Single cell type - IER3 - The Human Protein Atlas

IER3

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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.	IER3
Gene descriptionⁱ Full gene name according to HGNC.	Immediate early response 3
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, 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.	Glandular & Luminal cells - Unknown function (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 (Glandular and luminal cells, Suprabasal keratinocytes)
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.	0.44
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.	Group enriched (Central nervous system macrophage, Endothelial cell, Vascular associated smooth muscle cell, Choroid plexus epithelial 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.	Not detected in immune cells
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 (Glandular and luminal cells, Suprabasal keratinocytes)

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: Group enriched (Central nervous system macrophage, Endothelial cell, Vascular associated smooth muscle cell, Choroid plexus epithelial 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: Not detected in immune cells
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

IER3 is part of cluster 37 Glandular & Luminal cells - Unknown function with confidenceⁱ 1
334 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.
ARL5B	ADP ribosylation factor like GTPase 5B	0.7920	29
PPP1R15A	Protein phosphatase 1 regulatory subunit 15A	0.7203	80
MAFF	MAF bZIP transcription factor F	0.6936	37
GADD45A	Growth arrest and DNA damage inducible alpha	0.6734	37
EGR4	Early growth response 4	0.6613	37
ATF3	Activating transcription factor 3	0.6480	37
CITED4	Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 4	0.6249	37
IL1RL2	Interleukin 1 receptor like 2	0.6206	29
CDKN2AIP	CDKN2A interacting protein	0.6203	37
CLCF1	Cardiotrophin like cytokine factor 1	0.6189	37
ZBTB10	Zinc finger and BTB domain containing 10	0.6144	37
ULBP1	UL16 binding protein 1	0.6096	80
DNAJB1	DnaJ heat shock protein family (Hsp40) member B1	0.6083	80
HAP1	Huntingtin associated protein 1	0.6073	37
TUFT1	Tuftelin 1	0.6014	37

Adipocytes	281.9 nTPM
Breast	446.0 nTPM
Adipose tissue	117.8 nTPM

Alveolar cells type 1	98.8 nTPM
Lung	98.8 nTPM

Alveolar cells type 2	345.9 nTPM
Lung	345.9 nTPM

Astrocytes	2.5 nTPM
Brain	2.5 nTPM

B-cells	29.2 nTPM
Skin	179.6 nTPM
Esophagus	59.0 nTPM
Lymph node	33.4 nTPM
Salivary gland	23.5 nTPM
Thymus	20.1 nTPM
Adipose tissue	17.7 nTPM
Liver	14.5 nTPM
Lung	10.7 nTPM
Stomach	7.6 nTPM
Spleen	6.3 nTPM
Kidney	5.2 nTPM
PBMC	1.5 nTPM
Bone marrow	0.2 nTPM

Basal keratinocytes	985.4 nTPM
Tongue	1584.5 nTPM
Skin	386.3 nTPM

Basal squamous epithelial cells	808.2 nTPM
Esophagus	808.2 nTPM

Ciliated cells	527.3 nTPM
Fallopian tube	968.6 nTPM
Endometrium	942.0 nTPM
Lung	106.4 nTPM
Bronchus	92.0 nTPM

Club cells	388.1 nTPM
Lung	532.1 nTPM
Prostate	368.3 nTPM
Bronchus	263.9 nTPM

Distal enterocytes	827.3 nTPM
Colon	1447.4 nTPM
Rectum	207.3 nTPM

Endothelial cells	438.1 nTPM
Tongue	1287.0 nTPM
Esophagus	1221.5 nTPM
Fallopian tube	1060.2 nTPM
Skin	706.9 nTPM
Endometrium	697.4 nTPM
Salivary gland	533.5 nTPM
Thymus	393.9 nTPM
Skeletal muscle	364.3 nTPM
Vascular	359.9 nTPM
Breast	302.3 nTPM
Lung	300.1 nTPM
Prostate	232.6 nTPM
Placenta	105.6 nTPM
Testis	103.8 nTPM
Pancreas	98.2 nTPM
Ovary	55.7 nTPM
Liver	52.9 nTPM
Heart muscle	9.5 nTPM

