Single cell type - LOXL3 - The Human Protein Atlas

LOXL3

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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.	LOXL3
Gene descriptionⁱ Full gene name according to HGNC.	Lysyl oxidase like 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Enzymes Plasma proteins Potential drug targets
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.	Secreted, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	7

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.	Connective tissue cells - ECM organization (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 (Microglial cells, Hofbauer cells, Astrocytes, Pancreatic endocrine cells, Sertoli cells, Oligodendrocyte precursor cells, Monocytes, Melanocytes, Macrophages)
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.	0.78
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 enriched (Central nervous system macrophage)
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 (intermediate monocyte, non-classical monocyte)
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
Extracellular locationⁱ A possible secretion of the protein was predicted based on N-terminal signal sequence (signal peptide) predictions and transmembrane region predictions, and subsequently annotated for its local or systemic secretion based on literature, function, and protein and RNA expression data.	Protein predicted to be secreted

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 (Microglial cells, Hofbauer cells, Astrocytes, Pancreatic endocrine cells, Sertoli cells, Oligodendrocyte precursor cells, Monocytes, Melanocytes, Macrophages)

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 enriched (Central nervous system macrophage)

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 (intermediate monocyte, non-classical monocyte)
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

LOXL3 is part of cluster 50 Connective tissue cells - ECM organization with confidenceⁱ 1
176 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.
TGFBI	Transforming growth factor beta induced	0.6954	50
HGF	Hepatocyte growth factor	0.6688	50
FZD2	Frizzled class receptor 2	0.6532	50
DLK1	Delta like non-canonical Notch ligand 1	0.6449	50
CHAT	Choline O-acetyltransferase	0.6442	50
SLC18A3	Solute carrier family 18 member A3	0.6432	50
PITX2	Paired like homeodomain 2	0.6385	50
RTL1	Retrotransposon Gag like 1	0.6383	50
EGFL6	EGF like domain multiple 6	0.6318	50
HAPLN1	Hyaluronan and proteoglycan link protein 1	0.6300	50
PLAC1	Placenta enriched 1	0.6287	50
WNT2	Wnt family member 2	0.6268	50
DIO3	Iodothyronine deiodinase 3	0.6246	50
COLGALT1	Collagen beta(1-O)galactosyltransferase 1	0.5937	58
SPARC	Secreted protein acidic and cysteine rich	0.5892	50

IMMUNE CELLS

LOXL3 is part of cluster 40 Monocytes - Innate immune response with confidenceⁱ 1
228 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.
SLC24A4	Solute carrier family 24 member 4	1.0000	40
PGA5	Pepsinogen A5	1.0000	40
LIPN	Lipase family member N	1.0000	40
AP2A1	Adaptor related protein complex 2 subunit alpha 1	1.0000	40
CD300E	CD300e molecule	1.0000	40
PENK	Proenkephalin	1.0000	40
CDC42EP4	CDC42 effector protein 4	1.0000	40
FLII	FLII actin remodeling protein	1.0000	40
CXCL16	C-X-C motif chemokine ligand 16	1.0000	40
ATG3	Autophagy related 3	1.0000	40
SLC31A1	Solute carrier family 31 member 1	1.0000	40
SAT1	Spermidine/spermine N1-acetyltransferase 1	1.0000	40
CALML4	Calmodulin like 4	1.0000	40
TJP2	Tight junction protein 2	1.0000	40
ABHD11	Abhydrolase domain containing 11	1.0000	40

Adipocytes	0.5 nTPM
Breast	0.7 nTPM
Adipose tissue	0.4 nTPM

Alveolar cells type 1	0.9 nTPM
Lung	0.9 nTPM

Alveolar cells type 2	0.5 nTPM
Lung	0.5 nTPM

B-cells	0.3 nTPM
Skin	1.7 nTPM
Adipose tissue	0.8 nTPM
Bone marrow	0.7 nTPM
Salivary gland	0.4 nTPM
Lymph node	0.3 nTPM
Thymus	0.3 nTPM
Spleen	0.1 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Esophagus	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM

Basal keratinocytes	0.2 nTPM
Tongue	0.4 nTPM
Skin	0.0 nTPM

Ciliated cells	0.4 nTPM
Lung	0.7 nTPM
Fallopian tube	0.6 nTPM
Endometrium	0.4 nTPM
Bronchus	0.0 nTPM

