Single cell type - GATB - 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.	GATB
Gene descriptionⁱ Full gene name according to HGNC.	Glutamyl-tRNA amidotransferase subunit B
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Human disease related genes
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.	Muller glia cells - Retinal homeostasis (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 enriched (Müller glia)
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.	0.57
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 enriched (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: 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

GATB is part of cluster 11 Muller glia cells - Retinal homeostasis with confidenceⁱ 1
80 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.
PRSS35	Serine protease 35	0.8582	11
CRABP1	Cellular retinoic acid binding protein 1	0.8427	11
CRYAA	Crystallin alpha A	0.8395	11
FABP7	Fatty acid binding protein 7	0.8273	11
NPVF	Neuropeptide VF precursor	0.8241	11
TF	Transferrin	0.8208	11
DIPK1C	Divergent protein kinase domain 1C	0.8101	11
RAX	Retina and anterior neural fold homeobox	0.7997	11
SIX6	SIX homeobox 6	0.7960	11
GPR37	G protein-coupled receptor 37	0.7855	11
NR2E1	Nuclear receptor subfamily 2 group E member 1	0.7805	11
STAC2	SH3 and cysteine rich domain 2	0.7770	11
WIF1	WNT inhibitory factor 1	0.7739	11
DKK3	Dickkopf WNT signaling pathway inhibitor 3	0.7724	11
LIX1	Limb and CNS expressed 1	0.7718	11

IMMUNE CELLS

GATB is part of cluster 33 Non-specific - ATP binding with confidenceⁱ 0.92
757 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.
SMC1A	Structural maintenance of chromosomes 1A	1.0000	33
VPS52	VPS52 subunit of GARP complex	0.9762	33
DDX47	DEAD-box helicase 47	0.9762	33
TTF2	Transcription termination factor 2	0.9762	33
SMN1	Survival of motor neuron 1, telomeric	0.9762	33
CPSF1	Cleavage and polyadenylation specific factor 1	0.9524	33
ENSG00000273155	Novel LIPT1-MRPL30 readthrough	0.9524	33
ZNF335	Zinc finger protein 335	0.9524	33
USP38	Ubiquitin specific peptidase 38	0.9524	33
TMCO4	Transmembrane and coiled-coil domains 4	0.9524	33
GNE	Glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	0.9524	33
GEMIN6	Gem nuclear organelle associated protein 6	0.9524	33
SMPD4	Sphingomyelin phosphodiesterase 4	0.9524	33
PAN2	Poly(A) specific ribonuclease subunit PAN2	0.9524	33
MAU2	MAU2 sister chromatid cohesion factor	0.9524	33