Single cell type - IRF4 - The Human Protein Atlas

IRF4

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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.	IRF4
Gene descriptionⁱ Full gene name according to HGNC.	Interferon regulatory factor 4
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Cancer-related genes Disease related genes Transcription factors
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.	Dendritic cells - Antigen presentation (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 enriched (Dendritic 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.	0.89
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 enriched (Leukocyte)
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.	Group enriched (plasmacytoid DC, naive B-cell, myeloid DC, memory B-cell, T-reg)
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 enriched (Dendritic 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 enriched (Leukocyte)

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: Group enriched (plasmacytoid DC, naive B-cell, myeloid DC, memory B-cell, T-reg)
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

IRF4 is part of cluster 28 Dendritic cells - Antigen presentation with confidenceⁱ 1
245 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.
CXCR3	C-X-C motif chemokine receptor 3	0.8385	28
KRT71	Keratin 71	0.8200	28
RUBCN	Rubicon autophagy regulator	0.8147	28
BCL2L11	BCL2 like 11	0.8139	28
ENTPD7	Ectonucleoside triphosphate diphosphohydrolase 7	0.8095	28
FYTTD1	Forty-two-three domain containing 1	0.7904	28
SEL1L3	SEL1L family member 3	0.7767	28
PHEX	Phosphate regulating endopeptidase X-linked	0.7676	28
TENT4A	Terminal nucleotidyltransferase 4A	0.7454	28
PLD4	Phospholipase D family member 4	0.7257	28
IRF7	Interferon regulatory factor 7	0.7168	28
NOPCHAP1	NOP protein chaperone 1	0.7109	28
MYBL2	MYB proto-oncogene like 2	0.6995	61
ABHD15	Abhydrolase domain containing 15	0.6983	28
LILRA4	Leukocyte immunoglobulin like receptor A4	0.6867	28

IMMUNE CELLS

IRF4 is part of cluster 23 B-cells - Immunoglobulins with confidenceⁱ 0.97
208 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.
NPIPA9	Nuclear pore complex interacting protein family, member A9	1.0000	23
TLR10	Toll like receptor 10	1.0000	23
PARM1	Prostate androgen-regulated mucin-like protein 1	1.0000	23
KLF8	KLF transcription factor 8	1.0000	23
CCDC32	Coiled-coil domain containing 32	1.0000	23
SSPN	Sarcospan	0.9762	17
BANK1	B cell scaffold protein with ankyrin repeats 1	0.9762	23
ABCB9	ATP binding cassette subfamily B member 9	0.9762	23
ILDR1	Immunoglobulin like domain containing receptor 1	0.9762	23
FCRLA	Fc receptor like A	0.9762	23
QRSL1	Glutaminyl-tRNA amidotransferase subunit QRSL1	0.9762	23
MAP3K14	Mitogen-activated protein kinase kinase kinase 14	0.9762	23
PLA2G2D	Phospholipase A2 group IID	0.9762	17
POU2AF1	POU class 2 homeobox associating factor 1	0.9762	23
COL4A4	Collagen type IV alpha 4 chain	0.9762	23

Adipocytes	0.6 nTPM
Breast	1.0 nTPM
Adipose tissue	0.2 nTPM

Alveolar cells type 1	0.2 nTPM
Lung	0.2 nTPM

Alveolar cells type 2	3.9 nTPM
Lung	3.9 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	50.9 nTPM
Adipose tissue	159.3 nTPM
Stomach	85.2 nTPM
Lung	76.5 nTPM
Esophagus	59.0 nTPM
Lymph node	58.0 nTPM
Thymus	45.8 nTPM
Salivary gland	42.6 nTPM
Spleen	39.2 nTPM
Skin	32.2 nTPM
Bone marrow	29.9 nTPM
PBMC	29.2 nTPM
Liver	4.8 nTPM
Kidney	0.0 nTPM

Ciliated cells	0.3 nTPM
Fallopian tube	0.9 nTPM
Endometrium	0.2 nTPM
Bronchus	0.0 nTPM
Lung	0.0 nTPM

Club cells	0.1 nTPM
Lung	0.1 nTPM
Prostate	0.1 nTPM
Bronchus	0.0 nTPM

Dendritic cells	1174.0 nTPM
Adipose tissue	2297.7 nTPM
PBMC	50.4 nTPM

Endothelial cells	0.9 nTPM
Thymus	2.6 nTPM
Liver	2.5 nTPM
Prostate	2.4 nTPM
Heart muscle	2.1 nTPM
Vascular	1.3 nTPM
Skin	1.1 nTPM
Esophagus	0.8 nTPM
Tongue	0.8 nTPM
Placenta	0.6 nTPM
Salivary gland	0.6 nTPM
Endometrium	0.2 nTPM
Skeletal muscle	0.2 nTPM
Lung	0.2 nTPM
Ovary	0.2 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Breast	0.0 nTPM
Fallopian tube	0.0 nTPM

Enteroendocrine cells	0.1 nTPM
Colon	0.3 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Fibroblasts	2.6 nTPM
Thymus	8.4 nTPM
Salivary gland	7.8 nTPM
Adipose tissue	5.2 nTPM
Fallopian tube	4.8 nTPM
Prostate	2.6 nTPM
Vascular	2.0 nTPM
Breast	2.0 nTPM
Skeletal muscle	1.4 nTPM
Stomach	1.4 nTPM
Liver	1.2 nTPM
Skin	1.1 nTPM
Esophagus	1.0 nTPM
Placenta	0.9 nTPM
Lung	0.9 nTPM
Pancreas	0.5 nTPM
Heart muscle	0.0 nTPM

