Single cell type - EGR1 - The Human Protein Atlas

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.	EGR1
Gene descriptionⁱ Full gene name according to HGNC.	Early growth response 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Cancer-related genes Plasma proteins 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.	1

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.	Cell type enhanced (Skeletal myocytes, Basal prostatic 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.	0.35
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 (Vascular associated smooth muscle 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.	Immune cell enhanced (neutrophil)
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 type

Cell type enrichment

Single nuclei - Brain

Immune cells

Expression clustering

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 (Skeletal myocytes, Basal prostatic 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 enhanced (Vascular associated smooth muscle 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: Immune cell enhanced (neutrophil)
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

EGR1 is part of cluster 80 Non-specific - Transcription with confidenceⁱ 1
184 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.
FOS	Fos proto-oncogene, AP-1 transcription factor subunit	0.7418	80
JUN	Jun proto-oncogene, AP-1 transcription factor subunit	0.7364	80
CEBPD	CCAAT enhancer binding protein delta	0.7096	80
NR4A1	Nuclear receptor subfamily 4 group A member 1	0.6877	80
ATF3	Activating transcription factor 3	0.6582	37
FOSB	FosB proto-oncogene, AP-1 transcription factor subunit	0.6239	80
ZFP36	ZFP36 ring finger protein	0.6217	80
SERTAD1	SERTA domain containing 1	0.6090	80
KLF4	KLF transcription factor 4	0.6008	80
RHOB	Ras homolog family member B	0.5944	53
JUNB	JunB proto-oncogene, AP-1 transcription factor subunit	0.5750	80
MAT2A	Methionine adenosyltransferase 2A	0.5708	80
BTG2	BTG anti-proliferation factor 2	0.5619	80
PPP1R15A	Protein phosphatase 1 regulatory subunit 15A	0.5585	80
CSRNP1	Cysteine and serine rich nuclear protein 1	0.5532	80

IMMUNE CELLS

EGR1 is part of cluster 38 Monocytes & Neutrophils - Degranulation with confidenceⁱ 1
501 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.
STAT6	Signal transducer and activator of transcription 6	1.0000	38
SBF2	SET binding factor 2	1.0000	38
HMGCR	3-hydroxy-3-methylglutaryl-CoA reductase	0.9762	38
NCEH1	Neutral cholesterol ester hydrolase 1	0.9762	38
NUP58	Nucleoporin 58	0.9762	38
TTLL4	Tubulin tyrosine ligase like 4	0.9762	38
PRAM1	PML-RARA regulated adaptor molecule 1	0.9762	38
RIN2	Ras and Rab interactor 2	0.9762	38
CFP	Complement factor properdin	0.9762	38
PRLR	Prolactin receptor	0.9762	38
CC2D2A	Coiled-coil and C2 domain containing 2A	0.9762	38
CDH9	Cadherin 9	0.9762	38
LTA4H	Leukotriene A4 hydrolase	0.9762	38
HIPK3	Homeodomain interacting protein kinase 3	0.9762	38
MEFV	MEFV innate immuity regulator, pyrin	0.9762	38