Single cell type - NMI - The Human Protein Atlas

NMI

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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.	NMI
Gene descriptionⁱ Full gene name according to HGNC.	N-myc and STAT interactor
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Plasma 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.	Secreted, 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.	Monocytes - Innate immune response (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.	0.40
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 (Leukocyte, Central nervous system macrophage, 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.	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
Extracellular locationⁱ A possible secretion of the protein was predicted based on N-terminal signal sequence (signal peptide) predictions and transmembrane region predictions, and subsequently annotated for its local or systemic secretion based on literature, function, and protein and RNA expression data.	Protein predicted to be secreted

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: Cell type enhanced (Leukocyte, Central nervous system macrophage, 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: 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

NMI is part of cluster 29 Monocytes - Innate immune response with confidenceⁱ 1
447 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.
CASP4	Caspase 4	0.6450	19
VSIR	V-set immunoregulatory receptor	0.5908	29
PARP9	Poly(ADP-ribose) polymerase family member 9	0.5748	58
MNDA	Myeloid cell nuclear differentiation antigen	0.5634	74
TRIM21	Tripartite motif containing 21	0.5633	58
GMFG	Glia maturation factor gamma	0.5579	19
CPPED1	Calcineurin like phosphoesterase domain containing 1	0.5553	29
DDX60L	DExD/H-box 60 like	0.5421	58
CEBPE	CCAAT enhancer binding protein epsilon	0.5390	74
SCNM1	Sodium channel modifier 1	0.5366	28
EIF2AK2	Eukaryotic translation initiation factor 2 alpha kinase 2	0.5340	58
CARD8	Caspase recruitment domain family member 8	0.5303	19
NLRP12	NLR family pyrin domain containing 12	0.5295	29
MYO1F	Myosin IF	0.5229	19
ANP32A	Acidic nuclear phosphoprotein 32 family member A	0.5190	74

IMMUNE CELLS

NMI is part of cluster 28 Neutrophils - Unknown function with confidenceⁱ 0.99
118 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.
UBE2R2	Ubiquitin conjugating enzyme E2 R2	1.0000	28
BEST1	Bestrophin 1	1.0000	28
SH3GLB1	SH3 domain containing GRB2 like, endophilin B1	0.9762	35
PRKAR1A	Protein kinase cAMP-dependent type I regulatory subunit alpha	0.9762	28
YPEL5	Yippee like 5	0.9762	28
HNRNPH2	Heterogeneous nuclear ribonucleoprotein H2	0.9524	28
MCMBP	Minichromosome maintenance complex binding protein	0.9524	28
HCAR2	Hydroxycarboxylic acid receptor 2	0.9524	28
UBAP1	Ubiquitin associated protein 1	0.9524	28
NBEAL2	Neurobeachin like 2	0.9524	28
ISL2	ISL LIM homeobox 2	0.9524	28
EVA1B	Eva-1 homolog B	0.9524	35
RNF185	Ring finger protein 185	0.9524	28
CALCOCO2	Calcium binding and coiled-coil domain 2	0.9524	28
IRAG1	Inositol 1,4,5-triphosphate receptor associated 1	0.9524	28

Adipocytes	32.3 nTPM
Breast	43.0 nTPM
Adipose tissue	21.6 nTPM

Alveolar cells type 1	32.1 nTPM
Lung	32.1 nTPM

Alveolar cells type 2	26.6 nTPM
Lung	26.6 nTPM

Astrocytes	2.8 nTPM
Brain	2.8 nTPM

B-cells	26.7 nTPM
PBMC	69.3 nTPM
Skin	52.5 nTPM
Liver	43.5 nTPM
Lung	38.9 nTPM
Salivary gland	25.2 nTPM
Bone marrow	23.1 nTPM
Thymus	22.5 nTPM
Spleen	16.7 nTPM
Lymph node	13.8 nTPM
Adipose tissue	13.2 nTPM
Stomach	11.4 nTPM
Kidney	10.4 nTPM
Esophagus	5.9 nTPM

Ciliated cells	32.8 nTPM
Bronchus	41.7 nTPM
Endometrium	35.5 nTPM
Lung	28.2 nTPM
Fallopian tube	25.9 nTPM

