Single cell type - RNF180 - The Human Protein Atlas

RNF180

Search result

Field

Term

Cluster

Pathway

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.	RNF180
Gene descriptionⁱ Full gene name according to HGNC.	Ring finger protein 180
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Enzymes Metabolic 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.	Membrane, 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.	Neurons - 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 (Oligodendrocyte precursor cells, Inhibitory neurons, Excitatory 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.	0.61
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 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 (Oligodendrocyte precursor cells, Inhibitory neurons, Excitatory 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: 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

RNF180 is part of cluster 69 Neurons - Neuronal signaling with confidenceⁱ 1
331 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.
SLC44A5	Solute carrier family 44 member 5	0.6816	69
KCNK2	Potassium two pore domain channel subfamily K member 2	0.6709	69
SNTG1	Syntrophin gamma 1	0.6649	69
PCDH11X	Protocadherin 11 X-linked	0.6637	69
TRPC6	Transient receptor potential cation channel subfamily C member 6	0.6568	69
SHISA6	Shisa family member 6	0.6543	69
PPM1E	Protein phosphatase, Mg2+/Mn2+ dependent 1E	0.6389	69
NDST4	N-deacetylase and N-sulfotransferase 4	0.6300	69
CLVS1	Clavesin 1	0.6273	69
SCMH1	Scm polycomb group protein homolog 1	0.6235	69
PNMA6F	PNMA family member 6F	0.6105	69
KCNMB2	Potassium calcium-activated channel subfamily M regulatory beta subunit 2	0.6099	76
NBEA	Neurobeachin	0.6067	69
CDH9	Cadherin 9	0.6053	69
GLRA2	Glycine receptor alpha 2	0.6024	69

IMMUNE CELLS

RNF180 is part of cluster 46 Basophils - Proteolysis with confidenceⁱ 1
156 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.
ZNF638	Zinc finger protein 638	1.0000	46
ITGB8	Integrin subunit beta 8	1.0000	46
CABP5	Calcium binding protein 5	1.0000	46
CCNP	Cyclin P	1.0000	46
KLF5	KLF transcription factor 5	1.0000	46
MID1	Midline 1	1.0000	46
TPSD1	Tryptase delta 1	1.0000	46
L2HGDH	L-2-hydroxyglutarate dehydrogenase	1.0000	46
NLK	Nemo like kinase	1.0000	46
FRYL	FRY like transcription coactivator	1.0000	46
THSD7A	Thrombospondin type 1 domain containing 7A	1.0000	46
SEMA3C	Semaphorin 3C	1.0000	46
CTNNA2	Catenin alpha 2	1.0000	46
SNCAIP	Synuclein alpha interacting protein	1.0000	46
HIPK2	Homeodomain interacting protein kinase 2	1.0000	46

Adipocytes	9.4 nTPM
Adipose tissue	10.9 nTPM
Breast	7.9 nTPM

Alveolar cells type 1	14.4 nTPM
Lung	14.4 nTPM

Alveolar cells type 2	8.9 nTPM
Lung	8.9 nTPM

Astrocytes	48.9 nTPM
Brain	48.9 nTPM

B-cells	0.6 nTPM
Salivary gland	2.7 nTPM
Thymus	2.6 nTPM
Lung	1.3 nTPM
Adipose tissue	0.4 nTPM
Spleen	0.4 nTPM
Lymph node	0.1 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM

Ciliated cells	6.4 nTPM
Endometrium	12.6 nTPM
Fallopian tube	6.5 nTPM
Lung	5.9 nTPM
Bronchus	0.6 nTPM

Club cells	5.5 nTPM
Lung	9.0 nTPM
Prostate	6.4 nTPM
Bronchus	1.0 nTPM

Endothelial cells	8.4 nTPM
Prostate	17.1 nTPM
Salivary gland	14.9 nTPM
Vascular	13.1 nTPM
Liver	11.3 nTPM
Heart muscle	10.8 nTPM
Thymus	10.8 nTPM
Breast	10.5 nTPM
Fallopian tube	10.2 nTPM
Skeletal muscle	8.3 nTPM
Ovary	8.1 nTPM
Testis	7.9 nTPM
Tongue	7.4 nTPM
Esophagus	7.3 nTPM
Skin	4.5 nTPM
Endometrium	3.1 nTPM
Pancreas	2.6 nTPM
Lung	1.9 nTPM
Placenta	0.6 nTPM

