Single cell type - RIGI - The Human Protein Atlas

RIGI

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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.	RIGI
Gene descriptionⁱ Full gene name according to HGNC.	RNA sensor RIG-I
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Enzymes Human disease related genes Potential drug targets
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.	Non-specific - Transcription (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 (Microglial cells, Oligodendrocyte precursor cells, Astrocytes, Schwann 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.	0.65
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.	Cell type enhanced (Endothelial cell)
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 (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 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 (Microglial cells, Oligodendrocyte precursor cells, Astrocytes, Schwann 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: Cell type enhanced (Endothelial cell)

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 (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

RIGI is part of cluster 49 Non-specific - Transcription with confidenceⁱ 1
378 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.
ASXL1	ASXL transcriptional regulator 1	0.6621	80
NOD1	Nucleotide binding oligomerization domain containing 1	0.5868	49
GTF2H4	General transcription factor IIH subunit 4	0.5651	49
ST6GALNAC6	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 6	0.5637	49
TMEM35B	Transmembrane protein 35B	0.5554	49
ENSG00000285085	Novel protein	0.5452	49
NPHP3-ACAD11	NPHP3-ACAD11 readthrough (NMD candidate)	0.5340	49
CCL11	C-C motif chemokine ligand 11	0.5314	49
RASA4	RAS p21 protein activator 4	0.5193	49
ENSG00000286264	Novel protein	0.5180	49
MUSK	Muscle associated receptor tyrosine kinase	0.5167	2
STIMATE-MUSTN1	STIMATE-MUSTN1 readthrough	0.5116	49
TNFRSF10D	TNF receptor superfamily member 10d	0.5110	41
BRD2	Bromodomain containing 2	0.5082	80
TMED7-TICAM2	TMED7-TICAM2 readthrough	0.5023	49

IMMUNE CELLS

RIGI is part of cluster 24 Non-specific - Transcription with confidenceⁱ 0.9
516 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.
ROM1	Retinal outer segment membrane protein 1	0.9762	24
EPG5	Ectopic P-granules 5 autophagy tethering factor	0.9286	15
ZBTB37	Zinc finger and BTB domain containing 37	0.9286	15
IFNG	Interferon gamma	0.9048	24
ZNF626	Zinc finger protein 626	0.9048	24
IRAK2	Interleukin 1 receptor associated kinase 2	0.9048	24
SERPINE2	Serpin family E member 2	0.9048	24
ERBB2	Erb-b2 receptor tyrosine kinase 2	0.9048	24
PGGHG	Protein-glucosylgalactosylhydroxylysine glucosidase	0.9048	15
MIGA1	Mitoguardin 1	0.9048	24
DGKK	Diacylglycerol kinase kappa	0.8810	24
OGA	O-GlcNAcase	0.8810	20
DNAH14	Dynein axonemal heavy chain 14	0.8810	24
TMEM132C	Transmembrane protein 132C	0.8810	24
WRN	WRN RecQ like helicase	0.8810	24

Adipocytes	14.9 nTPM
Breast	17.4 nTPM
Adipose tissue	12.5 nTPM

Alveolar cells type 1	1.7 nTPM
Lung	1.7 nTPM

Alveolar cells type 2	6.5 nTPM
Lung	6.5 nTPM

B-cells	6.0 nTPM
Lymph node	13.6 nTPM
Kidney	10.4 nTPM
Liver	9.7 nTPM
Stomach	6.3 nTPM
Bone marrow	6.0 nTPM
Esophagus	5.9 nTPM
Thymus	5.9 nTPM
Skin	5.1 nTPM
Spleen	4.1 nTPM
Salivary gland	3.5 nTPM
PBMC	3.1 nTPM
Adipose tissue	2.9 nTPM
Lung	1.3 nTPM

Basal keratinocytes	1.2 nTPM
Tongue	1.7 nTPM
Skin	0.6 nTPM

Ciliated cells	2.3 nTPM
Endometrium	4.5 nTPM
Fallopian tube	1.9 nTPM
Lung	1.6 nTPM
Bronchus	1.2 nTPM

Club cells	2.2 nTPM
Lung	2.7 nTPM
Prostate	2.7 nTPM
Bronchus	1.1 nTPM

Endothelial cells	10.6 nTPM
Esophagus	40.2 nTPM
Skeletal muscle	31.6 nTPM
Heart muscle	15.4 nTPM
Ovary	14.6 nTPM
Vascular	12.5 nTPM
Tongue	10.9 nTPM
Thymus	9.7 nTPM
Salivary gland	8.5 nTPM
Lung	6.1 nTPM
Prostate	6.0 nTPM
Fallopian tube	5.7 nTPM
Skin	5.5 nTPM
Breast	5.3 nTPM
Pancreas	5.2 nTPM
Endometrium	4.8 nTPM
Testis	3.7 nTPM
Liver	2.5 nTPM
Placenta	2.3 nTPM

