Single cell type - AGAP6 - The Human Protein Atlas

AGAP6

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Pathway

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.	AGAP6
Gene descriptionⁱ Full gene name according to HGNC.	ArfGAP with GTPase domain, ankyrin repeat and PH domain 6
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.	Early spermatids - Spermatogenesis (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 (Early spermatids, Excitatory neurons, Astrocytes, Inhibitory neurons, Oligodendrocytes, Late spermatids, Oligodendrocyte precursor 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.	0.71
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.	Immune cell enhanced (basophil)
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 transcript level

ASSAYSⁱ

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 (Early spermatids, Excitatory neurons, Astrocytes, Inhibitory neurons, Oligodendrocytes, Late spermatids, Oligodendrocyte precursor 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: Immune cell enhanced (basophil)
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

AGAP6 is part of cluster 21 Early spermatids - Spermatogenesis with confidenceⁱ 0.67
337 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.
PEX5	Peroxisomal biogenesis factor 5	0.6451	21
NPIPA1	Nuclear pore complex interacting protein family member A1	0.6321	13
ASNS	Asparagine synthetase (glutamine-hydrolyzing)	0.6306	13
WDR37	WD repeat domain 37	0.6284	21
AGAP4	ArfGAP with GTPase domain, ankyrin repeat and PH domain 4	0.6086	13
SPDYE17	Speedy/RINGO cell cycle regulator family member E17	0.5951	13
SPDYE3	Speedy/RINGO cell cycle regulator family member E3	0.5948	13
FAM153A	Family with sequence similarity 153 member A	0.5881	13
FANCC	FA complementation group C	0.5543	21
ADAM20	ADAM metallopeptidase domain 20	0.5524	21
ZNF790	Zinc finger protein 790	0.5447	21
PACRGL	Parkin coregulated like	0.5435	13
FDXACB1	Ferredoxin-fold anticodon binding domain containing 1	0.5430	21
LRRC37A2	Leucine rich repeat containing 37 member A2	0.5428	21
NPIPB13	Nuclear pore complex interacting protein family, member B13	0.5406	13

Adipocytes	0.7 nTPM
Adipose tissue	1.0 nTPM
Breast	0.5 nTPM

Alveolar cells type 1	1.3 nTPM
Lung	1.3 nTPM

Alveolar cells type 2	1.5 nTPM
Lung	1.5 nTPM

B-cells	2.1 nTPM
PBMC	7.7 nTPM
Kidney	5.2 nTPM
Liver	4.8 nTPM
Salivary gland	3.0 nTPM
Adipose tissue	2.1 nTPM
Bone marrow	1.6 nTPM
Lung	1.3 nTPM
Spleen	1.0 nTPM
Thymus	0.7 nTPM
Lymph node	0.3 nTPM
Skin	0.0 nTPM
Esophagus	0.0 nTPM
Stomach	0.0 nTPM

Basal keratinocytes	1.9 nTPM
Skin	2.9 nTPM
Tongue	1.0 nTPM

Ciliated cells	2.6 nTPM
Bronchus	4.8 nTPM
Lung	3.7 nTPM
Endometrium	1.7 nTPM
Fallopian tube	0.3 nTPM

Club cells	1.6 nTPM
Lung	1.9 nTPM
Bronchus	1.4 nTPM
Prostate	1.4 nTPM

Endothelial cells	1.2 nTPM
Liver	5.0 nTPM
Skeletal muscle	2.0 nTPM
Testis	1.8 nTPM
Thymus	1.6 nTPM
Ovary	1.5 nTPM
Prostate	1.4 nTPM
Salivary gland	1.4 nTPM
Lung	1.3 nTPM
Vascular	1.3 nTPM
Tongue	1.0 nTPM
Endometrium	0.9 nTPM
Skin	0.8 nTPM
Esophagus	0.8 nTPM
Placenta	0.6 nTPM
Fallopian tube	0.5 nTPM
Heart muscle	0.2 nTPM
Pancreas	0.0 nTPM
Breast	0.0 nTPM

Enteroendocrine cells	2.3 nTPM
Small intestine	6.9 nTPM
Colon	0.1 nTPM
Rectum	0.0 nTPM

