Single cell type - MRI1 - The Human Protein Atlas

MRI1

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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.	MRI1
Gene descriptionⁱ Full gene name according to HGNC.	Methylthioribose-1-phosphate isomerase 1
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.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	2

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.	Low cell type specificity
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.	0.28
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: Low cell type specificity

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

MRI1 is part of cluster 55 Non-specific - Transcription with confidenceⁱ 1
709 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.
N4BP2L2	NEDD4 binding protein 2 like 2	0.5837	55
ZNF224	Zinc finger protein 224	0.5553	55
PNISR	PNN interacting serine and arginine rich protein	0.5457	55
TTC14	Tetratricopeptide repeat domain 14	0.5329	55
ZNF83	Zinc finger protein 83	0.5040	6
CWF19L2	CWF19 like cell cycle control factor 2	0.4985	55
ELMOD3	ELMO domain containing 3	0.4865	55
PIGL	Phosphatidylinositol glycan anchor biosynthesis class L	0.4853	8
ZFP14	ZFP14 zinc finger protein	0.4695	55
XNDC1N	XRCC1 N-terminal domain containing 1, N-terminal like	0.4636	55
GOLGA8B	Golgin A8 family member B	0.4549	55
NKTR	Natural killer cell triggering receptor	0.4544	55
ATF6B	Activating transcription factor 6 beta	0.4522	55
GON4L	Gon-4 like	0.4475	55
ZNF75A	Zinc finger protein 75a	0.4375	55

IMMUNE CELLS

MRI1 is part of cluster 13 Non-specific - Mitochondria with confidenceⁱ 0.82
458 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.
NOMO1	NODAL modulator 1	1.0000	13
AARSD1	Alanyl-tRNA synthetase domain containing 1	0.9762	13
USP40	Ubiquitin specific peptidase 40	0.9762	13
PRPF8	Pre-mRNA processing factor 8	0.9762	13
SLX4IP	SLX4 interacting protein	0.9762	30
STK16	Serine/threonine kinase 16	0.9524	13
EFCAB2	EF-hand calcium binding domain 2	0.9524	13
ENTPD7	Ectonucleoside triphosphate diphosphohydrolase 7	0.9524	13
CCT2	Chaperonin containing TCP1 subunit 2	0.9524	13
ARMC5	Armadillo repeat containing 5	0.9524	30
ESR2	Estrogen receptor 2	0.9524	30
WARS2	Tryptophanyl tRNA synthetase 2, mitochondrial	0.9524	13
PIGQ	Phosphatidylinositol glycan anchor biosynthesis class Q	0.9524	13
CUL7	Cullin 7	0.9524	30
RRP9	Ribosomal RNA processing 9, U3 small nucleolar RNA binding protein	0.9286	13

Adipocytes	8.2 nTPM
Adipose tissue	9.1 nTPM
Breast	7.3 nTPM

Alveolar cells type 1	9.3 nTPM
Lung	9.3 nTPM

Alveolar cells type 2	8.2 nTPM
Lung	8.2 nTPM

Astrocytes	14.2 nTPM
Brain	14.2 nTPM

B-cells	12.4 nTPM
Liver	24.2 nTPM
Salivary gland	18.4 nTPM
Kidney	15.6 nTPM
Thymus	15.2 nTPM
Adipose tissue	14.0 nTPM
PBMC	13.9 nTPM
Stomach	12.7 nTPM
Bone marrow	12.3 nTPM
Esophagus	11.8 nTPM
Spleen	8.4 nTPM
Lung	8.0 nTPM
Skin	3.4 nTPM
Lymph node	3.1 nTPM

Ciliated cells	14.6 nTPM
Bronchus	18.4 nTPM
Lung	15.9 nTPM
Fallopian tube	14.0 nTPM
Endometrium	10.2 nTPM

Club cells	12.1 nTPM
Prostate	13.7 nTPM
Bronchus	11.8 nTPM
Lung	10.9 nTPM

Endothelial cells	13.5 nTPM
Placenta	72.1 nTPM
Ovary	21.9 nTPM
Testis	16.5 nTPM
Prostate	12.3 nTPM
Endometrium	11.7 nTPM
Vascular	11.7 nTPM
Lung	11.1 nTPM
Thymus	10.6 nTPM
Skeletal muscle	10.0 nTPM
Salivary gland	9.9 nTPM
Breast	9.7 nTPM
Esophagus	8.3 nTPM
Skin	7.9 nTPM
Liver	7.6 nTPM
Tongue	7.5 nTPM
Heart muscle	6.3 nTPM
Fallopian tube	5.6 nTPM
Pancreas	2.6 nTPM