Enteroendocrine cells	410.3 nTPM
Colon	1083.7 nTPM
Rectum	95.6 nTPM
Small intestine	51.5 nTPM

Fibroblasts	448.4 nTPM
Skin	1030.6 nTPM
Fallopian tube	991.4 nTPM
Lung	898.8 nTPM
Skeletal muscle	740.3 nTPM
Pancreas	720.5 nTPM
Esophagus	534.3 nTPM
Thymus	483.3 nTPM
Stomach	383.3 nTPM
Breast	342.3 nTPM
Salivary gland	316.2 nTPM
Vascular	263.5 nTPM
Prostate	242.9 nTPM
Placenta	99.6 nTPM
Adipose tissue	81.3 nTPM
Liver	35.6 nTPM
Heart muscle	10.0 nTPM

Glandular and luminal cells	2947.6 nTPM
Endometrium	2947.6 nTPM

Granulocytes	500.8 nTPM
Fallopian tube	897.3 nTPM
Tongue	514.2 nTPM
Lung	90.8 nTPM

Bipolar cells	3.8 nTPM
Eye	3.8 nTPM

Cholangiocytes	213.7 nTPM
Liver	213.7 nTPM

Collecting duct cells	77.8 nTPM
Kidney	77.8 nTPM

Cone photoreceptor cells	0.0 nTPM
Eye	0.0 nTPM

Intestinal goblet cells	690.1 nTPM
Colon	1491.3 nTPM
Rectum	427.8 nTPM
Small intestine	151.3 nTPM

Lymphatic endothelial cells	147.9 nTPM
Fallopian tube	186.6 nTPM
Ovary	109.1 nTPM

Macrophages	1174.4 nTPM
Breast	3235.2 nTPM
Adipose tissue	3050.2 nTPM
Fallopian tube	2395.3 nTPM
Skin	2028.0 nTPM
Tongue	1700.1 nTPM
Endometrium	1699.2 nTPM
Esophagus	1564.4 nTPM
Prostate	1092.4 nTPM
Vascular	1081.2 nTPM
Skeletal muscle	1039.4 nTPM
Salivary gland	963.4 nTPM
Testis	634.2 nTPM
Stomach	488.7 nTPM
Spleen	486.2 nTPM
Pancreas	353.6 nTPM
Thymus	204.9 nTPM
Kidney	133.6 nTPM
Lung	132.8 nTPM
Bone marrow	31.4 nTPM

Paneth cells	618.0 nTPM
Colon	1389.6 nTPM
Rectum	343.6 nTPM
Small intestine	120.9 nTPM

Plasma cells	66.0 nTPM
Esophagus	181.9 nTPM
Fallopian tube	137.7 nTPM
Salivary gland	129.8 nTPM
Thymus	20.6 nTPM
Stomach	19.7 nTPM
Liver	19.0 nTPM
Spleen	13.0 nTPM
Bone marrow	6.0 nTPM

Schwann cells	233.0 nTPM
Esophagus	563.1 nTPM
Vascular	108.1 nTPM
Adipose tissue	27.7 nTPM

Serous glandular cells	670.4 nTPM
Tongue	954.5 nTPM
Salivary gland	386.3 nTPM

Smooth muscle cells	481.2 nTPM
Skin	1638.4 nTPM
Tongue	1177.2 nTPM
Fallopian tube	936.3 nTPM
Endometrium	910.5 nTPM
Esophagus	774.8 nTPM
Placenta	508.7 nTPM
Lung	359.7 nTPM
Breast	297.4 nTPM
Salivary gland	283.8 nTPM
Skeletal muscle	181.1 nTPM
Thymus	173.9 nTPM
Liver	101.9 nTPM
Prostate	93.7 nTPM
Ovary	90.1 nTPM
Adipose tissue	86.4 nTPM
Vascular	84.5 nTPM