Fibroblasts	1.1 nTPM
Liver	3.6 nTPM
Skeletal muscle	1.9 nTPM
Stomach	1.4 nTPM
Vascular	1.3 nTPM
Skin	1.2 nTPM
Lung	1.2 nTPM
Salivary gland	1.1 nTPM
Thymus	0.9 nTPM
Adipose tissue	0.8 nTPM
Breast	0.8 nTPM
Pancreas	0.7 nTPM
Prostate	0.7 nTPM
Esophagus	0.6 nTPM
Fallopian tube	0.6 nTPM
Placenta	0.5 nTPM
Heart muscle	0.2 nTPM

Granulocytes	0.8 nTPM
Lung	1.5 nTPM
Fallopian tube	0.8 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	0.6 nTPM
Rectum	1.0 nTPM
Small intestine	0.8 nTPM
Colon	0.0 nTPM

Lymphatic endothelial cells	0.3 nTPM
Fallopian tube	0.6 nTPM
Ovary	0.0 nTPM

Macrophages	1.1 nTPM
Vascular	2.3 nTPM
Salivary gland	2.2 nTPM
Bone marrow	2.0 nTPM
Skeletal muscle	1.7 nTPM
Prostate	1.7 nTPM
Tongue	1.7 nTPM
Thymus	1.6 nTPM
Adipose tissue	1.5 nTPM
Esophagus	1.3 nTPM
Lung	1.3 nTPM
Skin	1.1 nTPM
Kidney	0.9 nTPM
Fallopian tube	0.9 nTPM
Breast	0.7 nTPM
Testis	0.6 nTPM
Endometrium	0.0 nTPM
Pancreas	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	0.2 nTPM
Rectum	0.7 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Astrocytes	18.3 nTPM
Brain	18.3 nTPM

Cone photoreceptor cells	6.8 nTPM
Eye	6.8 nTPM

Plasma cells	1.8 nTPM
Esophagus	5.2 nTPM
Thymus	2.9 nTPM
Salivary gland	1.8 nTPM
Bone marrow	1.5 nTPM
Stomach	1.3 nTPM
Fallopian tube	1.3 nTPM
Spleen	0.7 nTPM
Liver	0.0 nTPM

Schwann cells	0.5 nTPM
Vascular	1.0 nTPM
Adipose tissue	0.4 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	1.3 nTPM
Salivary gland	2.6 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	1.2 nTPM
Salivary gland	3.5 nTPM
Liver	3.0 nTPM
Skeletal muscle	1.9 nTPM
Tongue	1.8 nTPM
Skin	1.4 nTPM
Placenta	1.3 nTPM
Vascular	1.3 nTPM
Thymus	0.9 nTPM
Ovary	0.9 nTPM
Endometrium	0.8 nTPM
Adipose tissue	0.7 nTPM
Prostate	0.6 nTPM
Breast	0.6 nTPM
Fallopian tube	0.3 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM

T-cells	1.7 nTPM
PBMC	7.3 nTPM
Liver	3.5 nTPM
Salivary gland	3.1 nTPM
Esophagus	2.4 nTPM
Tongue	2.4 nTPM
Skeletal muscle	2.3 nTPM
Thymus	1.6 nTPM
Vascular	1.6 nTPM
Skin	1.4 nTPM
Adipose tissue	1.3 nTPM
Bone marrow	1.3 nTPM
Endometrium	1.0 nTPM
Kidney	0.9 nTPM
Prostate	0.9 nTPM
Breast	0.8 nTPM
Lymph node	0.7 nTPM
Stomach	0.7 nTPM
Fallopian tube	0.6 nTPM
Spleen	0.5 nTPM
Lung	0.5 nTPM
Colon	0.0 nTPM

Undifferentiated cells	1.0 nTPM
Small intestine	1.8 nTPM
Rectum	1.0 nTPM
Colon	0.4 nTPM

Amygdala excitatory	14.6 nTPM
Amygdala	18.1 nTPM
Hypothalamus	16.0 nTPM
Hippocampus	15.7 nTPM
Cerebral cortex	15.1 nTPM
Basal ganglia	13.8 nTPM
Thalamus	9.1 nTPM

