Single cell type - AGAP2 - 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.	AGAP2
Gene descriptionⁱ Full gene name according to HGNC.	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2
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.	Non-specific - Cardiac endocrine signaling & maintenanc (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 (Neutrophils, Brain excitatory neurons, Neutrophil progenitors, Brain inhibitory neurons, Pericytes, Hematopoietic stem cells, NK-cells, T-cells, Retinal amacrine cells, Other brain neurons)
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.	0.82
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 (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 (Neutrophils, Neuronal cells, Mural cells, Stem 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: 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

AGAP2 is part of cluster 71 Non-specific - Cardiac endocrine signaling & maintenanc with confidenceⁱ 1
353 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.
ENSG00000282218	Novel protein, GOPC-ROS1 readthrough	0.5092	71
ELMO2	Engulfment and cell motility 2	0.5087	29
KPNA5	Karyopherin subunit alpha 5	0.5003	71
THPO	Thrombopoietin	0.4941	71
DLGAP3	DLG associated protein 3	0.4706	35
HAUS7	HAUS augmin like complex subunit 7	0.4587	71
GUCY1A2	Guanylate cyclase 1 soluble subunit alpha 2	0.4557	110
CELF2	CUGBP Elav-like family member 2	0.4469	29
MOCS1	Molybdenum cofactor synthesis 1	0.4462	71
CENPO	Centromere protein O	0.4453	71
SMIM12	Small integral membrane protein 12	0.4439	71
B4GALNT1	Beta-1,4-N-acetyl-galactosaminyltransferase 1	0.4433	35
DEFB124	Defensin beta 124	0.4384	71
GJE1	Gap junction protein epsilon 1	0.4268	71
CHRD	Chordin	0.4253	2

IMMUNE CELLS

AGAP2 is part of cluster 35 Neutrophils - Protein binding with confidenceⁱ 0.9
504 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.
SAMD9	Sterile alpha motif domain containing 9	0.9762	32
IRAK4	Interleukin 1 receptor associated kinase 4	0.9762	35
WDR26	WD repeat domain 26	0.9762	35
SDE2	SDE2 telomere maintenance homolog	0.9762	35
ETV3	ETS variant transcription factor 3	0.9762	35
POC1B	POC1 centriolar protein B	0.9762	32
FGF23	Fibroblast growth factor 23	0.9524	35
MAFF	MAF bZIP transcription factor F	0.9524	32
BAG5	BAG cochaperone 5	0.9524	35
ZER1	Zyg-11 related cell cycle regulator	0.9524	35
STK26	Serine/threonine kinase 26	0.9524	32
PLD1	Phospholipase D1	0.9524	42
BIN2	Bridging integrator 2	0.9524	35
STXBP3	Syntaxin binding protein 3	0.9286	35
STK38	Serine/threonine kinase 38	0.9286	35