Enteroendocrine cells	5.7 nTPM
Rectum	11.7 nTPM
Colon	5.2 nTPM
Small intestine	0.0 nTPM

Fibroblasts	11.6 nTPM
Adipose tissue	19.5 nTPM
Heart muscle	15.8 nTPM
Prostate	13.9 nTPM
Salivary gland	13.8 nTPM
Stomach	13.0 nTPM
Lung	12.6 nTPM
Placenta	11.5 nTPM
Vascular	10.9 nTPM
Liver	10.7 nTPM
Skeletal muscle	10.6 nTPM
Thymus	10.4 nTPM
Breast	10.2 nTPM
Fallopian tube	10.2 nTPM
Skin	8.3 nTPM
Esophagus	8.0 nTPM
Pancreas	7.0 nTPM

Granulocytes	10.0 nTPM
Lung	17.1 nTPM
Fallopian tube	8.1 nTPM
Tongue	4.9 nTPM

Intestinal goblet cells	9.5 nTPM
Rectum	12.0 nTPM
Small intestine	11.6 nTPM
Colon	4.9 nTPM

Lymphatic endothelial cells	17.8 nTPM
Ovary	27.3 nTPM
Fallopian tube	8.3 nTPM

Macrophages	7.4 nTPM
Salivary gland	12.9 nTPM
Prostate	12.8 nTPM
Testis	11.8 nTPM
Adipose tissue	11.5 nTPM
Vascular	10.8 nTPM
Bone marrow	9.1 nTPM
Lung	8.3 nTPM
Thymus	8.0 nTPM
Breast	7.7 nTPM
Tongue	7.2 nTPM
Skeletal muscle	6.9 nTPM
Skin	6.7 nTPM
Fallopian tube	6.7 nTPM
Pancreas	6.2 nTPM
Endometrium	6.1 nTPM
Kidney	3.5 nTPM
Stomach	2.6 nTPM
Esophagus	1.3 nTPM
Spleen	1.0 nTPM

Paneth cells	8.3 nTPM
Rectum	10.7 nTPM
Colon	7.2 nTPM
Small intestine	6.9 nTPM

Basal prostatic cells	15.3 nTPM
Prostate	15.3 nTPM

Basal squamous epithelial cells	8.6 nTPM
Esophagus	8.6 nTPM

Collecting duct cells	13.6 nTPM
Kidney	13.6 nTPM

Cytotrophoblasts	13.6 nTPM
Placenta	13.6 nTPM

Plasma cells	12.7 nTPM
Thymus	19.1 nTPM
Bone marrow	16.6 nTPM
Spleen	14.4 nTPM
Salivary gland	12.1 nTPM
Esophagus	10.4 nTPM
Liver	10.0 nTPM
Fallopian tube	9.6 nTPM
Stomach	9.2 nTPM

Schwann cells	16.9 nTPM
Esophagus	24.0 nTPM
Vascular	15.7 nTPM
Adipose tissue	10.9 nTPM

Serous glandular cells	8.3 nTPM
Salivary gland	12.2 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	14.1 nTPM
Ovary	26.0 nTPM
Lung	25.9 nTPM
Adipose tissue	22.5 nTPM
Prostate	14.6 nTPM
Thymus	13.2 nTPM
Liver	12.7 nTPM
Vascular	12.3 nTPM
Breast	12.3 nTPM
Esophagus	12.0 nTPM
Fallopian tube	11.6 nTPM
Tongue	11.1 nTPM
Placenta	11.0 nTPM
Endometrium	10.8 nTPM
Skin	10.8 nTPM
Skeletal muscle	10.7 nTPM
Salivary gland	8.8 nTPM

Suprabasal keratinocytes	10.8 nTPM
Skin	12.8 nTPM
Tongue	8.8 nTPM

T-cells	14.1 nTPM
PBMC	30.7 nTPM
Salivary gland	19.1 nTPM
Lung	18.5 nTPM
Thymus	17.8 nTPM
Kidney	16.8 nTPM
Adipose tissue	16.2 nTPM
Prostate	16.1 nTPM
Bone marrow	16.0 nTPM
Vascular	15.3 nTPM
Tongue	15.1 nTPM
Skin	14.4 nTPM
Fallopian tube	12.3 nTPM
Esophagus	12.2 nTPM
Skeletal muscle	11.7 nTPM
Endometrium	10.6 nTPM
Stomach	10.6 nTPM
Breast	9.8 nTPM
Colon	9.7 nTPM
Liver	8.9 nTPM
Spleen	8.0 nTPM
Lymph node	5.9 nTPM