Astrocyte	14.9 nTPM
Amygdala	19.2 nTPM
Hippocampus	17.2 nTPM
Midbrain	17.1 nTPM
Cerebral cortex	16.3 nTPM
Thalamus	15.6 nTPM
Basal ganglia	14.7 nTPM
Cerebellum	14.3 nTPM
Hypothalamus	14.2 nTPM
Pons	13.9 nTPM
Medulla oblongata	12.8 nTPM
Spinal cord	8.3 nTPM

Bergmann glia	17.8 nTPM
Pons	23.0 nTPM
Cerebellum	17.6 nTPM
Medulla oblongata	12.8 nTPM

Central nervous system macrophage	16.4 nTPM
Amygdala	21.8 nTPM
Hypothalamus	18.3 nTPM
Cerebellum	17.5 nTPM
Midbrain	17.3 nTPM
Thalamus	16.5 nTPM
Pons	16.2 nTPM
Basal ganglia	16.1 nTPM
Hippocampus	16.1 nTPM
Cerebral cortex	14.7 nTPM
Spinal cord	13.8 nTPM
Medulla oblongata	11.8 nTPM

Cerebellar inhibitory	16.2 nTPM
Midbrain	23.0 nTPM
Cerebellum	18.5 nTPM
Pons	15.3 nTPM
Medulla oblongata	13.3 nTPM
Spinal cord	11.0 nTPM

Cge interneuron	12.3 nTPM
Amygdala	13.4 nTPM
Hypothalamus	12.8 nTPM
Midbrain	12.5 nTPM
Thalamus	12.3 nTPM
Cerebral cortex	12.1 nTPM
Hippocampus	11.8 nTPM
Basal ganglia	11.1 nTPM

Choroid plexus epithelial cell	14.9 nTPM
Basal ganglia	25.1 nTPM
Medulla oblongata	20.7 nTPM
Hippocampus	8.3 nTPM
Thalamus	5.5 nTPM

Committed oligodendrocyte precursor	14.2 nTPM
Hippocampus	19.4 nTPM
Midbrain	18.5 nTPM
Amygdala	18.0 nTPM
Hypothalamus	15.7 nTPM
Pons	15.1 nTPM
Thalamus	14.9 nTPM
Cerebral cortex	13.9 nTPM
Basal ganglia	13.1 nTPM
Medulla oblongata	12.9 nTPM
Cerebellum	11.1 nTPM
Spinal cord	3.7 nTPM

Deep-layer corticothalamic and 6b	14.4 nTPM
Midbrain	16.6 nTPM
Hippocampus	14.9 nTPM
Hypothalamus	14.8 nTPM
Cerebral cortex	14.5 nTPM
Amygdala	14.0 nTPM
Basal ganglia	11.6 nTPM

Deep-layer intratelencephalic	15.4 nTPM
Hypothalamus	17.0 nTPM
Amygdala	15.9 nTPM
Hippocampus	15.5 nTPM
Cerebral cortex	15.4 nTPM
Basal ganglia	13.1 nTPM

Deep-layer near-projecting	14.0 nTPM
Amygdala	17.8 nTPM
Hippocampus	14.3 nTPM
Cerebral cortex	14.0 nTPM
Hypothalamus	12.8 nTPM
Basal ganglia	10.9 nTPM

Eccentric medium spiny neuron	15.1 nTPM
Hypothalamus	16.3 nTPM
Amygdala	16.2 nTPM
Thalamus	16.0 nTPM
Basal ganglia	15.0 nTPM
Cerebral cortex	14.4 nTPM
Hippocampus	12.8 nTPM

Endothelial cell	13.2 nTPM
Spinal cord	17.3 nTPM
Pons	16.2 nTPM
Thalamus	15.2 nTPM
Hypothalamus	14.9 nTPM
Cerebral cortex	13.4 nTPM
Medulla oblongata	13.3 nTPM
Basal ganglia	13.0 nTPM
Cerebellum	12.4 nTPM
Amygdala	11.2 nTPM
Midbrain	9.5 nTPM
Hippocampus	9.0 nTPM

Ependymal cell	10.5 nTPM
Amygdala	14.8 nTPM
Spinal cord	13.4 nTPM
Basal ganglia	12.7 nTPM
Hippocampus	11.6 nTPM
Thalamus	10.9 nTPM
Midbrain	10.2 nTPM
Medulla oblongata	7.2 nTPM
Hypothalamus	7.1 nTPM
Pons	6.3 nTPM