Enteroendocrine cells	6.5 nTPM
Small intestine	17.2 nTPM
Rectum	1.7 nTPM
Colon	0.5 nTPM

Fibroblasts	9.7 nTPM
Heart muscle	31.3 nTPM
Prostate	18.5 nTPM
Liver	16.6 nTPM
Vascular	13.8 nTPM
Lung	11.4 nTPM
Fallopian tube	10.4 nTPM
Stomach	10.1 nTPM
Placenta	6.4 nTPM
Salivary gland	6.4 nTPM
Skeletal muscle	6.2 nTPM
Thymus	5.4 nTPM
Esophagus	4.5 nTPM
Pancreas	4.3 nTPM
Skin	3.8 nTPM
Breast	3.7 nTPM
Adipose tissue	1.9 nTPM

Granulocytes	0.1 nTPM
Fallopian tube	0.4 nTPM
Lung	0.0 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	1.1 nTPM
Small intestine	1.8 nTPM
Rectum	0.9 nTPM
Colon	0.5 nTPM

Lymphatic endothelial cells	9.7 nTPM
Ovary	10.9 nTPM
Fallopian tube	8.5 nTPM

Macrophages	1.0 nTPM
Prostate	5.0 nTPM
Endometrium	2.5 nTPM
Vascular	2.4 nTPM
Thymus	1.9 nTPM
Salivary gland	1.7 nTPM
Esophagus	1.3 nTPM
Testis	1.2 nTPM
Tongue	1.2 nTPM
Kidney	0.9 nTPM
Breast	0.5 nTPM
Fallopian tube	0.5 nTPM
Skeletal muscle	0.4 nTPM
Lung	0.1 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Adipose tissue	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	7.1 nTPM
Small intestine	20.7 nTPM
Rectum	0.5 nTPM
Colon	0.0 nTPM

Basal prostatic cells	34.5 nTPM
Prostate	34.5 nTPM

Basal squamous epithelial cells	6.6 nTPM
Esophagus	6.6 nTPM

Bipolar cells	13.5 nTPM
Eye	13.5 nTPM

Collecting duct cells	13.6 nTPM
Kidney	13.6 nTPM

Plasma cells	0.5 nTPM
Fallopian tube	1.9 nTPM
Liver	1.0 nTPM
Salivary gland	0.9 nTPM
Thymus	0.3 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Schwann cells	14.1 nTPM
Esophagus	35.9 nTPM
Vascular	6.3 nTPM
Adipose tissue	0.0 nTPM

Serous glandular cells	4.6 nTPM
Salivary gland	9.3 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	21.5 nTPM
Vascular	44.7 nTPM
Skeletal muscle	37.9 nTPM
Prostate	32.2 nTPM
Thymus	31.6 nTPM
Lung	28.2 nTPM
Salivary gland	23.8 nTPM
Adipose tissue	21.2 nTPM
Ovary	20.2 nTPM
Fallopian tube	18.3 nTPM
Skin	18.0 nTPM
Breast	15.8 nTPM
Esophagus	14.4 nTPM
Liver	13.2 nTPM
Endometrium	12.2 nTPM
Tongue	9.3 nTPM
Placenta	2.1 nTPM

T-cells	0.6 nTPM
Prostate	4.4 nTPM
Endometrium	4.3 nTPM
Vascular	1.2 nTPM
Tongue	0.6 nTPM
Skeletal muscle	0.4 nTPM
Salivary gland	0.2 nTPM
Breast	0.2 nTPM
Fallopian tube	0.2 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Thymus	0.0 nTPM

Undifferentiated cells	1.6 nTPM
Small intestine	4.2 nTPM
Rectum	0.6 nTPM
Colon	0.2 nTPM

Amygdala excitatory	120.4 nTPM
Thalamus	142.9 nTPM
Hypothalamus	136.3 nTPM
Basal ganglia	134.5 nTPM
Amygdala	110.8 nTPM
Hippocampus	102.3 nTPM
Cerebral cortex	95.8 nTPM

