Single cell type - CD48 - 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.	CD48
Gene descriptionⁱ Full gene name according to HGNC.	CD48 molecule
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	CD markers Plasma proteins Transporters
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, Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	3

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.	Cell type enhanced (Monocytes, T-cells, NK-cells, B-cells, Granulocytes, Hofbauer cells, Kupffer cells, Schwann cells, Macrophages)
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.	0.80
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 (Leukocyte)
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
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 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: Cell type enhanced (Monocytes, T-cells, NK-cells, B-cells, Granulocytes, Hofbauer cells, Kupffer cells, Schwann cells, Macrophages)

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 (Leukocyte)

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

CD48 is part of cluster 19 NK-cells - Adaptive immune response with confidenceⁱ 0.9
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.
S1PR4	Sphingosine-1-phosphate receptor 4	0.7195	19
OR2A25	Olfactory receptor family 2 subfamily A member 25	0.6876	19
ICAM3	Intercellular adhesion molecule 3	0.6832	19
C16orf54	Chromosome 16 open reading frame 54	0.6450	78
IKZF1	IKAROS family zinc finger 1	0.6397	19
TRAC	T cell receptor alpha constant	0.6268	19
ZNF101	Zinc finger protein 101	0.6142	19
NOP53	NOP53 ribosome biogenesis factor	0.6105	64
GIMAP2	GTPase, IMAP family member 2	0.6086	19
OR4D1	Olfactory receptor family 4 subfamily D member 1	0.6071	19
LIMD2	LIM domain containing 2	0.6067	73
RPS29	Ribosomal protein S29	0.6005	64
SLC25A45	Solute carrier family 25 member 45	0.6002	55
TRAF3IP3	TRAF3 interacting protein 3	0.5965	19
RPL21	Ribosomal protein L21	0.5914	64

IMMUNE CELLS

CD48 is part of cluster 33 Non-specific - ATP binding with confidenceⁱ 0.87
757 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.
SH3KBP1	SH3 domain containing kinase binding protein 1	0.9524	33
COASY	Coenzyme A synthase	0.9286	33
ALDH3A2	Aldehyde dehydrogenase 3 family member A2	0.9286	33
SLC25A40	Solute carrier family 25 member 40	0.9286	33
DGCR6	DiGeorge syndrome critical region gene 6	0.9286	33
PYGB	Glycogen phosphorylase B	0.9286	33
EHD4	EH domain containing 4	0.9286	33
EIF3C	Eukaryotic translation initiation factor 3 subunit C	0.9048	33
MGST3	Microsomal glutathione S-transferase 3	0.9048	33
AHR	Aryl hydrocarbon receptor	0.9048	33
PLK3	Polo like kinase 3	0.8810	33
DCLRE1B	DNA cross-link repair 1B	0.8571	33
DMAC2	Distal membrane arm assembly component 2	0.8571	33
THAP11	THAP domain containing 11	0.8571	33
C1GALT1C1	C1GALT1 specific chaperone 1	0.8571	38