Single cell type - SERPINE1 - 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.	SERPINE1
Gene descriptionⁱ Full gene name according to HGNC.	Serpin family E member 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes Candidate cardiovascular disease genes Disease related genes FDA approved drug targets Human disease related genes 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.	Secreted
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.	Gonadal somatic cells - Mixed function (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 (Syncytiotrophoblasts, Ovarian stromal cells, Hepatic stellate cells, Decidual stromal cells, Migrating cytotrophoblasts, Fibroblasts, Vascular endothelial cells, Hepatocytes, Leydig 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.	0.69
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.	Group enriched (Endothelial cell, Central nervous system macrophage)
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 enriched (NK-cell)
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
Extracellular locationⁱ A possible secretion of the protein was predicted based on N-terminal signal sequence (signal peptide) predictions and transmembrane region predictions, and subsequently annotated for its local or systemic secretion based on literature, function, and protein and RNA expression data.	Protein predicted to be secreted

ASSAYSⁱ

Single cell type

Cell type enrichment

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 enhanced (Trophoblast cells, Stromal cells, Stellate 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: Group enriched (Endothelial cell, Central nervous system macrophage)

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 enriched (NK-cell)
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

SERPINE1 is part of cluster 94 Gonadal somatic cells - Mixed function with confidenceⁱ 1
128 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.
COLEC11	Collectin subfamily member 11	0.5578	94
TCF21	Transcription factor 21	0.5367	108
DAPK3	Death associated protein kinase 3	0.5193	62
LOXL2	Lysyl oxidase like 2	0.5135	12
SNRPB2	Small nuclear ribonucleoprotein polypeptide B2	0.5033	39
SLC25A17	Solute carrier family 25 member 17	0.4865	94
WWTR1	WW domain containing transcription regulator 1	0.4862	12
CYP1A1	Cytochrome P450 family 1 subfamily A member 1	0.4761	32
PWWP3B	PWWP domain containing 3B	0.4746	94
AKAP12	A-kinase anchoring protein 12	0.4745	12
CCDC68	Coiled-coil domain containing 68	0.4711	12
ACSM3	Acyl-CoA synthetase medium chain family member 3	0.4654	94
GREB1	Growth regulating estrogen receptor binding 1	0.4649	94
WFIKKN2	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	0.4576	94
RBP1	Retinol binding protein 1	0.4549	94

IMMUNE CELLS

SERPINE1 is part of cluster 14 Non-specific - Unknown function with confidenceⁱ 0.66
292 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.
ENSG00000288681	Novel protein	0.9762	15
CLASP1	Cytoplasmic linker associated protein 1	0.9524	15
ZNF578	Zinc finger protein 578	0.9524	5
SMIM24	Small integral membrane protein 24	0.9524	15
TIE1	Tyrosine kinase with immunoglobulin like and EGF like domains 1	0.9524	15
ANKMY2	Ankyrin repeat and MYND domain containing 2	0.9286	15
FZD6	Frizzled class receptor 6	0.9286	14
HOXA10	Homeobox A10	0.9286	15
CTSO	Cathepsin O	0.9286	24
CEBPZ	CCAAT enhancer binding protein zeta	0.9048	15
LRIF1	Ligand dependent nuclear receptor interacting factor 1	0.9048	14
RAB22A	RAB22A, member RAS oncogene family	0.9048	15
SPINK2	Serine peptidase inhibitor Kazal type 2	0.9048	14
ZNF614	Zinc finger protein 614	0.9048	5
ARL14EP	ADP ribosylation factor like GTPase 14 effector protein	0.9048	15