Single cell type - PUDP - 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.	PUDP
Gene descriptionⁱ Full gene name according to HGNC.	Pseudouridine 5'-phosphatase
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Enzymes
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.	Cytotrophoblasts - Mitochondria (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 (Cytotrophoblasts)
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.	0.43
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.	Low cell type specificity
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

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 (Cytotrophoblasts)

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: Low cell type specificity

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

PUDP is part of cluster 24 Cytotrophoblasts - Mitochondria with confidenceⁱ 1
235 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.
TRBV20OR9-2	T cell receptor beta variable 20/OR9-2 (non-functional)	0.6203	24
GJB7	Gap junction protein beta 7	0.6112	24
SMAGP	Small cell adhesion glycoprotein	0.6105	24
L1TD1	LINE1 type transposase domain containing 1	0.5960	24
SOX14	SRY-box transcription factor 14	0.5955	24
FBN2	Fibrillin 2	0.5939	24
GRAMD2A	GRAM domain containing 2A	0.5925	24
PAGE4	PAGE family member 4	0.5875	24
RMI2	RecQ mediated genome instability 2	0.5842	24
FOXO4	Forkhead box O4	0.5788	24
MAGEA8	MAGE family member A8	0.5753	24
HPDL	4-hydroxyphenylpyruvate dioxygenase like	0.5743	24
SLC27A6	Solute carrier family 27 member 6	0.5714	24
SLC12A9	Solute carrier family 12 member 9	0.5698	24
FADD	Fas associated via death domain	0.5651	24

IMMUNE CELLS

PUDP is part of cluster 33 Non-specific - ATP binding with confidenceⁱ 0.86
757 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.
SAMHD1	SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1	0.9762	33
NUDT14	Nudix hydrolase 14	0.9762	33
SLC25A3	Solute carrier family 25 member 3	0.9762	33
SETD7	SET domain containing 7, histone lysine methyltransferase	0.9762	33
CIBAR1	CBY1 interacting BAR domain containing 1	0.9524	33
CRAT	Carnitine O-acetyltransferase	0.9524	33
WRAP73	WD repeat containing, antisense to TP73	0.9524	33
PEPD	Peptidase D	0.9524	33
PCYOX1L	Prenylcysteine oxidase 1 like	0.9524	33
C1orf43	Chromosome 1 open reading frame 43	0.9524	26
UQCRC2	Ubiquinol-cytochrome c reductase core protein 2	0.9524	33
LDHA	Lactate dehydrogenase A	0.9286	33
OXA1L	OXA1L mitochondrial inner membrane protein	0.9286	33
MAN2C1	Mannosidase alpha class 2C member 1	0.9286	33
CAPRIN1	Cell cycle associated protein 1	0.9286	33