Single cell type - PADI2 - 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.	PADI2
Gene descriptionⁱ Full gene name according to HGNC.	Peptidyl arginine deiminase 2
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.	2

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.	Microglia - Neuroimmunity & neuroinflammation (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 (Cone photoreceptor cells, Myonuclei, Colonocytes, Neutrophils, Microglia, Oligodendrocytes, Rod photoreceptor cells, Goblet cells, Macrophages, Müller glia, Neutrophil progenitors)
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.	0.75
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 (Central nervous system macrophage, Oligodendrocyte, Astrocyte, Committed oligodendrocyte precursor)
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.	Group enriched (neutrophil, eosinophil)
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 (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 (Neuronal cells, Myocytes, Enterocytes, Neutrophils, Glial 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: Cell type enhanced (Central nervous system macrophage, Oligodendrocyte, Astrocyte, Committed oligodendrocyte precursor)

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: Group enriched (neutrophil, eosinophil)
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

PADI2 is part of cluster 74 Microglia - Neuroimmunity & neuroinflammation with confidenceⁱ 1
118 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.
LPCAT2	Lysophosphatidylcholine acyltransferase 2	0.5461	74
CD177	CD177 molecule	0.4347	48
TM6SF1	Transmembrane 6 superfamily member 1	0.4324	32
GAL3ST4	Galactose-3-O-sulfotransferase 4	0.4060	74
APOBR	Apolipoprotein B receptor	0.3989	48
ASCL4	Achaete-scute family bHLH transcription factor 4	0.3891	74
APAF1	Apoptotic peptidase activating factor 1	0.3869	37
HSPBAP1	HSPB1 associated protein 1	0.3820	24
KBTBD12	Kelch repeat and BTB domain containing 12	0.3800	74
DOCK8	Dedicator of cytokinesis 8	0.3780	74
MACIR	Macrophage immunometabolism regulator	0.3749	48
CLEC5A	C-type lectin domain containing 5A	0.3737	82
HK2	Hexokinase 2	0.3735	48
VASH1	Vasohibin 1	0.3717	74
GPAT3	Glycerol-3-phosphate acyltransferase 3	0.3686	82

IMMUNE CELLS

PADI2 is part of cluster 21 Neutrophils - Unknown function with confidenceⁱ 1
492 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.
ABAT	4-aminobutyrate aminotransferase	0.9762	21
MEGF9	Multiple EGF like domains 9	0.9762	21
CCNY	Cyclin Y	0.9762	38
ARHGEF40	Rho guanine nucleotide exchange factor 40	0.9762	21
GLIPR2	GLI pathogenesis related 2	0.9762	21
ALPK1	Alpha kinase 1	0.9762	21
FCGR2A	Fc gamma receptor IIa	0.9762	21
NUP214	Nucleoporin 214	0.9524	38
AGTRAP	Angiotensin II receptor associated protein	0.9524	21
TALDO1	Transaldolase 1	0.9524	21
H3-3A	H3.3 histone A	0.9524	21
RNF175	Ring finger protein 175	0.9524	38
IL1RN	Interleukin 1 receptor antagonist	0.9524	38
MICAL2	Microtubule associated monooxygenase, calponin and LIM domain containing 2	0.9524	38
SGK1	Serum/glucocorticoid regulated kinase 1	0.9524	21