14 molecule	0.6807	58
CTSB	Cathepsin B	0.6730	58
AIF1	Allograft inflammatory factor 1	0.6649	29
CSF1R	Colony stimulating factor 1 receptor	0.6643	58
CD68	CD68 molecule	0.6642	58
MS4A6A	Membrane spanning 4-domains A6A	0.6606	58
CYBB	Cytochrome b-245 beta chain	0.6583	29
IFI30	IFI30 lysosomal thiol reductase	0.6571	29

IMMUNE CELLS

LILRB4 is part of cluster 10 Non-specific - Membrane trafficking with confidenceⁱ 0.95
408 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.
COPZ1	COPI coat complex subunit zeta 1	1.0000	10
TBC1D9B	TBC1 domain family member 9B	1.0000	10
MYDGF	Myeloid derived growth factor	0.9762	44
ENSG00000283761	Novel protein	0.9762	10
ENSG00000271810	Novel protein, PPM1J-RHOC readthrough	0.9762	10
ENSG00000267001	Novel protein	0.9762	10
SFT2D2	SFT2 domain containing 2	0.9762	10
CLN8	CLN8 transmembrane ER and ERGIC protein	0.9762	10
ARPP21	CAMP regulated phosphoprotein 21	0.9762	44
GPRC5C	G protein-coupled receptor class C group 5 member C	0.9762	44
KIRREL3	Kirre like nephrin family adhesion molecule 3	0.9762	10
UCHL3	Ubiquitin C-terminal hydrolase L3	0.9762	44
SLC1A5	Solute carrier family 1 member 5	0.9762	10
SCARB2	Scavenger receptor class B member 2	0.9524	10
CAPNS1	Calpain small subunit 1	0.9524	10

Adipocytes	0.3 nTPM
Breast	0.7 nTPM
Adipose tissue	0.0 nTPM

Alveolar cells type 1	0.2 nTPM
Lung	0.2 nTPM

Alveolar cells type 2	0.4 nTPM
Lung	0.4 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	4.5 nTPM
Lung	28.2 nTPM
Liver	9.7 nTPM
Kidney	5.2 nTPM
PBMC	4.6 nTPM
Skin	3.4 nTPM
Adipose tissue	2.9 nTPM
Spleen	1.4 nTPM
Salivary gland	1.1 nTPM
Thymus	1.0 nTPM
Lymph node	0.6 nTPM
Stomach	0.4 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

Ciliated cells	0.9 nTPM
Lung	3.3 nTPM
Fallopian tube	0.5 nTPM
Endometrium	0.0 nTPM
Bronchus	0.0 nTPM

Club cells	0.9 nTPM
Lung	2.6 nTPM
Prostate	0.3 nTPM
Bronchus	0.0 nTPM

Dendritic cells	185.8 nTPM
PBMC	215.8 nTPM
Adipose tissue	155.8 nTPM

Endothelial cells	0.6 nTPM
Lung	1.9 nTPM
Vascular	1.8 nTPM
Salivary gland	1.2 nTPM
Tongue	1.2 nTPM
Placenta	1.1 nTPM
Heart muscle	0.9 nTPM
Thymus	0.8 nTPM
Skin	0.4 nTPM
Skeletal muscle	0.2 nTPM
Prostate	0.2 nTPM
Fallopian tube	0.1 nTPM
Ovary	0.1 nTPM
Testis	0.0 nTPM
Liver	0.0 nTPM
Endometrium	0.0 nTPM
Pancreas	0.0 nTPM
Esophagus	0.0 nTPM
Breast	0.0 nTPM

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

Fibroblasts	0.2 nTPM
Vascular	1.4 nTPM
Placenta	0.6 nTPM
Salivary gland	0.6 nTPM
Thymus	0.4 nTPM
Skin	0.3 nTPM
Esophagus	0.2 nTPM
Adipose tissue	0.1 nTPM
Breast	0.1 nTPM
Fallopian tube	0.1 nTPM
Heart muscle	0.0 nTPM
Liver	0.0 nTPM
Pancreas	0.0 nTPM
Skeletal muscle	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM

Granulocytes	0.1 nTPM
Fallopian tube	0.2 nTPM
Lung	0.0 nTPM
Tongue	0.0 nTPM

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

Lymphatic endothelial cells	0.0 nTPM
Fallopian tube	0.1 nTPM
Ovary	0.0 nTPM

Macrophages	86.8 nTPM
Pancreas	238.4 nTPM
Breast	126.0 nTPM
Kidney	112.4 nTPM
Stomach	110.6 nTPM
Vascular	105.3 nTPM
Bone marrow	102.4 nTPM
Fallopian tube	89.7 nTPM
Esophagus	82.2 nTPM
Prostate	80.8 nTPM
Thymus	80.5 nTPM
Spleen	79.2 nTPM
Salivary gland	74.9 nTPM
Endometrium	70.7 nTPM
Adipose tissue	63.1 nTPM
Skin	55.7 nTPM
Lung	54.1 nTPM
Skeletal muscle	51.7 nTPM
Testis	49.0 nTPM
Tongue	22.4 nTPM

