Single cell type - IFI6 - The Human Protein Atlas

IFI6

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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.	IFI6
Gene descriptionⁱ Full gene name according to HGNC.	Interferon alpha inducible protein 6
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
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.	Cytotrophoblasts - Mitochondria (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.	Group enriched (Syncytiotrophoblasts, Cytotrophoblasts, Extravillous trophoblasts)
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.	0.60
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.	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: Group enriched (Syncytiotrophoblasts, Cytotrophoblasts, Extravillous trophoblasts)

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: 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

IFI6 is part of cluster 24 Cytotrophoblasts - Mitochondria with confidenceⁱ 1
235 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.
FOXO4	Forkhead box O4	0.9410	24
PAGE4	PAGE family member 4	0.9387	24
VGLL1	Vestigial like family member 1	0.9328	24
MAGEA8	MAGE family member A8	0.9240	24
SMAGP	Small cell adhesion glycoprotein	0.9201	24
XAGE3	X antigen family member 3	0.9151	24
SOX14	SRY-box transcription factor 14	0.9119	24
GRAMD2A	GRAM domain containing 2A	0.8971	24
TRBV20OR9-2	T cell receptor beta variable 20/OR9-2 (non-functional)	0.8932	24
PEG10	Paternally expressed 10	0.8917	24
DUSP9	Dual specificity phosphatase 9	0.8873	24
MORC4	MORC family CW-type zinc finger 4	0.8832	24
MBNL3	Muscleblind like splicing regulator 3	0.8828	24
MLLT1	MLLT1 super elongation complex subunit	0.8780	24
NRK	Nik related kinase	0.8754	24

IMMUNE CELLS

IFI6 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.
DYNC1LI2	Dynein cytoplasmic 1 light intermediate chain 2	1.0000	28
CKLF-CMTM1	CKLF-CMTM1 readthrough	0.9762	35
IGSF23	Immunoglobulin superfamily member 23	0.9762	28
IFIT1	Interferon induced protein with tetratricopeptide repeats 1	0.9762	28
DDX60L	DExD/H-box 60 like	0.9762	28
FPR2	Formyl peptide receptor 2	0.9762	28
PFKFB3	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	0.9762	28
SLC25A44	Solute carrier family 25 member 44	0.9762	28
CARHSP1	Calcium regulated heat stable protein 1	0.9762	28
RCBTB2	RCC1 and BTB domain containing protein 2	0.9762	28
ATXN1	Ataxin 1	0.9762	28
NFE2L2	NFE2 like bZIP transcription factor 2	0.9762	28
MTMR3	Myotubularin related protein 3	0.9762	21
FYB1	FYN binding protein 1	0.9762	21
RAB7A	RAB7A, member RAS oncogene family	0.9762	28

Adipocytes	104.1 nTPM
Adipose tissue	125.4 nTPM
Breast	82.8 nTPM

Alveolar cells type 1	41.3 nTPM
Lung	41.3 nTPM

Alveolar cells type 2	12.6 nTPM
Lung	12.6 nTPM

Astrocytes	5.0 nTPM
Brain	5.0 nTPM

B-cells	14.5 nTPM
Skin	25.4 nTPM
Bone marrow	24.8 nTPM
Adipose tissue	23.9 nTPM
Stomach	20.7 nTPM
Spleen	18.0 nTPM
Lymph node	15.8 nTPM
Thymus	13.8 nTPM
Lung	12.1 nTPM
Kidney	10.4 nTPM
PBMC	9.2 nTPM
Esophagus	5.9 nTPM
Liver	4.8 nTPM
Salivary gland	4.0 nTPM

Ciliated cells	42.9 nTPM
Lung	55.5 nTPM
Endometrium	49.1 nTPM
Bronchus	40.5 nTPM
Fallopian tube	26.6 nTPM

Club cells	30.2 nTPM
Lung	39.2 nTPM
Prostate	27.5 nTPM
Bronchus	23.7 nTPM

Endothelial cells	99.6 nTPM
Ovary	376.9 nTPM
Skeletal muscle	266.8 nTPM
Testis	189.2 nTPM
Placenta	186.8 nTPM
Esophagus	163.2 nTPM
Skin	129.0 nTPM
Endometrium	69.6 nTPM
Thymus	58.4 nTPM
Lung	57.6 nTPM
Breast	50.1 nTPM
Fallopian tube	44.5 nTPM
Pancreas	38.8 nTPM
Tongue	35.1 nTPM
Vascular	31.7 nTPM
Liver	29.0 nTPM
Prostate	26.8 nTPM
Salivary gland	25.8 nTPM
Heart muscle	13.6 nTPM