Club cells	24.8 nTPM
Bronchus	37.5 nTPM
Lung	21.6 nTPM
Prostate	15.2 nTPM

Endothelial cells	41.4 nTPM
Heart muscle	102.5 nTPM
Placenta	67.6 nTPM
Testis	57.7 nTPM
Skeletal muscle	45.9 nTPM
Lung	45.7 nTPM
Ovary	43.6 nTPM
Fallopian tube	41.0 nTPM
Breast	38.7 nTPM
Thymus	36.0 nTPM
Endometrium	35.3 nTPM
Pancreas	33.6 nTPM
Vascular	30.8 nTPM
Skin	30.7 nTPM
Tongue	30.7 nTPM
Salivary gland	29.5 nTPM
Prostate	26.5 nTPM
Liver	25.2 nTPM
Esophagus	24.6 nTPM

Enteroendocrine cells	16.7 nTPM
Colon	24.6 nTPM
Small intestine	13.7 nTPM
Rectum	11.7 nTPM

Fibroblasts	15.6 nTPM
Heart muscle	27.0 nTPM
Pancreas	26.3 nTPM
Breast	23.5 nTPM
Skeletal muscle	21.2 nTPM
Adipose tissue	19.8 nTPM
Skin	16.4 nTPM
Fallopian tube	15.3 nTPM
Lung	14.9 nTPM
Esophagus	13.7 nTPM
Vascular	13.6 nTPM
Thymus	12.3 nTPM
Liver	11.9 nTPM
Salivary gland	10.9 nTPM
Prostate	9.9 nTPM
Stomach	8.6 nTPM
Placenta	4.6 nTPM

Granulocytes	26.3 nTPM
Lung	36.8 nTPM
Fallopian tube	22.7 nTPM
Tongue	19.4 nTPM

Intestinal goblet cells	24.7 nTPM
Small intestine	28.2 nTPM
Colon	24.6 nTPM
Rectum	21.2 nTPM

Lymphatic endothelial cells	30.6 nTPM
Fallopian tube	34.0 nTPM
Ovary	27.3 nTPM

Macrophages	42.3 nTPM
Kidney	84.1 nTPM
Lung	65.5 nTPM
Spleen	65.2 nTPM
Pancreas	55.5 nTPM
Bone marrow	53.7 nTPM
Skeletal muscle	51.1 nTPM
Testis	50.2 nTPM
Fallopian tube	46.9 nTPM
Endometrium	44.9 nTPM
Breast	42.1 nTPM
Thymus	38.7 nTPM
Vascular	38.3 nTPM
Prostate	31.6 nTPM
Stomach	30.9 nTPM
Adipose tissue	30.8 nTPM
Salivary gland	25.7 nTPM
Tongue	25.2 nTPM
Esophagus	12.8 nTPM
Skin	11.1 nTPM

Paneth cells	23.4 nTPM
Small intestine	38.0 nTPM
Rectum	25.0 nTPM
Colon	7.2 nTPM

Basal keratinocytes	19.3 nTPM
Tongue	26.1 nTPM
Skin	12.6 nTPM

Basal respiratory cells	44.5 nTPM
Bronchus	44.5 nTPM

Bipolar cells	0.2 nTPM
Eye	0.2 nTPM

Cone photoreceptor cells	0.0 nTPM
Eye	0.0 nTPM

Plasma cells	14.8 nTPM
Liver	28.5 nTPM
Spleen	23.1 nTPM
Bone marrow	21.1 nTPM
Thymus	14.4 nTPM
Salivary gland	9.8 nTPM
Fallopian tube	8.4 nTPM
Stomach	7.5 nTPM
Esophagus	5.2 nTPM

Schwann cells	26.9 nTPM
Adipose tissue	48.8 nTPM
Vascular	19.9 nTPM
Esophagus	12.0 nTPM

Serous glandular cells	9.0 nTPM
Salivary gland	13.6 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	14.1 nTPM
Liver	36.9 nTPM
Placenta	25.3 nTPM
Skeletal muscle	19.8 nTPM
Breast	16.8 nTPM
Ovary	16.4 nTPM
Vascular	13.6 nTPM
Fallopian tube	13.0 nTPM
Lung	11.8 nTPM
Endometrium	11.7 nTPM
Tongue	11.4 nTPM
Thymus	11.1 nTPM
Skin	8.8 nTPM
Esophagus	8.4 nTPM
Prostate	7.3 nTPM
Adipose tissue	6.7 nTPM
Salivary gland	6.7 nTPM