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

Plasma cells	42.4 nTPM
Liver	109.7 nTPM
Thymus	99.7 nTPM
Bone marrow	72.5 nTPM
Spleen	38.2 nTPM
Salivary gland	16.6 nTPM
Stomach	2.1 nTPM
Fallopian tube	0.3 nTPM
Esophagus	0.0 nTPM

Schwann cells	0.3 nTPM
Vascular	0.5 nTPM
Adipose tissue	0.4 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	0.9 nTPM
Salivary gland	1.8 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	0.3 nTPM
Liver	1.3 nTPM
Vascular	1.3 nTPM
Thymus	0.7 nTPM
Salivary gland	0.5 nTPM
Placenta	0.3 nTPM
Skin	0.3 nTPM
Ovary	0.3 nTPM
Endometrium	0.2 nTPM
Fallopian tube	0.1 nTPM
Skeletal muscle	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Tongue	0.0 nTPM
Breast	0.0 nTPM

T-cells	0.6 nTPM
Skeletal muscle	2.3 nTPM
Colon	1.9 nTPM
Vascular	1.6 nTPM
Lung	1.3 nTPM
Kidney	0.9 nTPM
PBMC	0.9 nTPM
Liver	0.8 nTPM
Salivary gland	0.7 nTPM
Endometrium	0.2 nTPM
Adipose tissue	0.2 nTPM
Thymus	0.2 nTPM
Fallopian tube	0.2 nTPM
Bone marrow	0.1 nTPM
Tongue	0.1 nTPM
Breast	0.1 nTPM
Skin	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Prostate	0.0 nTPM

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

Amygdala excitatory	0.1 nTPM
Basal ganglia	0.3 nTPM
Hippocampus	0.2 nTPM
Amygdala	0.1 nTPM
Cerebral cortex	0.1 nTPM
Hypothalamus	0.1 nTPM
Thalamus	0.0 nTPM

Astrocyte	0.4 nTPM
Spinal cord	1.0 nTPM
Midbrain	0.7 nTPM
Basal ganglia	0.6 nTPM
Cerebellum	0.6 nTPM
Cerebral cortex	0.3 nTPM
Hippocampus	0.3 nTPM
Amygdala	0.2 nTPM
Medulla oblongata	0.2 nTPM
Hypothalamus	0.1 nTPM
Pons	0.1 nTPM
Thalamus	0.1 nTPM

Bergmann glia	0.1 nTPM
Cerebellum	0.2 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	157.6 nTPM
Basal ganglia	204.9 nTPM
Medulla oblongata	191.0 nTPM
Midbrain	180.0 nTPM
Pons	167.2 nTPM
Cerebellum	166.2 nTPM
Spinal cord	156.6 nTPM
Thalamus	154.2 nTPM
Cerebral cortex	148.8 nTPM
Hippocampus	141.7 nTPM
Hypothalamus	115.1 nTPM
Amygdala	107.9 nTPM

Cerebellar inhibitory	0.3 nTPM
Medulla oblongata	0.6 nTPM
Cerebellum	0.3 nTPM
Midbrain	0.3 nTPM
Pons	0.2 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	0.3 nTPM
Midbrain	1.0 nTPM
Basal ganglia	0.3 nTPM
Thalamus	0.3 nTPM
Amygdala	0.2 nTPM
Hippocampus	0.2 nTPM
Hypothalamus	0.2 nTPM
Cerebral cortex	0.1 nTPM

Choroid plexus epithelial cell	0.1 nTPM
Medulla oblongata	0.3 nTPM
Basal ganglia	0.2 nTPM
Hippocampus	0.0 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	0.3 nTPM
Basal ganglia	1.6 nTPM
Midbrain	0.8 nTPM
Cerebral cortex	0.6 nTPM
Hippocampus	0.5 nTPM
Amygdala	0.0 nTPM
Cerebellum	0.0 nTPM
Hypothalamus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM
Thalamus	0.0 nTPM

Deep-layer corticothalamic and 6b	0.1 nTPM
Amygdala	0.2 nTPM
Basal ganglia	0.2 nTPM
Cerebral cortex	0.1 nTPM
Hippocampus	0.1 nTPM
Hypothalamus	0.1 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	0.1 nTPM
Basal ganglia	0.2 nTPM
Hypothalamus	0.2 nTPM
Amygdala	0.1 nTPM
Cerebral cortex	0.1 nTPM
Hippocampus	0.1 nTPM

Deep-layer near-projecting	0.3 nTPM
Hypothalamus	0.6 nTPM
Hippocampus	0.3 nTPM
Amygdala	0.2 nTPM
Basal ganglia	0.2 nTPM
Cerebral cortex	0.2 nTPM

Eccentric medium spiny neuron	0.1 nTPM
Amygdala	0.2 nTPM
Basal ganglia	0.2 nTPM
Hypothalamus	0.1 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Thalamus	0.0 nTPM

Endothelial cell	0.5 nTPM
Spinal cord	1.7 nTPM
Medulla oblongata	1.0 nTPM
Basal ganglia	0.9 nTPM
Cerebral cortex	0.6 nTPM
Pons	0.6 nTPM
Thalamus	0.6 nTPM
Amygdala	0.0 nTPM
Cerebellum	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM