Single cell type - LRBA - The Human Protein Atlas

LRBA

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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.	LRBA
Gene descriptionⁱ Full gene name according to HGNC.	LPS responsive beige-like anchor protein
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Human disease related genes Plasma proteins
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.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	13

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.	Oligodendrocyte precursor - Unknown function (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 (Oligodendrocyte precursor cells, Excitatory neurons, Oligodendrocytes, Inhibitory neurons, Microglial 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.	0.41
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.	Low cell type specificity
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.	Low immune cell specificity
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 (Oligodendrocyte precursor cells, Excitatory neurons, Oligodendrocytes, Inhibitory neurons, Microglial 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: Low cell type specificity

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: Low immune cell specificity
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

LRBA is part of cluster 76 Oligodendrocyte precursor - Unknown function with confidenceⁱ 1
210 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.
IGF1R	Insulin like growth factor 1 receptor	0.4980	37
IKZF2	IKAROS family zinc finger 2	0.4618	78
USP43	Ubiquitin specific peptidase 43	0.4552	37
RAD54B	RAD54 homolog B	0.4451	34
RABGAP1L	RAB GTPase activating protein 1 like	0.4378	68
PCCA	Propionyl-CoA carboxylase subunit alpha	0.4339	37
ZSCAN25	Zinc finger and SCAN domain containing 25	0.4331	76
POC1B	POC1 centriolar protein B	0.4247	37
ATP2C1	ATPase secretory pathway Ca2+ transporting 1	0.4191	34
XYLT1	Xylosyltransferase 1	0.4136	76
ZNF611	Zinc finger protein 611	0.4084	37
OXNAD1	Oxidoreductase NAD binding domain containing 1	0.4083	78
CHURC1-FNTB	CHURC1-FNTB readthrough	0.4081	76
PPP1R9A	Protein phosphatase 1 regulatory subunit 9A	0.4059	76
BTRC	Beta-transducin repeat containing E3 ubiquitin protein ligase	0.3970	76

IMMUNE CELLS

LRBA is part of cluster 3 Non-specific - Nuclear processes with confidenceⁱ 0.96
471 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.
ZFP90	ZFP90 zinc finger protein	0.9762	3
TSTD2	Thiosulfate sulfurtransferase like domain containing 2	0.9524	3
ZNF280B	Zinc finger protein 280B	0.9524	3
ZNF75D	Zinc finger protein 75D	0.9524	3
ZNF764	Zinc finger protein 764	0.9524	3
ZNF226	Zinc finger protein 226	0.9524	3
PGAP3	Post-GPI attachment to proteins phospholipase 3	0.9524	3
ARPC5L	Actin related protein 2/3 complex subunit 5 like	0.9524	3
S100PBP	S100P binding protein	0.9524	3
MACF1	Microtubule actin crosslinking factor 1	0.9286	3
ZNF195	Zinc finger protein 195	0.9286	3
PPP3CC	Protein phosphatase 3 catalytic subunit gamma	0.9286	3
PLCL2	Phospholipase C like 2	0.9286	3
RCN2	Reticulocalbin 2	0.9286	3
TRIM68	Tripartite motif containing 68	0.9286	3

Adipocytes	11.3 nTPM
Adipose tissue	11.9 nTPM
Breast	10.7 nTPM

Alveolar cells type 1	34.7 nTPM
Lung	34.7 nTPM

Alveolar cells type 2	36.5 nTPM
Lung	36.5 nTPM

Astrocytes	140.9 nTPM
Brain	140.9 nTPM

B-cells	40.5 nTPM
Bone marrow	61.7 nTPM
Lymph node	55.2 nTPM
Spleen	54.9 nTPM
Stomach	54.0 nTPM
Kidney	52.0 nTPM
Salivary gland	40.4 nTPM
Thymus	39.2 nTPM
PBMC	35.4 nTPM
Esophagus	35.4 nTPM
Liver	33.8 nTPM
Adipose tissue	32.9 nTPM
Lung	20.1 nTPM
Skin	11.9 nTPM

Ciliated cells	53.8 nTPM
Lung	68.9 nTPM
Fallopian tube	50.8 nTPM
Endometrium	50.4 nTPM
Bronchus	45.3 nTPM

