Single cell type - LRRC61 - 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.	LRRC61
Gene descriptionⁱ Full gene name according to HGNC.	Leucine rich repeat containing 61
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.	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.	Renal epithelial cells - Ion transport & homeostasis (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 (Renal collecting duct principal cells, Loop of henle epithelial cells, Renal collecting duct intercalated cells, Papillary tip epithelial cells, Renal connecting tubule cells, Proximal tubule cells, Podocytes, Fallopian tube ciliated cells, Distal convoluted tubule cells, Epicardial 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.	0.83
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.	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

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 (Ductal cells, Renal nephron 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: 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

LRRC61 is part of cluster 64 Renal epithelial cells - Ion transport & homeostasis with confidenceⁱ 1
105 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.
IFNE	Interferon epsilon	0.8797	64
FAM50B	Family with sequence similarity 50 member B	0.8186	64
FAM83H	Family with sequence similarity 83 member H	0.8016	64
MRPS6	Mitochondrial ribosomal protein S6	0.7997	64
EVPLL	Envoplakin like	0.7987	64
RNASE10	Ribonuclease A family member 10 (inactive)	0.7921	64
KLRG2	Killer cell lectin like receptor G2	0.7753	64
ANKRD45	Ankyrin repeat domain 45	0.7743	64
SLC14A2	Solute carrier family 14 member 2	0.7722	64
AGRN	Agrin	0.7691	64
ENSG00000285085	Novel protein	0.7652	64
WNT9B	Wnt family member 9B	0.7633	64
HS3ST6	Heparan sulfate-glucosamine 3-sulfotransferase 6	0.7581	64
TMEM238L	Transmembrane protein 238 like	0.7477	64
AQP2	Aquaporin 2	0.7454	64

IMMUNE CELLS

LRRC61 is part of cluster 12 Non-specific - Mitochondrial translation with confidenceⁱ 0.99
566 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.
BUD23	BUD23 rRNA methyltransferase and ribosome maturation factor	0.9762	12
MRPS21	Mitochondrial ribosomal protein S21	0.9762	12
ZNF589	Zinc finger protein 589	0.9762	12
MRPL17	Mitochondrial ribosomal protein L17	0.9762	12
CBX5	Chromobox 5	0.9762	12
FKBP3	FKBP prolyl isomerase 3	0.9524	12
HEMK1	HemK methyltransferase family member 1	0.9524	12
HMGN1	High mobility group nucleosome binding domain 1	0.9524	12
SBF1	SET binding factor 1	0.9286	12
NOP56	NOP56 ribonucleoprotein	0.9286	12
GPX7	Glutathione peroxidase 7	0.9286	12
LSM8	LSM8 homolog, U6 small nuclear RNA associated	0.9286	12
HIRIP3	HIRA interacting protein 3	0.9286	12
ZNRD2	Zinc ribbon domain containing 2	0.9286	12
SRP72	Signal recognition particle 72	0.9286	12