Astrocyte	108.8 nTPM
Hypothalamus	142.7 nTPM
Basal ganglia	134.9 nTPM
Midbrain	128.5 nTPM
Amygdala	124.9 nTPM
Thalamus	123.9 nTPM
Pons	105.2 nTPM
Hippocampus	94.6 nTPM
Medulla oblongata	90.8 nTPM
Spinal cord	84.7 nTPM
Cerebellum	84.6 nTPM
Cerebral cortex	81.8 nTPM

Bergmann glia	110.7 nTPM
Medulla oblongata	119.3 nTPM
Cerebellum	110.7 nTPM
Pons	102.1 nTPM

Central nervous system macrophage	28.1 nTPM
Amygdala	42.4 nTPM
Hypothalamus	40.8 nTPM
Spinal cord	29.4 nTPM
Thalamus	28.7 nTPM
Basal ganglia	26.8 nTPM
Hippocampus	26.6 nTPM
Midbrain	26.3 nTPM
Cerebral cortex	26.0 nTPM
Pons	21.3 nTPM
Medulla oblongata	20.5 nTPM
Cerebellum	20.1 nTPM

Cerebellar inhibitory	126.2 nTPM
Spinal cord	132.0 nTPM
Medulla oblongata	127.6 nTPM
Pons	126.9 nTPM
Cerebellum	123.9 nTPM
Midbrain	120.4 nTPM

Cge interneuron	146.2 nTPM
Hypothalamus	156.4 nTPM
Amygdala	153.9 nTPM
Cerebral cortex	146.1 nTPM
Midbrain	144.7 nTPM
Thalamus	142.5 nTPM
Basal ganglia	141.3 nTPM
Hippocampus	138.7 nTPM

Choroid plexus epithelial cell	152.0 nTPM
Basal ganglia	221.7 nTPM
Thalamus	139.8 nTPM
Hippocampus	124.8 nTPM
Medulla oblongata	121.7 nTPM

Committed oligodendrocyte precursor	110.7 nTPM
Spinal cord	147.2 nTPM
Hippocampus	146.2 nTPM
Cerebellum	123.7 nTPM
Cerebral cortex	122.2 nTPM
Amygdala	117.3 nTPM
Midbrain	108.4 nTPM
Pons	101.8 nTPM
Medulla oblongata	96.8 nTPM
Basal ganglia	93.6 nTPM
Hypothalamus	93.5 nTPM
Thalamus	67.1 nTPM

Deep-layer corticothalamic and 6b	117.7 nTPM
Hypothalamus	149.9 nTPM
Amygdala	134.4 nTPM
Hippocampus	120.3 nTPM
Cerebral cortex	110.9 nTPM
Basal ganglia	98.7 nTPM
Midbrain	92.1 nTPM

Deep-layer intratelencephalic	107.6 nTPM
Amygdala	122.3 nTPM
Hypothalamus	114.9 nTPM
Hippocampus	104.4 nTPM
Cerebral cortex	102.2 nTPM
Basal ganglia	94.2 nTPM

Deep-layer near-projecting	148.1 nTPM
Hypothalamus	179.4 nTPM
Amygdala	156.5 nTPM
Cerebral cortex	140.8 nTPM
Basal ganglia	140.1 nTPM
Hippocampus	123.9 nTPM

Eccentric medium spiny neuron	169.4 nTPM
Hypothalamus	187.8 nTPM
Amygdala	181.8 nTPM
Thalamus	173.7 nTPM
Cerebral cortex	161.7 nTPM
Basal ganglia	159.8 nTPM
Hippocampus	151.7 nTPM

Endothelial cell	69.2 nTPM
Amygdala	91.7 nTPM
Medulla oblongata	87.2 nTPM
Hypothalamus	84.4 nTPM
Cerebral cortex	80.6 nTPM
Midbrain	73.7 nTPM
Basal ganglia	66.2 nTPM
Pons	66.2 nTPM
Hippocampus	64.1 nTPM
Thalamus	56.5 nTPM
Spinal cord	48.3 nTPM
Cerebellum	42.6 nTPM

Ependymal cell	88.6 nTPM
Spinal cord	122.7 nTPM
Amygdala	103.5 nTPM
Basal ganglia	98.7 nTPM
Hypothalamus	96.4 nTPM
Midbrain	85.7 nTPM
Hippocampus	80.6 nTPM
Thalamus	74.1 nTPM
Pons	71.9 nTPM
Medulla oblongata	64.1 nTPM