Single cell type - AMIGO2 - 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.	AMIGO2
Gene descriptionⁱ Full gene name according to HGNC.	Adhesion molecule with Ig like 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.	Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	3

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.	Neurons - Neurotransmission & signaling (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 (Breast myoepithelial cells, Platelets, Epididymal basal cells, Endometrial glandular cells, Urothelial cells, Smooth muscle cells, Epididymal efferent duct ciliated cells, Vascular smooth muscle cells, Epididymal efferent duct absorptive cells, Endometrial luminal cells, Fallopian tube ciliated 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.	0.66
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 (Vascular associated smooth muscle cell, Midbrain-derived inhibitory)
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 (Secretory gland support, Platelets, Basal 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 (Vascular associated smooth muscle cell, Midbrain-derived inhibitory)

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

AMIGO2 is part of cluster 98 Neurons - Neurotransmission & signaling with confidenceⁱ 1
318 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.
GPR151	G protein-coupled receptor 151	0.5617	98
LRRC55	Leucine rich repeat containing 55	0.5613	98
OR2A25	Olfactory receptor family 2 subfamily A member 25	0.5333	98
CHRNB3	Cholinergic receptor nicotinic beta 3 subunit	0.5138	98
POU4F1	POU class 4 homeobox 1	0.5016	98
GNG8	G protein subunit gamma 8	0.4707	47
MAGED4	MAGE family member D4	0.4697	98
MC4R	Melanocortin 4 receptor	0.4599	109
GPR179	G protein-coupled receptor 179	0.4509	98
PCED1B	PC-esterase domain containing 1B	0.4508	9
NGB	Neuroglobin	0.4412	98
SLC7A4	Solute carrier family 7 member 4	0.4274	98
SNCG	Synuclein gamma	0.4245	69
KRTAP10-4	Keratin associated protein 10-4	0.4150	98
NWD2	NACHT and WD repeat domain containing 2	0.4131	109

IMMUNE CELLS

AMIGO2 is part of cluster 11 T-cells - Unknown function with confidenceⁱ 1
119 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.
ARHGEF4	Rho guanine nucleotide exchange factor 4	1.0000	11
HOXB2	Homeobox B2	1.0000	11
RPF2	Ribosome production factor 2 homolog	0.9762	3
LY9	Lymphocyte antigen 9	0.9762	11
SUPT3H	SPT3 homolog, SAGA and STAGA complex component	0.9762	3
B4GAT1	Beta-1,4-glucuronyltransferase 1	0.9762	3
ZNF510	Zinc finger protein 510	0.9524	1
MRPS6	Mitochondrial ribosomal protein S6	0.9524	1
DHRS3	Dehydrogenase/reductase 3	0.9524	11
ZNF337	Zinc finger protein 337	0.9524	11
ESYT2	Extended synaptotagmin 2	0.9524	1
AK5	Adenylate kinase 5	0.9286	11
NBL1	NBL1, DAN family BMP antagonist	0.9286	11
CAPN5	Calpain 5	0.9286	11
DCBLD1	Discoidin, CUB and LCCL domain containing 1	0.9286	11