Single cell type - SNX24 - 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.	SNX24
Gene descriptionⁱ Full gene name according to HGNC.	Sorting nexin 24
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.	4

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 (Esophageal apical cells, Kupffer 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.	0.43
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 (non-classical monocyte)
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 (Apical squamous epithelial 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: Immune cell enhanced (non-classical monocyte)
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

SNX24 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.
WWP1	WW domain containing E3 ubiquitin protein ligase 1	0.4906	72
LGMN	Legumain	0.4375	72
SLC38A6	Solute carrier family 38 member 6	0.4367	72
RGL1	Ral guanine nucleotide dissociation stimulator like 1	0.4204	72
DNAAF9	Dynein axonemal assembly factor 9	0.3874	72
NMRK1	Nicotinamide riboside kinase 1	0.3869	84
EDA	Ectodysplasin A	0.3794	72
SIGLEC1	Sialic acid binding Ig like lectin 1	0.3793	72
SLC46A1	Solute carrier family 46 member 1	0.3724	72
FRMD4B	FERM domain containing 4B	0.3680	72
FCHO2	FCH and mu domain containing endocytic adaptor 2	0.3669	72
SNX6	Sorting nexin 6	0.3640	72
CMKLR1	Chemerin chemokine-like receptor 1	0.3611	72
BLVRB	Biliverdin reductase B	0.3551	84
DEAF1	DEAF1 transcription factor	0.3549	84

IMMUNE CELLS

SNX24 is part of cluster 37 Monocytes & Neutrophils - Innate immune response with confidenceⁱ 0.98
275 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.
GRIN3A	Glutamate ionotropic receptor NMDA type subunit 3A	1.0000	37
RABGGTA	Rab geranylgeranyltransferase subunit alpha	1.0000	37
CEBPG	CCAAT enhancer binding protein gamma	1.0000	37
OCRL	OCRL inositol polyphosphate-5-phosphatase	0.9762	40
CALHM2	Calcium homeostasis modulator family member 2	0.9762	37
MYOF	Myoferlin	0.9762	40
MYO1G	Myosin IG	0.9762	33
ACP2	Acid phosphatase 2, lysosomal	0.9762	37
TSKS	Testis specific serine kinase substrate	0.9762	40
TUBA1B	Tubulin alpha 1b	0.9762	37
ACOT9	Acyl-CoA thioesterase 9	0.9762	40
PSMA4	Proteasome 20S subunit alpha 4	0.9762	37
CCRL2	C-C motif chemokine receptor like 2	0.9762	37
PHF19	PHD finger protein 19	0.9762	33
PCDH12	Protocadherin 12	0.9762	40