Suprabasal keratinocytes	20.9 nTPM
Tongue	22.0 nTPM
Skin	19.7 nTPM

T-cells	30.8 nTPM
Kidney	58.5 nTPM
PBMC	57.5 nTPM
Colon	43.9 nTPM
Liver	42.7 nTPM
Lung	40.9 nTPM
Fallopian tube	33.4 nTPM
Bone marrow	33.0 nTPM
Vascular	31.0 nTPM
Endometrium	30.5 nTPM
Prostate	30.3 nTPM
Thymus	30.1 nTPM
Breast	28.8 nTPM
Skeletal muscle	28.7 nTPM
Spleen	25.8 nTPM
Adipose tissue	23.0 nTPM
Salivary gland	21.5 nTPM
Stomach	21.2 nTPM
Tongue	19.2 nTPM
Lymph node	17.2 nTPM
Skin	15.4 nTPM
Esophagus	14.6 nTPM

Undifferentiated cells	29.1 nTPM
Small intestine	39.9 nTPM
Colon	26.4 nTPM
Rectum	21.1 nTPM

Amygdala excitatory	0.2 nTPM
Hypothalamus	0.4 nTPM
Amygdala	0.3 nTPM
Cerebral cortex	0.2 nTPM
Hippocampus	0.2 nTPM
Basal ganglia	0.1 nTPM
Thalamus	0.0 nTPM

Astrocyte	6.8 nTPM
Amygdala	8.8 nTPM
Midbrain	7.8 nTPM
Thalamus	7.5 nTPM
Hippocampus	7.2 nTPM
Cerebral cortex	6.9 nTPM
Hypothalamus	6.8 nTPM
Basal ganglia	6.7 nTPM
Medulla oblongata	6.1 nTPM
Pons	6.1 nTPM
Spinal cord	5.6 nTPM
Cerebellum	4.9 nTPM

Bergmann glia	4.6 nTPM
Cerebellum	5.3 nTPM
Medulla oblongata	4.3 nTPM
Pons	4.3 nTPM

Central nervous system macrophage	29.9 nTPM
Amygdala	36.3 nTPM
Thalamus	31.7 nTPM
Midbrain	31.3 nTPM
Basal ganglia	30.4 nTPM
Hippocampus	30.3 nTPM
Cerebral cortex	30.0 nTPM
Medulla oblongata	28.6 nTPM
Pons	28.4 nTPM
Hypothalamus	28.3 nTPM
Spinal cord	27.1 nTPM
Cerebellum	26.4 nTPM

Cerebellar inhibitory	0.1 nTPM
Cerebellum	0.1 nTPM
Pons	0.1 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	0.3 nTPM
Basal ganglia	0.6 nTPM
Thalamus	0.4 nTPM
Cerebral cortex	0.3 nTPM
Hippocampus	0.2 nTPM
Hypothalamus	0.2 nTPM
Midbrain	0.2 nTPM
Amygdala	0.1 nTPM

Choroid plexus epithelial cell	1.7 nTPM
Basal ganglia	4.4 nTPM
Medulla oblongata	2.5 nTPM
Hippocampus	0.0 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	4.0 nTPM
Spinal cord	11.0 nTPM
Midbrain	5.9 nTPM
Amygdala	4.5 nTPM
Basal ganglia	3.8 nTPM
Hippocampus	3.6 nTPM
Pons	3.5 nTPM
Cerebellum	3.2 nTPM
Cerebral cortex	3.2 nTPM
Hypothalamus	2.0 nTPM
Thalamus	1.6 nTPM
Medulla oblongata	1.3 nTPM

Deep-layer corticothalamic and 6b	0.0 nTPM
Basal ganglia	0.1 nTPM
Cerebral cortex	0.1 nTPM
Amygdala	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	0.1 nTPM
Amygdala	0.2 nTPM
Basal ganglia	0.2 nTPM
Cerebral cortex	0.2 nTPM
Hippocampus	0.2 nTPM
Hypothalamus	0.1 nTPM

Deep-layer near-projecting	0.2 nTPM
Amygdala	0.4 nTPM
Hippocampus	0.3 nTPM
Hypothalamus	0.2 nTPM
Cerebral cortex	0.1 nTPM
Basal ganglia	0.0 nTPM

Eccentric medium spiny neuron	0.1 nTPM
Thalamus	0.3 nTPM
Amygdala	0.2 nTPM
Cerebral cortex	0.2 nTPM
Basal ganglia	0.1 nTPM
Hypothalamus	0.1 nTPM
Hippocampus	0.0 nTPM

Endothelial cell	27.7 nTPM
Pons	36.2 nTPM
Hippocampus	31.7 nTPM
Spinal cord	31.1 nTPM
Medulla oblongata	30.8 nTPM
Cerebral cortex	30.0 nTPM
Cerebellum	27.1 nTPM
Amygdala	25.7 nTPM
Thalamus	25.4 nTPM
Hypothalamus	24.8 nTPM
Midbrain	21.7 nTPM
Basal ganglia	20.5 nTPM