Single cell type - BRI3 - 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.	BRI3
Gene descriptionⁱ Full gene name according to HGNC.	Brain protein I3
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.	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.	Macrophages - Phagocytosis & lysosomal degradation (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 (Neutrophils, Hofbauer cells, Early spermatids, Alveolar cells type 2)
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.	0.31
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.	Immune cell enhanced (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

ASSAYSⁱ

Single cell type

Cell type enrichment

Single nuclei - Brain

Immune cells

Expression clustering

SINGLE CELL TYPESⁱ A summary of normalized single cell RNA (nCPM) from all single cell types. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. * Single nuclei Read more
Single cell type groups RNA single cell type group specificity: Cell type enhanced (Neutrophils)

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: Immune cell enhanced (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

BRI3 is part of cluster 72 Macrophages - Phagocytosis & lysosomal degradation with confidenceⁱ 1
247 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.
FTL	Ferritin light chain	0.6849	72
ACP5	Acid phosphatase 5, tartrate resistant	0.6566	72
PNPLA6	Patatin like phospholipase domain containing 6	0.6513	72
DCSTAMP	Dendrocyte expressed seven transmembrane protein	0.6320	72
CCL18	C-C motif chemokine ligand 18	0.6296	72
FCGR1A	Fc gamma receptor Ia	0.6218	72
MARCO	Macrophage receptor with collagenous structure	0.6068	72
ATP6V0B	ATPase H+ transporting V0 subunit b	0.6058	72
DNASE2	Deoxyribonuclease 2, lysosomal	0.5953	72
CHIT1	Chitinase 1	0.5937	72
CYP27A1	Cytochrome P450 family 27 subfamily A member 1	0.5926	72
ATP6AP1	ATPase H+ transporting accessory protein 1	0.5924	72
GRN	Granulin precursor	0.5915	72
CTSD	Cathepsin D	0.5830	72
IGSF6	Immunoglobulin superfamily member 6	0.5821	31

IMMUNE CELLS

BRI3 is part of cluster 7 Non-specific - Innate immune response with confidenceⁱ 1
237 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.
PLAUR	Plasminogen activator, urokinase receptor	1.0000	7
RAB1B	RAB1B, member RAS oncogene family	1.0000	7
GNAI2	G protein subunit alpha i2	1.0000	7
NACC2	NACC family member 2	1.0000	7
RAC1	Rac family small GTPase 1	1.0000	7
ENSG00000260861	Novel protein, SIRPB1-SIRPD readthrough	0.9762	7
OAZ2	Ornithine decarboxylase antizyme 2	0.9762	7
CLEC1B	C-type lectin domain family 1 member B	0.9762	7
SCLT1	Sodium channel and clathrin linker 1	0.9762	7
BIN3	Bridging integrator 3	0.9762	7
GALNS	Galactosamine (N-acetyl)-6-sulfatase	0.9762	7
ABHD2	Abhydrolase domain containing 2, acylglycerol lipase	0.9762	7
MPP1	MAGUK p55 scaffold protein 1	0.9762	7
RHOT1	Ras homolog family member T1	0.9762	7
VPS18	VPS18 core subunit of CORVET and HOPS complexes	0.9762	7