Club cells	0.2 nTPM
Lung	0.7 nTPM
Bronchus	0.0 nTPM
Prostate	0.0 nTPM

Endothelial cells	0.6 nTPM
Esophagus	1.8 nTPM
Heart muscle	1.0 nTPM
Breast	0.9 nTPM
Vascular	0.8 nTPM
Ovary	0.8 nTPM
Endometrium	0.7 nTPM
Thymus	0.7 nTPM
Testis	0.6 nTPM
Placenta	0.6 nTPM
Tongue	0.6 nTPM
Skin	0.4 nTPM
Salivary gland	0.4 nTPM
Fallopian tube	0.4 nTPM
Lung	0.3 nTPM
Prostate	0.3 nTPM
Skeletal muscle	0.1 nTPM
Liver	0.0 nTPM
Pancreas	0.0 nTPM

Enteroendocrine cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Fibroblasts	6.4 nTPM
Pancreas	24.4 nTPM
Skeletal muscle	12.8 nTPM
Esophagus	11.5 nTPM
Stomach	7.2 nTPM
Adipose tissue	6.7 nTPM
Vascular	6.0 nTPM
Breast	5.7 nTPM
Skin	4.8 nTPM
Placenta	4.0 nTPM
Prostate	4.0 nTPM
Thymus	3.8 nTPM
Fallopian tube	3.5 nTPM
Salivary gland	3.4 nTPM
Heart muscle	3.2 nTPM
Lung	1.5 nTPM
Liver	0.0 nTPM

Granulocytes	0.7 nTPM
Lung	1.5 nTPM
Fallopian tube	0.6 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	0.2 nTPM
Colon	0.2 nTPM
Rectum	0.2 nTPM
Small intestine	0.0 nTPM

Lymphatic endothelial cells	0.1 nTPM
Fallopian tube	0.2 nTPM
Ovary	0.0 nTPM

Macrophages	10.2 nTPM
Esophagus	18.0 nTPM
Breast	15.2 nTPM
Spleen	13.0 nTPM
Stomach	12.9 nTPM
Fallopian tube	12.9 nTPM
Adipose tissue	11.7 nTPM
Salivary gland	11.5 nTPM
Thymus	11.3 nTPM
Bone marrow	11.1 nTPM
Vascular	10.3 nTPM
Prostate	9.9 nTPM
Testis	9.3 nTPM
Lung	9.2 nTPM
Kidney	8.0 nTPM
Tongue	6.3 nTPM
Pancreas	6.2 nTPM
Skeletal muscle	6.0 nTPM
Skin	5.6 nTPM
Endometrium	5.5 nTPM

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

Astrocytes	13.3 nTPM
Brain	13.3 nTPM

Endometrial stromal cells	4.3 nTPM
Endometrium	4.3 nTPM

Plasma cells	0.3 nTPM
Thymus	0.6 nTPM
Spleen	0.5 nTPM
Stomach	0.4 nTPM
Salivary gland	0.4 nTPM
Fallopian tube	0.3 nTPM
Liver	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

Schwann cells	4.3 nTPM
Vascular	10.4 nTPM
Adipose tissue	2.3 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	0.4 nTPM
Salivary gland	0.8 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	4.2 nTPM
Placenta	19.6 nTPM
Lung	7.1 nTPM
Vascular	5.5 nTPM
Skeletal muscle	4.7 nTPM
Endometrium	4.1 nTPM
Thymus	3.8 nTPM
Skin	3.5 nTPM
Breast	3.0 nTPM
Adipose tissue	2.7 nTPM
Tongue	2.7 nTPM
Esophagus	2.4 nTPM
Prostate	2.4 nTPM
Ovary	2.1 nTPM
Fallopian tube	1.6 nTPM
Salivary gland	0.9 nTPM
Liver	0.4 nTPM

T-cells	0.3 nTPM
Skin	1.4 nTPM
Endometrium	0.8 nTPM
Tongue	0.8 nTPM
Lymph node	0.5 nTPM
Lung	0.5 nTPM
Bone marrow	0.4 nTPM
Salivary gland	0.4 nTPM
Adipose tissue	0.3 nTPM
Spleen	0.3 nTPM
Thymus	0.3 nTPM
PBMC	0.2 nTPM
Prostate	0.2 nTPM
Breast	0.2 nTPM
Stomach	0.1 nTPM
Fallopian tube	0.1 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Vascular	0.0 nTPM

Undifferentiated cells	0.4 nTPM
Colon	0.7 nTPM
Rectum	0.3 nTPM
Small intestine	0.1 nTPM