Granulocytes	6.1 nTPM
Tongue	9.7 nTPM
Fallopian tube	8.1 nTPM
Lung	0.5 nTPM

Intestinal goblet cells	0.2 nTPM
Colon	0.7 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Lymphatic endothelial cells	0.4 nTPM
Fallopian tube	0.8 nTPM
Ovary	0.0 nTPM

Macrophages	23.9 nTPM
Adipose tissue	94.6 nTPM
Tongue	84.9 nTPM
Endometrium	77.5 nTPM
Esophagus	36.0 nTPM
Fallopian tube	26.0 nTPM
Skeletal muscle	24.0 nTPM
Skin	23.4 nTPM
Stomach	23.1 nTPM
Breast	17.9 nTPM
Salivary gland	9.1 nTPM
Spleen	9.0 nTPM
Thymus	5.6 nTPM
Prostate	5.1 nTPM
Testis	5.0 nTPM
Kidney	4.4 nTPM
Vascular	4.1 nTPM
Pancreas	2.1 nTPM
Lung	2.0 nTPM
Bone marrow	0.0 nTPM

Paneth cells	0.1 nTPM
Rectum	0.2 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Plasma cells	199.5 nTPM
Stomach	345.9 nTPM
Bone marrow	246.1 nTPM
Spleen	226.1 nTPM
Thymus	225.3 nTPM
Fallopian tube	206.2 nTPM
Esophagus	140.3 nTPM
Salivary gland	108.8 nTPM
Liver	97.1 nTPM

Schwann cells	2.0 nTPM
Adipose tissue	5.9 nTPM
Esophagus	0.0 nTPM
Vascular	0.0 nTPM

Serous glandular cells	5.8 nTPM
Tongue	8.8 nTPM
Salivary gland	2.7 nTPM

Smooth muscle cells	0.8 nTPM
Thymus	2.5 nTPM
Breast	2.4 nTPM
Esophagus	1.2 nTPM
Lung	1.2 nTPM
Tongue	1.2 nTPM
Skin	0.8 nTPM
Placenta	0.7 nTPM
Liver	0.4 nTPM
Salivary gland	0.4 nTPM
Vascular	0.4 nTPM
Endometrium	0.3 nTPM
Adipose tissue	0.2 nTPM
Fallopian tube	0.2 nTPM
Ovary	0.1 nTPM
Skeletal muscle	0.0 nTPM
Prostate	0.0 nTPM

T-cells	38.7 nTPM
Stomach	91.1 nTPM
Tongue	80.3 nTPM
Adipose tissue	78.0 nTPM
Esophagus	65.7 nTPM
Fallopian tube	65.6 nTPM
Vascular	59.9 nTPM
Prostate	54.6 nTPM
Colon	48.7 nTPM
Lung	47.1 nTPM
Spleen	33.5 nTPM
Thymus	31.3 nTPM
Breast	31.2 nTPM
Endometrium	27.0 nTPM
Salivary gland	26.5 nTPM
Lymph node	23.4 nTPM
Skeletal muscle	21.5 nTPM
Skin	11.9 nTPM
Bone marrow	8.0 nTPM
Liver	3.2 nTPM
PBMC	2.9 nTPM
Kidney	1.8 nTPM

Undifferentiated cells	0.1 nTPM
Rectum	0.3 nTPM
Colon	0.1 nTPM
Small intestine	0.0 nTPM

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

Astrocyte	0.0 nTPM
Amygdala	0.1 nTPM
Basal ganglia	0.1 nTPM
Cerebral cortex	0.1 nTPM
Hippocampus	0.1 nTPM
Medulla oblongata	0.1 nTPM
Thalamus	0.1 nTPM
Cerebellum	0.0 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM

Bergmann glia	0.0 nTPM
Cerebellum	0.1 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	1.3 nTPM
Spinal cord	4.4 nTPM
Hypothalamus	1.8 nTPM
Cerebellum	1.7 nTPM
Amygdala	1.4 nTPM
Medulla oblongata	1.2 nTPM
Pons	0.9 nTPM
Basal ganglia	0.7 nTPM
Thalamus	0.7 nTPM
Hippocampus	0.6 nTPM
Midbrain	0.6 nTPM
Cerebral cortex	0.4 nTPM

Cerebellar inhibitory	0.3 nTPM
Pons	1.2 nTPM
Cerebellum	0.1 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	0.1 nTPM
Midbrain	0.2 nTPM
Amygdala	0.1 nTPM
Basal ganglia	0.1 nTPM
Cerebral cortex	0.1 nTPM
Hippocampus	0.1 nTPM
Hypothalamus	0.1 nTPM
Thalamus	0.0 nTPM

Choroid plexus epithelial cell	0.0 nTPM
Basal ganglia	0.1 nTPM
Hippocampus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	0.1 nTPM
Hypothalamus	1.4 nTPM
Thalamus	0.2 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebellum	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM

Deep-layer corticothalamic and 6b	0.1 nTPM
Basal ganglia	0.2 nTPM
Amygdala	0.1 nTPM
Cerebral cortex	0.1 nTPM
Hippocampus	0.1 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM

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

Deep-layer near-projecting	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

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

Endothelial cell	0.2 nTPM
Hypothalamus	1.2 nTPM
Pons	0.6 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebellum	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Spinal cord	0.0 nTPM
Thalamus	0.0 nTPM