Club cells	31.6 nTPM
Prostate	35.9 nTPM
Lung	29.6 nTPM
Bronchus	29.3 nTPM

Dendritic cells	24.6 nTPM
Adipose tissue	27.6 nTPM
PBMC	21.6 nTPM

Endothelial cells	14.9 nTPM
Heart muscle	41.4 nTPM
Salivary gland	20.4 nTPM
Tongue	18.9 nTPM
Prostate	17.4 nTPM
Vascular	16.0 nTPM
Liver	15.1 nTPM
Testis	15.0 nTPM
Thymus	14.9 nTPM
Skeletal muscle	13.7 nTPM
Endometrium	13.3 nTPM
Breast	13.2 nTPM
Fallopian tube	12.7 nTPM
Skin	12.6 nTPM
Esophagus	11.2 nTPM
Ovary	11.2 nTPM
Lung	10.3 nTPM
Placenta	6.2 nTPM
Pancreas	5.2 nTPM

Enteroendocrine cells	32.5 nTPM
Rectum	50.3 nTPM
Colon	26.5 nTPM
Small intestine	20.6 nTPM

Fibroblasts	11.3 nTPM
Placenta	20.8 nTPM
Heart muscle	19.3 nTPM
Salivary gland	16.4 nTPM
Esophagus	14.8 nTPM
Skeletal muscle	12.3 nTPM
Stomach	11.5 nTPM
Vascular	10.6 nTPM
Breast	10.2 nTPM
Skin	9.9 nTPM
Liver	9.5 nTPM
Thymus	8.8 nTPM
Fallopian tube	8.7 nTPM
Adipose tissue	8.4 nTPM
Prostate	7.3 nTPM
Lung	6.4 nTPM
Pancreas	5.9 nTPM

Granulocytes	19.0 nTPM
Fallopian tube	20.8 nTPM
Tongue	19.4 nTPM
Lung	16.6 nTPM

Intestinal goblet cells	24.8 nTPM
Rectum	33.9 nTPM
Small intestine	24.8 nTPM
Colon	15.7 nTPM

Lymphatic endothelial cells	20.6 nTPM
Ovary	27.3 nTPM
Fallopian tube	13.8 nTPM

Macrophages	13.0 nTPM
Tongue	28.6 nTPM
Bone marrow	19.3 nTPM
Salivary gland	19.1 nTPM
Prostate	15.9 nTPM
Endometrium	14.8 nTPM
Skin	13.4 nTPM
Kidney	13.3 nTPM
Stomach	12.9 nTPM
Breast	12.5 nTPM
Skeletal muscle	12.1 nTPM
Fallopian tube	12.1 nTPM
Adipose tissue	11.9 nTPM
Esophagus	11.6 nTPM
Vascular	10.3 nTPM
Testis	9.9 nTPM
Thymus	8.4 nTPM
Spleen	8.0 nTPM
Lung	7.9 nTPM
Pancreas	4.1 nTPM

Basal keratinocytes	26.4 nTPM
Tongue	31.4 nTPM
Skin	21.5 nTPM

Basal prostatic cells	28.2 nTPM
Prostate	28.2 nTPM

Basal respiratory cells	20.3 nTPM
Bronchus	20.3 nTPM

Basal squamous epithelial cells	29.9 nTPM
Esophagus	29.9 nTPM

Paneth cells	18.0 nTPM
Small intestine	27.6 nTPM
Rectum	22.8 nTPM
Colon	3.6 nTPM

Plasma cells	28.3 nTPM
Esophagus	41.6 nTPM
Bone marrow	36.2 nTPM
Stomach	34.3 nTPM
Thymus	31.8 nTPM
Fallopian tube	25.7 nTPM
Spleen	24.3 nTPM
Salivary gland	17.0 nTPM
Liver	15.5 nTPM

Schwann cells	18.7 nTPM
Adipose tissue	34.7 nTPM
Esophagus	12.0 nTPM
Vascular	9.4 nTPM

Serous glandular cells	34.1 nTPM
Salivary gland	41.8 nTPM
Tongue	26.5 nTPM

Smooth muscle cells	11.1 nTPM
Prostate	23.1 nTPM
Salivary gland	21.9 nTPM
Tongue	14.1 nTPM
Vascular	12.2 nTPM
Adipose tissue	12.0 nTPM
Liver	11.9 nTPM
Thymus	11.7 nTPM
Ovary	11.0 nTPM
Endometrium	10.8 nTPM
Breast	10.5 nTPM
Skeletal muscle	9.2 nTPM
Skin	9.0 nTPM
Fallopian tube	7.6 nTPM
Placenta	5.0 nTPM
Lung	4.7 nTPM
Esophagus	2.4 nTPM