Enteroendocrine cells	1.0 nTPM
Rectum	1.7 nTPM
Colon	1.2 nTPM
Small intestine	0.0 nTPM

Fibroblasts	6.4 nTPM
Stomach	28.8 nTPM
Esophagus	26.6 nTPM
Skeletal muscle	7.4 nTPM
Breast	5.2 nTPM
Vascular	5.0 nTPM
Fallopian tube	4.7 nTPM
Prostate	4.6 nTPM
Thymus	4.0 nTPM
Adipose tissue	3.7 nTPM
Salivary gland	3.3 nTPM
Liver	2.4 nTPM
Lung	2.3 nTPM
Skin	1.9 nTPM
Heart muscle	1.7 nTPM
Pancreas	0.5 nTPM
Placenta	0.0 nTPM

Granulocytes	3.8 nTPM
Tongue	4.9 nTPM
Lung	3.5 nTPM
Fallopian tube	3.1 nTPM

Intestinal goblet cells	1.0 nTPM
Small intestine	1.9 nTPM
Colon	0.5 nTPM
Rectum	0.5 nTPM

Lymphatic endothelial cells	5.3 nTPM
Ovary	5.5 nTPM
Fallopian tube	5.2 nTPM

Macrophages	3.6 nTPM
Vascular	9.8 nTPM
Breast	6.8 nTPM
Esophagus	6.4 nTPM
Kidney	5.3 nTPM
Skeletal muscle	4.6 nTPM
Testis	4.3 nTPM
Fallopian tube	4.2 nTPM
Lung	4.1 nTPM
Spleen	4.0 nTPM
Prostate	3.2 nTPM
Tongue	3.0 nTPM
Thymus	2.9 nTPM
Salivary gland	2.4 nTPM
Pancreas	2.1 nTPM
Bone marrow	2.0 nTPM
Endometrium	1.8 nTPM
Adipose tissue	1.8 nTPM
Skin	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	2.9 nTPM
Colon	3.6 nTPM
Small intestine	3.5 nTPM
Rectum	1.7 nTPM

Astrocytes	19.5 nTPM
Brain	19.5 nTPM

Early spermatids	0.7 nTPM
Testis	0.7 nTPM

Endometrial stromal cells	2.6 nTPM
Endometrium	2.6 nTPM

Plasma cells	6.7 nTPM
Esophagus	26.0 nTPM
Fallopian tube	7.7 nTPM
Stomach	7.5 nTPM
Salivary gland	4.0 nTPM
Spleen	3.6 nTPM
Thymus	2.0 nTPM
Bone marrow	1.5 nTPM
Liver	1.0 nTPM

Schwann cells	18.8 nTPM
Esophagus	47.9 nTPM
Vascular	7.8 nTPM
Adipose tissue	0.8 nTPM

Serous glandular cells	1.4 nTPM
Salivary gland	2.8 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	5.7 nTPM
Esophagus	28.8 nTPM
Adipose tissue	12.0 nTPM
Skeletal muscle	11.2 nTPM
Breast	8.3 nTPM
Ovary	5.9 nTPM
Vascular	3.6 nTPM
Lung	3.5 nTPM
Thymus	3.4 nTPM
Tongue	3.3 nTPM
Endometrium	2.5 nTPM
Salivary gland	2.4 nTPM
Liver	2.1 nTPM
Fallopian tube	1.7 nTPM
Prostate	1.2 nTPM
Skin	1.1 nTPM
Placenta	0.7 nTPM

T-cells	8.0 nTPM
Esophagus	21.9 nTPM
Spleen	17.1 nTPM
Lymph node	14.4 nTPM
Bone marrow	13.0 nTPM
Vascular	11.7 nTPM
Stomach	10.2 nTPM
Breast	10.1 nTPM
PBMC	8.7 nTPM
Skeletal muscle	8.3 nTPM
Thymus	7.6 nTPM
Fallopian tube	6.3 nTPM
Endometrium	5.2 nTPM
Prostate	4.8 nTPM
Adipose tissue	4.7 nTPM
Salivary gland	4.4 nTPM
Liver	3.9 nTPM
Tongue	3.8 nTPM
Skin	3.5 nTPM
Lung	3.4 nTPM
Colon	2.9 nTPM
Kidney	2.7 nTPM

Undifferentiated cells	0.5 nTPM
Colon	0.6 nTPM
Small intestine	0.6 nTPM
Rectum	0.4 nTPM

