Single cell type - VPREB1 - 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.	VPREB1
Gene descriptionⁱ Full gene name according to HGNC.	V-set pre-B cell surrogate light chain 1
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.	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.	NK-cells - Adaptive 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.	Not detected
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.	Not detected
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.	Not detected
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 (memory B-cell, naive B-cell)
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 (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: Not detected

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: Not detected

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 (memory B-cell, naive B-cell)
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

VPREB1 is part of cluster 19 NK-cells - Adaptive immune response with confidenceⁱ 1
266 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.
OR9I1	Olfactory receptor family 9 subfamily I member 1	0.6794	19
NCR2	Natural cytotoxicity triggering receptor 2	0.6372	19
CD160	CD160 molecule	0.6203	19
TRDC	T cell receptor delta constant	0.6190	19
LIM2	Lens intrinsic membrane protein 2	0.6111	19
OR2A25	Olfactory receptor family 2 subfamily A member 25	0.6088	19
CORO1A	Coronin 1A	0.6079	19
TRAF3IP3	TRAF3 interacting protein 3	0.6075	19
KLRF2	Killer cell lectin like receptor F2	0.6063	19
ANXA2R	Annexin A2 receptor	0.5903	19
MFNG	MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	0.5872	19
UTS2	Urotensin 2	0.5816	19
CHST12	Carbohydrate sulfotransferase 12	0.5789	19
TMIGD2	Transmembrane and immunoglobulin domain containing 2	0.5775	19
OR4D1	Olfactory receptor family 4 subfamily D member 1	0.5766	19

IMMUNE CELLS

VPREB1 is part of cluster 34 B-cells - Unknown function with confidenceⁱ 1
112 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.
PIK3C2B	Phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 beta	1.0000	34
SLC38A11	Solute carrier family 38 member 11	1.0000	34
APBB2	Amyloid beta precursor protein binding family B member 2	1.0000	34
BEND5	BEN domain containing 5	1.0000	34
SCN3A	Sodium voltage-gated channel alpha subunit 3	1.0000	34
LIX1	Limb and CNS expressed 1	1.0000	34
SLC2A5	Solute carrier family 2 member 5	1.0000	34
CD72	CD72 molecule	1.0000	34
NT5E	5'-nucleotidase ecto	1.0000	34
CHL1	Cell adhesion molecule L1 like	1.0000	34
DBNDD1	Dysbindin domain containing 1	1.0000	34
HIP1R	Huntingtin interacting protein 1 related	1.0000	34
BCAS4	Breast carcinoma amplified sequence 4	1.0000	34
CCN2	Cellular communication network factor 2	1.0000	34
ANGPTL1	Angiopoietin like 1	1.0000	34