Single cell type - PGAM2 - 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.	PGAM2
Gene descriptionⁱ Full gene name according to HGNC.	Phosphoglycerate mutase 2
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Enzymes Human disease related genes Metabolic proteins Plasma proteins Potential drug targets
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.	Late spermatids - Spermiogenesis: Maturation (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 (Late spermatids)
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.	0.87
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 (Upper rhombic lip, Astrocyte, Ependymal cell, 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.	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 type

Cell type summary (DVP)

Single nuclei - Brain

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: Cell type enriched (Spermatogenic cell types)

DVP - RNA AND PROTEIN ABUNDANCE COMPARISONⁱ

RNA cell type specificity:	Cell type enhanced (Skeletal myofibers)	Agreement detection:	Yes (0.70)
Protein cell type specificity:	Cell type enriched (Skeletal myofibers)	Agreement expression:	Yes (0.83)
RNA tau score:	0.76	Overlap:	Elevated - Overlap
Protein tau score:	0.78

	RNA expression (nCPM)ⁱ This plot shows the expression profile (RNAseq) based on selected single cell/nuclei cell type clusters from the single cell type summary above, shown as normalized CPM (nCPM). Learn more about the selection of clusters here Note, this RNA overview is based on a selected portion of the data above (covering the whole body and more cell types), with the goal to match the DVP data. Read more	Protein abundance (intensity)ⁱ This plot show quantitative protein detection using Deep Visual Proteomics (DVP). Learn more about the protein intensity here. Read more
Neurons
Astrocytes and Neuropil
Microglia and Neuropil
Pancreatic islets
Ciliated cells
Alveolar cells type 1
Alveolar cells type 2
Large ducts
Collecting ducts
Hepatocytes
Glomeruli
Proximal tubules
Distal tubules
Granulosa cells
Keratinocytes
Pancreas epithelial cells
Secretory cells
Oocytes
Cardiomyocytes
Skeletal myofibers
Capillaries
Smooth muscle cells
Neutrophils
Macrophages
CD4 T-cells
CD8 T-cells
B-cells

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Cell type enhanced (Upper rhombic lip, Astrocyte, Ependymal cell, 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: 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

PGAM2 is part of cluster 56 Late spermatids - Spermiogenesis: Maturation with confidenceⁱ 1
234 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.
HSPB9	Heat shock protein family B (small) member 9	0.9587	56
ODF2	Outer dense fiber of sperm tails 2	0.9200	56
PLAAT5	Phospholipase A and acyltransferase 5	0.9042	56
C11orf42	Chromosome 11 open reading frame 42	0.9040	56
LEMD1	LEM domain containing 1	0.9020	56
SPEM1	Spermatid maturation 1	0.9013	56
GAPDHS	Glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	0.8965	56
ALKBH7	AlkB homolog 7	0.8940	56
P3R3URF	PIK3R3 upstream open reading frame	0.8930	56
PRM3	Protamine 3	0.8918	56
ENSG00000187186	Novel protein	0.8907	56
TMEM239	Transmembrane protein 239	0.8898	56
TMCO5A	Transmembrane and coiled-coil domains 5A	0.8881	56
C12orf54	Chromosome 12 open reading frame 54	0.8853	56
TEX53	Testis expressed 53	0.8773	56