Single cell type - RNF165 - 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.	RNF165
Gene descriptionⁱ Full gene name according to HGNC.	Ring finger protein 165
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Enzymes
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.	6

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.	Horizontal & Bipolar cells - Neuronal signaling (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 (Horizontal cells, Cone photoreceptor cells, Rod photoreceptor cells, Excitatory neurons, Oligodendrocyte precursor cells, Inhibitory neurons)
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.	0.76
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 (NK-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: Cell type enhanced (Horizontal cells, Cone photoreceptor cells, Rod photoreceptor cells, Excitatory neurons, Oligodendrocyte precursor cells, Inhibitory neurons)

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 (NK-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

RNF165 is part of cluster 71 Horizontal & Bipolar cells - Neuronal signaling with confidenceⁱ 1
205 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.
GPRIN1	G protein regulated inducer of neurite outgrowth 1	0.5976	71
SBK1	SH3 domain binding kinase 1	0.5973	34
SLC12A5	Solute carrier family 12 member 5	0.5936	71
CELSR3	Cadherin EGF LAG seven-pass G-type receptor 3	0.5875	71
RPS6KL1	Ribosomal protein S6 kinase like 1	0.5734	71
GDAP1	Ganglioside induced differentiation associated protein 1	0.5724	71
LRTM2	Leucine rich repeats and transmembrane domains 2	0.5634	71
LRRTM2	Leucine rich repeat transmembrane neuronal 2	0.5618	34
PACSIN1	Protein kinase C and casein kinase substrate in neurons 1	0.5555	66
PDZD4	PDZ domain containing 4	0.5550	19
C1QL3	Complement C1q like 3	0.5544	34
SNCB	Synuclein beta	0.5330	71
STXBP1	Syntaxin binding protein 1	0.5276	66
DRD2	Dopamine receptor D2	0.5251	71
ACAP3	ArfGAP with coiled-coil, ankyrin repeat and PH domains 3	0.5239	66

IMMUNE CELLS

RNF165 is part of cluster 15 NK-cells - Unknown function with confidenceⁱ 1
158 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.
PRDM16	PR/SET domain 16	1.0000	15
SPRY2	Sprouty RTK signaling antagonist 2	1.0000	15
TNFRSF11A	TNF receptor superfamily member 11a	1.0000	15
ENSG00000285025	Mitochondrial elongation factor 1	0.9762	15
AGK	Acylglycerol kinase	0.9762	15
HOXA10	Homeobox A10	0.9762	15
GOLGA8O	Golgin A8 family member O	0.9762	15
CYTL1	Cytokine like 1	0.9762	15
LGALS9B	Galectin 9B	0.9762	15
PTGER1	Prostaglandin E receptor 1	0.9762	15
ZNF221	Zinc finger protein 221	0.9762	15
CABLES1	Cdk5 and Abl enzyme substrate 1	0.9762	15
RRN3	RRN3 homolog, RNA polymerase I transcription factor	0.9762	15
SMIM24	Small integral membrane protein 24	0.9524	15
CLASP1	Cytoplasmic linker associated protein 1	0.9524	15