Single cell type - MATR3 - 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.	MATR3
Gene descriptionⁱ Full gene name according to HGNC.	Matrin 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	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.	11

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 - Neuronal 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.	Group enriched (Inhibitory neurons, Oligodendrocytes, Excitatory neurons, Oligodendrocyte precursor cells, Astrocytes, Microglial 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.	0.91
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

Single nuclei - Brain

Immune cells

Expression clustering

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: Group enriched (Inhibitory neurons, Oligodendrocytes, Excitatory neurons, Oligodendrocyte precursor cells, Astrocytes, Microglial cells)

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

MATR3 is part of cluster 69 Neurons - Neuronal signaling with confidenceⁱ 1
331 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.
GPHN	Gephyrin	0.9155	69
APBA1	Amyloid beta precursor protein binding family A member 1	0.8701	69
ARMCX5-GPRASP2	ARMCX5-GPRASP2 readthrough	0.8496	69
BCL2L2-PABPN1	BCL2L2-PABPN1 readthrough	0.8342	69
UTP14C	UTP14C small subunit processome component	0.8341	69
FAM185A	Family with sequence similarity 185 member A	0.8267	69
AUTS2	Activator of transcription and developmental regulator AUTS2	0.7963	69
CELF6	CUGBP Elav-like family member 6	0.7860	69
ZSWIM5	Zinc finger SWIM-type containing 5	0.7831	69
ARNT2	Aryl hydrocarbon receptor nuclear translocator 2	0.7740	69
ZC3H12B	Zinc finger CCCH-type containing 12B	0.7702	69
DAB1	DAB adaptor protein 1	0.7609	69
ECE2	Endothelin converting enzyme 2	0.7574	69
GRIK2	Glutamate ionotropic receptor kainate type subunit 2	0.7490	69
HIVEP3	HIVEP zinc finger 3	0.7438	69

IMMUNE CELLS

MATR3 is part of cluster 43 Non-specific - Transcription & Translation with confidenceⁱ 0.99
433 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.
FDFT1	Farnesyl-diphosphate farnesyltransferase 1	0.9762	43
H2BC7	H2B clustered histone 7	0.9762	43
H4C16	H4 histone 16	0.9762	18
R3HDM2	R3H domain containing 2	0.9762	43
GJB6	Gap junction protein beta 6	0.9762	43
ZNF343	Zinc finger protein 343	0.9524	18
H4C6	H4 clustered histone 6	0.9524	43
FOXO1	Forkhead box O1	0.9524	43
KIAA1328	KIAA1328	0.9524	43
NAF1	Nuclear assembly factor 1 ribonucleoprotein	0.9524	43
IL9R	Interleukin 9 receptor	0.9524	14
EPB41L5	Erythrocyte membrane protein band 4.1 like 5	0.9524	43
CAMK2D	Calcium/calmodulin dependent protein kinase II delta	0.9286	18
CHAC2	ChaC glutathione specific gamma-glutamylcyclotransferase 2	0.9286	43
BTBD2	BTB domain containing 2	0.9286	18