Amygdala excitatory	26.3 nTPM
Thalamus	37.7 nTPM
Amygdala	31.8 nTPM
Hippocampus	27.6 nTPM
Cerebral cortex	23.1 nTPM
Hypothalamus	19.2 nTPM
Basal ganglia	18.7 nTPM

Astrocyte	43.1 nTPM
Amygdala	57.2 nTPM
Cerebral cortex	51.6 nTPM
Hypothalamus	48.0 nTPM
Basal ganglia	46.3 nTPM
Hippocampus	45.3 nTPM
Medulla oblongata	44.8 nTPM
Thalamus	39.4 nTPM
Midbrain	38.0 nTPM
Spinal cord	37.2 nTPM
Cerebellum	35.3 nTPM
Pons	30.7 nTPM

Bergmann glia	44.4 nTPM
Medulla oblongata	51.1 nTPM
Pons	41.7 nTPM
Cerebellum	40.3 nTPM

Central nervous system macrophage	80.5 nTPM
Amygdala	98.8 nTPM
Basal ganglia	95.9 nTPM
Hypothalamus	88.0 nTPM
Thalamus	83.6 nTPM
Midbrain	78.9 nTPM
Medulla oblongata	75.3 nTPM
Hippocampus	75.1 nTPM
Spinal cord	74.8 nTPM
Pons	74.4 nTPM
Cerebellum	70.4 nTPM
Cerebral cortex	70.3 nTPM

Cerebellar inhibitory	15.3 nTPM
Pons	20.9 nTPM
Medulla oblongata	16.6 nTPM
Midbrain	16.5 nTPM
Cerebellum	14.5 nTPM
Spinal cord	8.2 nTPM

Cge interneuron	24.0 nTPM
Midbrain	26.0 nTPM
Basal ganglia	25.9 nTPM
Cerebral cortex	25.1 nTPM
Thalamus	24.3 nTPM
Amygdala	24.1 nTPM
Hippocampus	23.5 nTPM
Hypothalamus	19.0 nTPM

Choroid plexus epithelial cell	32.1 nTPM
Basal ganglia	45.2 nTPM
Medulla oblongata	36.2 nTPM
Thalamus	24.7 nTPM
Hippocampus	22.2 nTPM

Committed oligodendrocyte precursor	30.9 nTPM
Midbrain	42.0 nTPM
Hypothalamus	38.9 nTPM
Cerebral cortex	38.6 nTPM
Spinal cord	36.8 nTPM
Hippocampus	34.9 nTPM
Amygdala	32.7 nTPM
Basal ganglia	27.4 nTPM
Thalamus	24.5 nTPM
Cerebellum	22.2 nTPM
Medulla oblongata	21.9 nTPM
Pons	20.4 nTPM

Deep-layer corticothalamic and 6b	18.5 nTPM
Basal ganglia	22.1 nTPM
Amygdala	21.4 nTPM
Hippocampus	19.8 nTPM
Cerebral cortex	19.6 nTPM
Hypothalamus	19.1 nTPM
Midbrain	8.9 nTPM

Deep-layer intratelencephalic	24.3 nTPM
Amygdala	33.7 nTPM
Hippocampus	25.7 nTPM
Basal ganglia	22.9 nTPM
Cerebral cortex	19.8 nTPM
Hypothalamus	19.6 nTPM

Deep-layer near-projecting	22.0 nTPM
Basal ganglia	25.6 nTPM
Amygdala	25.0 nTPM
Hippocampus	21.5 nTPM
Cerebral cortex	20.6 nTPM
Hypothalamus	17.1 nTPM

Eccentric medium spiny neuron	20.9 nTPM
Hippocampus	25.3 nTPM
Amygdala	22.0 nTPM
Cerebral cortex	21.5 nTPM
Basal ganglia	19.2 nTPM
Hypothalamus	19.1 nTPM
Thalamus	18.5 nTPM

Endothelial cell	162.8 nTPM
Hypothalamus	184.9 nTPM
Cerebellum	175.8 nTPM
Midbrain	175.8 nTPM
Basal ganglia	168.7 nTPM
Medulla oblongata	161.0 nTPM
Thalamus	161.0 nTPM
Cerebral cortex	157.9 nTPM
Spinal cord	157.1 nTPM
Hippocampus	153.2 nTPM
Pons	151.0 nTPM
Amygdala	144.2 nTPM

Ependymal cell	37.5 nTPM
Spinal cord	47.9 nTPM
Hippocampus	43.4 nTPM
Medulla oblongata	42.6 nTPM
Thalamus	40.1 nTPM
Amygdala	39.8 nTPM
Basal ganglia	35.4 nTPM
Midbrain	31.7 nTPM
Hypothalamus	28.6 nTPM
Pons	28.3 nTPM