Amygdala excitatory	3.3 nTPM
Thalamus	7.7 nTPM
Amygdala	3.8 nTPM
Hippocampus	3.1 nTPM
Basal ganglia	2.4 nTPM
Cerebral cortex	1.6 nTPM
Hypothalamus	0.9 nTPM

Astrocyte	21.4 nTPM
Hippocampus	26.1 nTPM
Cerebral cortex	24.4 nTPM
Thalamus	22.5 nTPM
Amygdala	22.4 nTPM
Cerebellum	22.0 nTPM
Hypothalamus	21.3 nTPM
Midbrain	21.2 nTPM
Pons	19.9 nTPM
Medulla oblongata	19.6 nTPM
Basal ganglia	19.3 nTPM
Spinal cord	16.8 nTPM

Bergmann glia	24.2 nTPM
Medulla oblongata	32.0 nTPM
Cerebellum	24.7 nTPM
Pons	15.8 nTPM

Central nervous system macrophage	111.4 nTPM
Amygdala	137.8 nTPM
Hippocampus	126.9 nTPM
Cerebellum	118.3 nTPM
Hypothalamus	116.9 nTPM
Midbrain	116.6 nTPM
Cerebral cortex	113.3 nTPM
Pons	108.3 nTPM
Thalamus	105.0 nTPM
Basal ganglia	100.1 nTPM
Medulla oblongata	95.0 nTPM
Spinal cord	87.1 nTPM

Cerebellar inhibitory	0.3 nTPM
Medulla oblongata	0.6 nTPM
Cerebellum	0.4 nTPM
Pons	0.4 nTPM
Midbrain	0.3 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	11.5 nTPM
Midbrain	13.8 nTPM
Hypothalamus	13.3 nTPM
Amygdala	12.4 nTPM
Cerebral cortex	11.6 nTPM
Basal ganglia	10.8 nTPM
Hippocampus	9.7 nTPM
Thalamus	8.6 nTPM

Choroid plexus epithelial cell	3.4 nTPM
Hippocampus	5.5 nTPM
Medulla oblongata	5.0 nTPM
Basal ganglia	3.1 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	11.5 nTPM
Midbrain	16.0 nTPM
Cerebellum	15.9 nTPM
Cerebral cortex	15.2 nTPM
Spinal cord	14.7 nTPM
Hippocampus	14.0 nTPM
Medulla oblongata	12.9 nTPM
Basal ganglia	10.4 nTPM
Amygdala	9.6 nTPM
Pons	8.9 nTPM
Hypothalamus	5.5 nTPM
Thalamus	3.4 nTPM

Deep-layer corticothalamic and 6b	0.8 nTPM
Hypothalamus	1.3 nTPM
Basal ganglia	1.2 nTPM
Cerebral cortex	1.0 nTPM
Amygdala	0.9 nTPM
Hippocampus	0.4 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	3.1 nTPM
Basal ganglia	4.6 nTPM
Amygdala	4.0 nTPM
Hypothalamus	3.5 nTPM
Hippocampus	1.7 nTPM
Cerebral cortex	1.6 nTPM

Deep-layer near-projecting	0.4 nTPM
Hypothalamus	0.9 nTPM
Amygdala	0.5 nTPM
Basal ganglia	0.3 nTPM
Cerebral cortex	0.3 nTPM
Hippocampus	0.0 nTPM

Eccentric medium spiny neuron	0.3 nTPM
Amygdala	0.6 nTPM
Thalamus	0.4 nTPM
Basal ganglia	0.3 nTPM
Cerebral cortex	0.3 nTPM
Hypothalamus	0.2 nTPM
Hippocampus	0.0 nTPM

Endothelial cell	2.3 nTPM
Cerebellum	3.9 nTPM
Medulla oblongata	3.1 nTPM
Basal ganglia	2.8 nTPM
Cerebral cortex	2.6 nTPM
Hypothalamus	2.5 nTPM
Amygdala	2.2 nTPM
Hippocampus	1.9 nTPM
Pons	1.9 nTPM
Spinal cord	1.7 nTPM
Thalamus	1.7 nTPM
Midbrain	0.9 nTPM

Ependymal cell	20.6 nTPM
Basal ganglia	28.3 nTPM
Hypothalamus	26.8 nTPM
Hippocampus	24.1 nTPM
Amygdala	19.9 nTPM
Pons	19.6 nTPM
Midbrain	19.0 nTPM
Medulla oblongata	18.7 nTPM
Thalamus	17.4 nTPM
Spinal cord	11.5 nTPM