Enteroendocrine cells	8.8 nTPM
Rectum	18.4 nTPM
Small intestine	6.9 nTPM
Colon	1.0 nTPM

Fibroblasts	58.5 nTPM
Esophagus	179.9 nTPM
Stomach	122.5 nTPM
Skin	113.7 nTPM
Skeletal muscle	95.2 nTPM
Adipose tissue	84.6 nTPM
Breast	76.9 nTPM
Prostate	38.3 nTPM
Placenta	37.3 nTPM
Lung	35.9 nTPM
Vascular	30.3 nTPM
Thymus	30.1 nTPM
Liver	27.3 nTPM
Fallopian tube	26.8 nTPM
Pancreas	13.5 nTPM
Salivary gland	13.3 nTPM
Heart muscle	10.5 nTPM

Granulocytes	15.1 nTPM
Lung	17.1 nTPM
Tongue	14.6 nTPM
Fallopian tube	13.6 nTPM

Intestinal goblet cells	18.4 nTPM
Small intestine	23.5 nTPM
Rectum	23.1 nTPM
Colon	8.6 nTPM

Lymphatic endothelial cells	278.2 nTPM
Ovary	523.7 nTPM
Fallopian tube	32.6 nTPM

Macrophages	86.8 nTPM
Lung	324.6 nTPM
Esophagus	195.2 nTPM
Kidney	150.5 nTPM
Stomach	146.6 nTPM
Spleen	123.3 nTPM
Bone marrow	116.5 nTPM
Fallopian tube	97.4 nTPM
Skeletal muscle	91.6 nTPM
Pancreas	76.1 nTPM
Testis	67.0 nTPM
Adipose tissue	63.9 nTPM
Endometrium	50.4 nTPM
Thymus	36.5 nTPM
Breast	33.8 nTPM
Vascular	28.1 nTPM
Prostate	18.5 nTPM
Skin	15.6 nTPM
Tongue	7.3 nTPM
Salivary gland	7.1 nTPM

Paneth cells	9.3 nTPM
Small intestine	20.7 nTPM
Rectum	7.3 nTPM
Colon	0.0 nTPM

Basal keratinocytes	6.1 nTPM
Skin	6.6 nTPM
Tongue	5.6 nTPM

Basal prostatic cells	8.0 nTPM
Prostate	8.0 nTPM

Basal squamous epithelial cells	15.7 nTPM
Esophagus	15.7 nTPM

Bipolar cells	4.4 nTPM
Eye	4.4 nTPM

Plasma cells	68.0 nTPM
Esophagus	192.3 nTPM
Stomach	157.9 nTPM
Spleen	55.3 nTPM
Bone marrow	49.8 nTPM
Salivary gland	34.5 nTPM
Fallopian tube	22.2 nTPM
Thymus	16.4 nTPM
Liver	16.0 nTPM

Schwann cells	109.3 nTPM
Esophagus	227.6 nTPM
Vascular	95.1 nTPM
Adipose tissue	5.1 nTPM

Serous glandular cells	5.6 nTPM
Salivary gland	6.8 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	52.9 nTPM
Ovary	172.5 nTPM
Placenta	150.9 nTPM
Skeletal muscle	94.1 nTPM
Esophagus	80.5 nTPM
Adipose tissue	43.9 nTPM
Liver	40.3 nTPM
Vascular	39.3 nTPM
Lung	38.8 nTPM
Skin	35.7 nTPM
Breast	34.5 nTPM
Tongue	29.9 nTPM
Endometrium	27.3 nTPM
Thymus	23.4 nTPM
Prostate	14.0 nTPM
Salivary gland	10.7 nTPM
Fallopian tube	10.1 nTPM

T-cells	38.1 nTPM
Stomach	64.2 nTPM
Bone marrow	62.6 nTPM
Kidney	61.2 nTPM
Esophagus	60.8 nTPM
Spleen	60.5 nTPM
Adipose tissue	58.3 nTPM
Skin	42.1 nTPM
Skeletal muscle	40.1 nTPM
PBMC	38.0 nTPM
Breast	37.2 nTPM
Lymph node	36.9 nTPM
Lung	35.1 nTPM
Endometrium	33.4 nTPM
Colon	31.2 nTPM
Thymus	28.8 nTPM
Liver	25.2 nTPM
Fallopian tube	22.9 nTPM
Prostate	20.0 nTPM
Vascular	18.9 nTPM
Tongue	12.8 nTPM
Salivary gland	11.0 nTPM

Undifferentiated cells	9.2 nTPM
Small intestine	20.0 nTPM
Colon	4.9 nTPM
Rectum	2.7 nTPM