Suprabasal keratinocytes	2113.7 nTPM
Tongue	3973.5 nTPM
Skin	253.9 nTPM

T-cells	103.9 nTPM
Endometrium	361.6 nTPM
Breast	350.2 nTPM
Tongue	234.2 nTPM
Colon	170.6 nTPM
Vascular	168.8 nTPM
Skin	163.7 nTPM
Esophagus	146.0 nTPM
Prostate	123.4 nTPM
Fallopian tube	108.8 nTPM
Skeletal muscle	68.1 nTPM
Lymph node	62.8 nTPM
Spleen	51.4 nTPM
Lung	37.4 nTPM
Salivary gland	34.9 nTPM
Adipose tissue	22.6 nTPM
Stomach	17.8 nTPM
Thymus	17.3 nTPM
Liver	14.8 nTPM
Kidney	14.2 nTPM
PBMC	8.0 nTPM
Bone marrow	4.7 nTPM

Undifferentiated cells	386.9 nTPM
Colon	727.8 nTPM
Rectum	284.8 nTPM
Small intestine	148.0 nTPM

Amygdala excitatory	2.9 nTPM
Basal ganglia	4.2 nTPM
Thalamus	4.1 nTPM
Amygdala	2.9 nTPM
Hippocampus	2.8 nTPM
Cerebral cortex	2.6 nTPM
Hypothalamus	0.8 nTPM

Astrocyte	3.2 nTPM
Pons	5.3 nTPM
Medulla oblongata	4.6 nTPM
Spinal cord	4.5 nTPM
Hypothalamus	3.9 nTPM
Basal ganglia	3.7 nTPM
Cerebral cortex	3.4 nTPM
Hippocampus	2.6 nTPM
Midbrain	2.6 nTPM
Thalamus	1.9 nTPM
Amygdala	1.5 nTPM
Cerebellum	1.5 nTPM

Bergmann glia	4.2 nTPM
Medulla oblongata	6.4 nTPM
Pons	4.3 nTPM
Cerebellum	1.9 nTPM

Central nervous system macrophage	94.8 nTPM
Spinal cord	128.1 nTPM
Basal ganglia	125.7 nTPM
Medulla oblongata	120.9 nTPM
Cerebellum	106.4 nTPM
Cerebral cortex	102.6 nTPM
Hypothalamus	90.1 nTPM
Hippocampus	89.9 nTPM
Pons	84.0 nTPM
Midbrain	76.2 nTPM
Thalamus	61.8 nTPM
Amygdala	56.6 nTPM

Cerebellar inhibitory	1.2 nTPM
Pons	2.7 nTPM
Midbrain	2.2 nTPM
Medulla oblongata	1.1 nTPM
Cerebellum	0.3 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	3.3 nTPM
Basal ganglia	4.6 nTPM
Midbrain	4.1 nTPM
Cerebral cortex	3.8 nTPM
Hippocampus	3.7 nTPM
Amygdala	2.8 nTPM
Thalamus	2.3 nTPM
Hypothalamus	1.5 nTPM

Choroid plexus epithelial cell	28.8 nTPM
Thalamus	41.1 nTPM
Basal ganglia	27.4 nTPM
Medulla oblongata	24.4 nTPM
Hippocampus	22.2 nTPM

Committed oligodendrocyte precursor	2.3 nTPM
Basal ganglia	8.8 nTPM
Pons	5.3 nTPM
Medulla oblongata	3.9 nTPM
Hypothalamus	2.0 nTPM
Thalamus	1.8 nTPM
Midbrain	1.7 nTPM
Hippocampus	1.0 nTPM
Amygdala	0.6 nTPM
Cerebral cortex	0.6 nTPM
Cerebellum	0.0 nTPM
Spinal cord	0.0 nTPM

Deep-layer corticothalamic and 6b	3.3 nTPM
Hippocampus	5.1 nTPM
Amygdala	4.3 nTPM
Cerebral cortex	4.0 nTPM
Basal ganglia	3.6 nTPM
Hypothalamus	1.7 nTPM
Midbrain	1.1 nTPM