Single cell type - XXYLT1 - The Human Protein Atlas

XXYLT1

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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.	XXYLT1
Gene descriptionⁱ Full gene name according to HGNC.	Xyloside xylosyltransferase 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Enzymes
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.	Lymphatic endothelial cells - Lymph vessel development (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 (Inhibitory neurons)
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.	0.46
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 (plasmacytoid DC)
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 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 (Inhibitory neurons)

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 (plasmacytoid DC)
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

XXYLT1 is part of cluster 54 Lymphatic endothelial cells - Lymph vessel development with confidenceⁱ 1
108 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.
PALM	Paralemmin	0.5460	54
POGLUT2	Protein O-glucosyltransferase 2	0.5116	50
KIF3C	Kinesin family member 3C	0.4783	34
ITGA9	Integrin subunit alpha 9	0.4699	54
APP	Amyloid beta precursor protein	0.4693	54
SHC1	SHC adaptor protein 1	0.4666	54
TRIOBP	TRIO and F-actin binding protein	0.4639	54
FGD1	FYVE, RhoGEF and PH domain containing 1	0.4621	9
RNF112	Ring finger protein 112	0.4576	34
PLAGL1	PLAG1 like zinc finger 1	0.4574	50
PPFIBP1	PPFIA binding protein 1	0.4438	54
COL5A2	Collagen type V alpha 2 chain	0.4398	50
DCHS1	Dachsous cadherin-related 1	0.4396	41
SCN3B	Sodium voltage-gated channel beta subunit 3	0.4359	54
DBN1	Drebrin 1	0.4317	45

IMMUNE CELLS

XXYLT1 is part of cluster 29 Non-specific - Unknown function with confidenceⁱ 0.81
401 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.
ZFAT	Zinc finger and AT-hook domain containing	1.0000	29
PLD4	Phospholipase D family member 4	1.0000	29
EGLN3	Egl-9 family hypoxia inducible factor 3	1.0000	29
ITM2C	Integral membrane protein 2C	0.9762	8
PDXP	Pyridoxal phosphatase	0.9762	29
FTCDNL1	Formiminotransferase cyclodeaminase N-terminal like	0.9762	29
HIGD1A	HIG1 hypoxia inducible domain family member 1A	0.9762	29
LMNB2	Lamin B2	0.9762	29
RNASEH2C	Ribonuclease H2 subunit C	0.9762	8
MFSD12	Major facilitator superfamily domain containing 12	0.9762	29
STK11IP	Serine/threonine kinase 11 interacting protein	0.9762	29
TDG	Thymine DNA glycosylase	0.9762	29
TMEM53	Transmembrane protein 53	0.9762	29
ZFYVE26	Zinc finger FYVE-type containing 26	0.9762	8
ERCC1	ERCC excision repair 1, endonuclease non-catalytic subunit	0.9762	29

Adipocytes	11.0 nTPM
Adipose tissue	11.3 nTPM
Breast	10.8 nTPM

Alveolar cells type 1	3.3 nTPM
Lung	3.3 nTPM

Alveolar cells type 2	3.3 nTPM
Lung	3.3 nTPM

Astrocytes	14.2 nTPM
Brain	14.2 nTPM

B-cells	3.2 nTPM
Stomach	6.3 nTPM
Kidney	5.2 nTPM
Thymus	4.6 nTPM
Salivary gland	4.2 nTPM
Bone marrow	4.0 nTPM
Lung	4.0 nTPM
Skin	3.4 nTPM
Lymph node	3.4 nTPM
PBMC	3.1 nTPM
Spleen	2.2 nTPM
Adipose tissue	1.6 nTPM
Liver	0.0 nTPM
Esophagus	0.0 nTPM

Ciliated cells	5.0 nTPM
Lung	6.8 nTPM
Fallopian tube	5.2 nTPM
Endometrium	4.8 nTPM
Bronchus	3.2 nTPM

