Single cell type - RPS4Y2 - 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.	RPS4Y2
Gene descriptionⁱ Full gene name according to HGNC.	Ribosomal protein S4 Y-linked 2
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Ribosomal 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.	1

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.	B-cells - Adaptive immunity: Humoral 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.	Group enriched (B-cells, Differentiating spermatogonia, Undifferentiated spermatogonia, Early primary spermatocytes, Prostatic glandular 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.	0.97
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.	Immune cell enriched (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: Group enriched (B-cells, Spermatogenic cell types, Glandular 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: 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: Immune cell enriched (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

RPS4Y2 is part of cluster 87 B-cells - Adaptive immunity: Humoral response with confidenceⁱ 1
200 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.
FCER2	Fc epsilon receptor II	0.8239	87
CXCR5	C-X-C motif chemokine receptor 5	0.8001	87
BANK1	B cell scaffold protein with ankyrin repeats 1	0.7660	87
CNR2	Cannabinoid receptor 2	0.7539	87
LY9	Lymphocyte antigen 9	0.7497	87
IGLJ3	Immunoglobulin lambda joining 3	0.7477	87
VPREB3	V-set pre-B cell surrogate light chain 3	0.7308	87
CR2	Complement C3d receptor 2	0.7301	87
PAX5	Paired box 5	0.7257	87
TNFRSF13C	TNF receptor superfamily member 13C	0.7214	87
FCRLA	Fc receptor like A	0.7206	87
CD19	CD19 molecule	0.7084	87
SHISAL2A	Shisa like 2A	0.7016	87
BTLA	B and T lymphocyte associated	0.6776	87
MS4A1	Membrane spanning 4-domains A1	0.6654	87

IMMUNE CELLS

RPS4Y2 is part of cluster 20 Non-specific - DNA binding 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.
ELAVL2	ELAV like RNA binding protein 2	1.0000	20
NSUN7	NOP2/Sun RNA methyltransferase family member 7	1.0000	20
CYP1A2	Cytochrome P450 family 1 subfamily A member 2	1.0000	20
MAB21L3	Mab-21 like 3	1.0000	20
FADS6	Fatty acid desaturase 6	1.0000	20
HECW1	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1.0000	20
FANCD2OS	FANCD2 opposite strand	1.0000	20
OR7G2	Olfactory receptor family 7 subfamily G member 2	1.0000	20
FBLIM1	Filamin binding LIM protein 1	0.9762	20
ARGFX	Arginine-fifty homeobox	0.9762	20
OR5AS1	Olfactory receptor family 5 subfamily AS member 1	0.9762	20
SLC35E3	Solute carrier family 35 member E3	0.9762	20
ATP23	ATP23 metallopeptidase and ATP synthase assembly factor homolog	0.9762	20
SPACA7	Sperm acrosome associated 7	0.9762	20
MIPOL1	Mirror-image polydactyly 1	0.9762	20