Undifferentiated cells	9.7 nTPM
Rectum	11.0 nTPM
Small intestine	9.4 nTPM
Colon	8.7 nTPM

Amygdala excitatory	45.2 nTPM
Cerebral cortex	54.3 nTPM
Basal ganglia	53.3 nTPM
Thalamus	50.4 nTPM
Amygdala	47.6 nTPM
Hippocampus	36.8 nTPM
Hypothalamus	29.1 nTPM

Astrocyte	31.2 nTPM
Pons	38.5 nTPM
Medulla oblongata	38.2 nTPM
Basal ganglia	38.0 nTPM
Thalamus	35.0 nTPM
Hypothalamus	33.3 nTPM
Midbrain	32.9 nTPM
Cerebral cortex	30.7 nTPM
Hippocampus	30.2 nTPM
Cerebellum	29.7 nTPM
Amygdala	21.2 nTPM
Spinal cord	15.2 nTPM

Bergmann glia	49.1 nTPM
Medulla oblongata	66.1 nTPM
Cerebellum	48.1 nTPM
Pons	33.1 nTPM

Central nervous system macrophage	34.3 nTPM
Cerebral cortex	43.9 nTPM
Medulla oblongata	40.9 nTPM
Basal ganglia	40.6 nTPM
Hippocampus	38.0 nTPM
Thalamus	34.4 nTPM
Cerebellum	33.4 nTPM
Pons	33.4 nTPM
Midbrain	32.7 nTPM
Hypothalamus	32.6 nTPM
Amygdala	29.4 nTPM
Spinal cord	18.0 nTPM

Cerebellar inhibitory	29.8 nTPM
Cerebellum	37.0 nTPM
Midbrain	36.4 nTPM
Medulla oblongata	32.8 nTPM
Pons	26.5 nTPM
Spinal cord	16.5 nTPM

Cge interneuron	41.4 nTPM
Basal ganglia	49.7 nTPM
Cerebral cortex	48.6 nTPM
Amygdala	44.6 nTPM
Hippocampus	44.6 nTPM
Midbrain	38.9 nTPM
Thalamus	35.0 nTPM
Hypothalamus	28.6 nTPM

Choroid plexus epithelial cell	31.5 nTPM
Medulla oblongata	40.2 nTPM
Hippocampus	38.8 nTPM
Thalamus	27.4 nTPM
Basal ganglia	19.6 nTPM

Committed oligodendrocyte precursor	24.9 nTPM
Medulla oblongata	45.2 nTPM
Midbrain	35.3 nTPM
Cerebral cortex	30.4 nTPM
Cerebellum	27.0 nTPM
Basal ganglia	26.3 nTPM
Hippocampus	24.8 nTPM
Thalamus	24.1 nTPM
Amygdala	23.1 nTPM
Pons	19.5 nTPM
Hypothalamus	17.8 nTPM
Spinal cord	0.0 nTPM

Deep-layer corticothalamic and 6b	56.3 nTPM
Basal ganglia	79.1 nTPM
Amygdala	59.6 nTPM
Cerebral cortex	59.3 nTPM
Midbrain	53.3 nTPM
Hippocampus	51.4 nTPM
Hypothalamus	35.4 nTPM

Deep-layer intratelencephalic	54.4 nTPM
Basal ganglia	77.5 nTPM
Amygdala	60.3 nTPM
Cerebral cortex	52.8 nTPM
Hippocampus	49.6 nTPM
Hypothalamus	32.0 nTPM

Deep-layer near-projecting	59.8 nTPM
Hippocampus	76.1 nTPM
Basal ganglia	71.7 nTPM
Amygdala	68.3 nTPM
Cerebral cortex	55.6 nTPM
Hypothalamus	27.2 nTPM

Eccentric medium spiny neuron	37.5 nTPM
Amygdala	45.9 nTPM
Cerebral cortex	43.9 nTPM
Basal ganglia	42.8 nTPM
Thalamus	33.4 nTPM
Hippocampus	30.3 nTPM
Hypothalamus	28.9 nTPM

Endothelial cell	23.9 nTPM
Cerebellum	34.1 nTPM
Amygdala	26.8 nTPM
Cerebral cortex	25.6 nTPM
Hippocampus	25.0 nTPM
Hypothalamus	24.8 nTPM
Medulla oblongata	24.6 nTPM
Thalamus	24.3 nTPM
Midbrain	23.6 nTPM
Basal ganglia	20.5 nTPM
Spinal cord	17.3 nTPM
Pons	16.2 nTPM