Amygdala excitatory	8.4 nTPM
Thalamus	21.8 nTPM
Basal ganglia	8.2 nTPM
Amygdala	6.8 nTPM
Hypothalamus	5.9 nTPM
Hippocampus	4.5 nTPM
Cerebral cortex	3.3 nTPM

Astrocyte	9.5 nTPM
Spinal cord	15.5 nTPM
Medulla oblongata	13.0 nTPM
Basal ganglia	12.7 nTPM
Thalamus	9.7 nTPM
Hypothalamus	8.5 nTPM
Midbrain	8.4 nTPM
Hippocampus	8.3 nTPM
Cerebellum	7.5 nTPM
Pons	7.2 nTPM
Cerebral cortex	7.0 nTPM
Amygdala	6.6 nTPM

Bergmann glia	2.7 nTPM
Pons	4.3 nTPM
Cerebellum	3.7 nTPM
Medulla oblongata	0.0 nTPM

Central nervous system macrophage	11.1 nTPM
Spinal cord	19.4 nTPM
Basal ganglia	17.1 nTPM
Medulla oblongata	13.9 nTPM
Thalamus	11.2 nTPM
Hypothalamus	10.2 nTPM
Midbrain	9.8 nTPM
Pons	9.8 nTPM
Cerebellum	8.8 nTPM
Cerebral cortex	7.3 nTPM
Hippocampus	7.1 nTPM
Amygdala	7.0 nTPM

Cerebellar inhibitory	8.3 nTPM
Pons	15.9 nTPM
Medulla oblongata	10.7 nTPM
Midbrain	5.9 nTPM
Spinal cord	5.5 nTPM
Cerebellum	3.5 nTPM

Cge interneuron	34.2 nTPM
Thalamus	57.7 nTPM
Midbrain	45.9 nTPM
Basal ganglia	40.6 nTPM
Amygdala	28.5 nTPM
Cerebral cortex	26.4 nTPM
Hippocampus	22.4 nTPM
Hypothalamus	17.7 nTPM

Choroid plexus epithelial cell	16.0 nTPM
Hippocampus	25.0 nTPM
Medulla oblongata	17.4 nTPM
Thalamus	13.7 nTPM
Basal ganglia	7.9 nTPM

Committed oligodendrocyte precursor	31.1 nTPM
Medulla oblongata	49.1 nTPM
Spinal cord	47.8 nTPM
Midbrain	47.0 nTPM
Cerebellum	46.0 nTPM
Pons	40.7 nTPM
Basal ganglia	27.4 nTPM
Hippocampus	19.7 nTPM
Cerebral cortex	19.6 nTPM
Amygdala	16.9 nTPM
Thalamus	14.6 nTPM
Hypothalamus	13.0 nTPM

Deep-layer corticothalamic and 6b	7.3 nTPM
Midbrain	15.5 nTPM
Basal ganglia	8.4 nTPM
Cerebral cortex	5.3 nTPM
Hippocampus	5.2 nTPM
Hypothalamus	4.6 nTPM
Amygdala	4.5 nTPM

Deep-layer intratelencephalic	11.2 nTPM
Amygdala	15.7 nTPM
Basal ganglia	13.1 nTPM
Hippocampus	11.4 nTPM
Cerebral cortex	9.6 nTPM
Hypothalamus	6.4 nTPM

Deep-layer near-projecting	4.6 nTPM
Basal ganglia	9.1 nTPM
Hippocampus	4.6 nTPM
Cerebral cortex	4.1 nTPM
Hypothalamus	2.8 nTPM
Amygdala	2.3 nTPM

Eccentric medium spiny neuron	5.5 nTPM
Amygdala	6.3 nTPM
Hypothalamus	6.1 nTPM
Basal ganglia	5.7 nTPM
Cerebral cortex	5.7 nTPM
Thalamus	5.6 nTPM
Hippocampus	3.7 nTPM

Endothelial cell	200.4 nTPM
Medulla oblongata	302.5 nTPM
Thalamus	240.0 nTPM
Pons	232.8 nTPM
Midbrain	206.0 nTPM
Cerebral cortex	205.9 nTPM
Cerebellum	203.7 nTPM
Spinal cord	196.8 nTPM
Basal ganglia	191.1 nTPM
Amygdala	159.8 nTPM
Hippocampus	152.6 nTPM
Hypothalamus	112.9 nTPM

Ependymal cell	34.9 nTPM
Medulla oblongata	50.3 nTPM
Spinal cord	47.9 nTPM
Pons	38.1 nTPM
Thalamus	37.7 nTPM
Midbrain	35.6 nTPM
Hippocampus	31.4 nTPM
Basal ganglia	29.8 nTPM
Amygdala	22.2 nTPM
Hypothalamus	21.4 nTPM