Suprabasal keratinocytes	32.6 nTPM
Tongue	40.9 nTPM
Skin	24.3 nTPM

T-cells	47.8 nTPM
Bone marrow	71.1 nTPM
Stomach	68.3 nTPM
Tongue	63.9 nTPM
Spleen	63.4 nTPM
Esophagus	60.8 nTPM
Lymph node	53.4 nTPM
Adipose tissue	50.1 nTPM
PBMC	49.8 nTPM
Skeletal muscle	49.5 nTPM
Fallopian tube	48.0 nTPM
Kidney	47.0 nTPM
Thymus	42.9 nTPM
Prostate	41.5 nTPM
Salivary gland	41.4 nTPM
Breast	41.4 nTPM
Lung	38.9 nTPM
Skin	38.6 nTPM
Liver	37.9 nTPM
Endometrium	35.3 nTPM
Vascular	34.6 nTPM
Colon	25.3 nTPM

Undifferentiated cells	27.7 nTPM
Rectum	32.2 nTPM
Small intestine	30.6 nTPM
Colon	20.2 nTPM

Amygdala excitatory	313.5 nTPM
Amygdala	342.6 nTPM
Hypothalamus	342.6 nTPM
Hippocampus	338.6 nTPM
Cerebral cortex	319.9 nTPM
Basal ganglia	284.2 nTPM
Thalamus	253.2 nTPM

Astrocyte	283.8 nTPM
Amygdala	394.5 nTPM
Hypothalamus	356.6 nTPM
Basal ganglia	308.8 nTPM
Hippocampus	291.4 nTPM
Cerebral cortex	283.0 nTPM
Thalamus	274.5 nTPM
Midbrain	262.2 nTPM
Medulla oblongata	249.0 nTPM
Spinal cord	247.8 nTPM
Pons	230.9 nTPM
Cerebellum	223.4 nTPM

Bergmann glia	313.2 nTPM
Cerebellum	353.7 nTPM
Medulla oblongata	319.7 nTPM
Pons	266.1 nTPM

Central nervous system macrophage	459.2 nTPM
Amygdala	629.8 nTPM
Hypothalamus	573.9 nTPM
Basal ganglia	489.7 nTPM
Midbrain	462.1 nTPM
Thalamus	447.0 nTPM
Hippocampus	435.0 nTPM
Pons	417.2 nTPM
Spinal cord	415.1 nTPM
Cerebral cortex	401.9 nTPM
Cerebellum	398.7 nTPM
Medulla oblongata	380.3 nTPM

Cerebellar inhibitory	345.9 nTPM
Medulla oblongata	367.5 nTPM
Spinal cord	360.2 nTPM
Cerebellum	353.3 nTPM
Midbrain	345.3 nTPM
Pons	303.3 nTPM

Cge interneuron	221.8 nTPM
Hypothalamus	268.4 nTPM
Amygdala	251.7 nTPM
Midbrain	212.6 nTPM
Thalamus	211.9 nTPM
Basal ganglia	208.5 nTPM
Cerebral cortex	199.9 nTPM
Hippocampus	199.7 nTPM

Choroid plexus epithelial cell	1117.0 nTPM
Basal ganglia	1546.2 nTPM
Hippocampus	1059.4 nTPM
Medulla oblongata	977.1 nTPM
Thalamus	885.1 nTPM

Committed oligodendrocyte precursor	278.4 nTPM
Amygdala	342.8 nTPM
Medulla oblongata	318.9 nTPM
Hypothalamus	312.0 nTPM
Thalamus	297.6 nTPM
Cerebral cortex	285.6 nTPM
Basal ganglia	278.1 nTPM
Hippocampus	269.8 nTPM
Pons	256.7 nTPM
Cerebellum	250.5 nTPM
Spinal cord	228.1 nTPM
Midbrain	222.6 nTPM

Deep-layer corticothalamic and 6b	307.3 nTPM
Hypothalamus	348.9 nTPM
Amygdala	340.0 nTPM
Cerebral cortex	321.5 nTPM
Basal ganglia	296.6 nTPM
Hippocampus	290.5 nTPM
Midbrain	246.3 nTPM

Deep-layer intratelencephalic	296.2 nTPM
Amygdala	341.5 nTPM
Hypothalamus	335.9 nTPM
Hippocampus	272.6 nTPM
Cerebral cortex	267.1 nTPM
Basal ganglia	263.7 nTPM

Deep-layer near-projecting	246.5 nTPM
Hypothalamus	275.5 nTPM
Amygdala	272.1 nTPM
Cerebral cortex	257.1 nTPM
Basal ganglia	220.6 nTPM
Hippocampus	207.2 nTPM

Eccentric medium spiny neuron	451.1 nTPM
Thalamus	484.1 nTPM
Amygdala	476.8 nTPM
Hypothalamus	470.2 nTPM
Basal ganglia	458.5 nTPM
Cerebral cortex	429.9 nTPM
Hippocampus	387.2 nTPM