Single cell type - PSME1 - 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.	PSME1
Gene descriptionⁱ Full gene name according to HGNC.	Proteasome activator subunit 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Plasma 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.	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.	Langerhans cells - Innate immune response (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.	Low cell type specificity
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.	0.27
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 (Leukocyte, Pericyte, 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.	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: Low cell type specificity

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 (Leukocyte, Pericyte, 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: 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

PSME1 is part of cluster 14 Langerhans cells - Innate immune response with confidenceⁱ 1
131 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.
PSMB9	Proteasome 20S subunit beta 9	0.6561	14
PSME2	Proteasome activator subunit 2	0.6235	15
B2M	Beta-2-microglobulin	0.6207	14
HLA-C	Major histocompatibility complex, class I, C	0.5963	14
PSMB10	Proteasome 20S subunit beta 10	0.5939	7
HLA-B	Major histocompatibility complex, class I, B	0.5694	14
HLA-F	Major histocompatibility complex, class I, F	0.5666	14
PSMB8	Proteasome 20S subunit beta 8	0.5634	14
MYO1G	Myosin IG	0.5539	14
TAP1	Transporter 1, ATP binding cassette subfamily B member	0.5484	14
LSP1	Lymphocyte specific protein 1	0.5352	14
IRF2	Interferon regulatory factor 2	0.5179	14
PFN1	Profilin 1	0.5126	14
BTN3A3	Butyrophilin subfamily 3 member A3	0.5120	19
IFI35	Interferon induced protein 35	0.5118	14

IMMUNE CELLS

PSME1 is part of cluster 37 Monocytes & Neutrophils - Innate immune response with confidenceⁱ 0.93
275 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.
CHMP5	Charged multivesicular body protein 5	1.0000	37
USB1	U6 snRNA biogenesis phosphodiesterase 1	0.9762	37
RRP12	Ribosomal RNA processing 12 homolog	0.9524	37
ZYX	Zyxin	0.9524	37
PICALM	Phosphatidylinositol binding clathrin assembly protein	0.9524	7
SPTLC1	Serine palmitoyltransferase long chain base subunit 1	0.9286	37
CATSPERG	Cation channel sperm associated auxiliary subunit gamma	0.9286	37
CPPED1	Calcineurin like phosphoesterase domain containing 1	0.9286	37
RAB2A	RAB2A, member RAS oncogene family	0.9286	37
TMEM30A	Transmembrane protein 30A	0.9286	37
RBCK1	RANBP2-type and C3HC4-type zinc finger containing 1	0.9286	28
RAP1GAP2	RAP1 GTPase activating protein 2	0.9286	37
BCL2A1	BCL2 related protein A1	0.9286	37
RAB5A	RAB5A, member RAS oncogene family	0.9286	37
WAC	WW domain containing adaptor with coiled-coil	0.9048	28