Single cell type - PGAM4 - 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.	PGAM4
Gene descriptionⁱ Full gene name according to HGNC.	Phosphoglycerate mutase family member 4
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes Metabolic 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.	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.	Cardiomyocytes - Cardiac muscle contraction & structure (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.	Not detected
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.	Not detected
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.	Not available
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 type

Cell type enrichment

Immune cells

Expression clustering

SINGLE CELL TYPESⁱ A summary of normalized single cell RNA (nCPM) from all single cell types. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. * Single nuclei Read more
Single cell type groups RNA single cell type group specificity: Not detected

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.

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

PGAM4 is part of cluster 60 Cardiomyocytes - Cardiac muscle contraction & structure with confidenceⁱ 1
246 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.
MPI	Mannose phosphate isomerase	0.5184	60
PYM1	PYM homolog 1, exon junction complex associated factor	0.4706	85
STRADB	STE20 related adaptor beta	0.4475	60
PPP1R13L	Protein phosphatase 1 regulatory subunit 13 like	0.4330	60
TPI1	Triosephosphate isomerase 1	0.4270	85
PMVK	Phosphomevalonate kinase	0.4251	85
ZNF225	Zinc finger protein 225	0.4128	60
PSMB6	Proteasome 20S subunit beta 6	0.4113	39
MRPL37	Mitochondrial ribosomal protein L37	0.4105	97
MFSD8	Major facilitator superfamily domain containing 8	0.4051	60
ZNF606	Zinc finger protein 606	0.4009	60
ICMT	Isoprenylcysteine carboxyl methyltransferase	0.3993	60
P2RY2	Purinergic receptor P2Y2	0.3991	85
CYP2J2	Cytochrome P450 family 2 subfamily J member 2	0.3984	60
ZFYVE19	Zinc finger FYVE-type containing 19	0.3983	63

IMMUNE CELLS

PGAM4 is part of cluster 38 Monocytes & Neutrophils - Degranulation with confidenceⁱ 0.93
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.
TBC1D2	TBC1 domain family member 2	1.0000	38
POTEG	POTE ankyrin domain family member G	1.0000	38
PANK2	Pantothenate kinase 2	1.0000	38
ZNG1A	Zn regulated GTPase metalloprotein activator 1A	1.0000	38
RILPL2	Rab interacting lysosomal protein like 2	1.0000	38
C19orf38	Chromosome 19 open reading frame 38	0.9762	38
TMEM176A	Transmembrane protein 176A	0.9762	26
FKBP1C	FKBP prolyl isomerase family member 1C	0.9762	38
CLK3	CDC like kinase 3	0.9762	38
PRDX3	Peroxiredoxin 3	0.9762	38
SHKBP1	SH3KBP1 binding protein 1	0.9762	38
UBXN11	UBX domain protein 11	0.9762	38
ACTA1	Actin alpha 1, skeletal muscle	0.9762	38
CREG1	Cellular repressor of E1A stimulated genes 1	0.9762	38
HADHB	Hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit beta	0.9762	38