Club cells	5.3 nTPM
Lung	6.0 nTPM
Bronchus	5.3 nTPM
Prostate	4.5 nTPM

Endothelial cells	10.1 nTPM
Placenta	23.3 nTPM
Lung	16.7 nTPM
Breast	14.9 nTPM
Endometrium	14.0 nTPM
Pancreas	12.9 nTPM
Liver	12.6 nTPM
Esophagus	10.0 nTPM
Thymus	9.3 nTPM
Tongue	9.3 nTPM
Prostate	8.4 nTPM
Salivary gland	8.3 nTPM
Vascular	7.8 nTPM
Skeletal muscle	6.9 nTPM
Fallopian tube	6.9 nTPM
Ovary	6.7 nTPM
Testis	6.4 nTPM
Skin	5.1 nTPM
Heart muscle	1.7 nTPM

Enteroendocrine cells	8.7 nTPM
Small intestine	10.3 nTPM
Colon	9.1 nTPM
Rectum	6.7 nTPM

Fibroblasts	10.9 nTPM
Pancreas	18.9 nTPM
Liver	17.8 nTPM
Esophagus	15.6 nTPM
Adipose tissue	14.9 nTPM
Placenta	13.8 nTPM
Skin	12.7 nTPM
Skeletal muscle	11.4 nTPM
Breast	11.0 nTPM
Thymus	10.5 nTPM
Fallopian tube	10.4 nTPM
Vascular	9.9 nTPM
Salivary gland	9.0 nTPM
Lung	7.0 nTPM
Prostate	5.9 nTPM
Stomach	5.8 nTPM
Heart muscle	0.0 nTPM

Granulocytes	4.2 nTPM
Tongue	4.9 nTPM
Fallopian tube	4.2 nTPM
Lung	3.5 nTPM

Intestinal goblet cells	2.3 nTPM
Colon	3.2 nTPM
Small intestine	2.4 nTPM
Rectum	1.4 nTPM

Lymphatic endothelial cells	15.6 nTPM
Ovary	16.4 nTPM
Fallopian tube	14.8 nTPM

Macrophages	10.1 nTPM
Bone marrow	24.3 nTPM
Endometrium	21.5 nTPM
Spleen	20.1 nTPM
Fallopian tube	14.6 nTPM
Esophagus	14.1 nTPM
Adipose tissue	12.7 nTPM
Skeletal muscle	9.8 nTPM
Prostate	9.1 nTPM
Breast	8.7 nTPM
Salivary gland	8.4 nTPM
Thymus	8.2 nTPM
Tongue	7.2 nTPM
Lung	6.5 nTPM
Vascular	6.2 nTPM
Testis	5.6 nTPM
Skin	5.6 nTPM
Stomach	5.1 nTPM
Pancreas	4.1 nTPM
Kidney	0.9 nTPM

Paneth cells	0.4 nTPM
Rectum	1.2 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Basal keratinocytes	8.9 nTPM
Tongue	13.9 nTPM
Skin	3.9 nTPM

Basal squamous epithelial cells	9.5 nTPM
Esophagus	9.5 nTPM

Bipolar cells	5.4 nTPM
Eye	5.4 nTPM

Cholangiocytes	1.9 nTPM
Liver	1.9 nTPM

Plasma cells	2.5 nTPM
Spleen	5.5 nTPM
Thymus	4.6 nTPM
Liver	3.5 nTPM
Bone marrow	3.0 nTPM
Fallopian tube	1.6 nTPM
Stomach	1.3 nTPM
Salivary gland	0.4 nTPM
Esophagus	0.0 nTPM

Schwann cells	3.7 nTPM
Vascular	5.7 nTPM
Adipose tissue	5.5 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	3.7 nTPM
Tongue	4.4 nTPM
Salivary gland	3.0 nTPM

Smooth muscle cells	7.9 nTPM
Placenta	15.4 nTPM
Lung	14.1 nTPM
Endometrium	11.2 nTPM
Adipose tissue	11.1 nTPM
Thymus	8.8 nTPM
Esophagus	8.4 nTPM
Tongue	8.4 nTPM
Vascular	7.9 nTPM
Liver	7.6 nTPM
Fallopian tube	6.3 nTPM
Breast	6.1 nTPM
Skeletal muscle	4.6 nTPM
Prostate	4.3 nTPM
Skin	4.2 nTPM
Salivary gland	4.0 nTPM
Ovary	3.5 nTPM

Suprabasal keratinocytes	15.2 nTPM
Tongue	22.4 nTPM
Skin	8.0 nTPM

T-cells	5.2 nTPM
Stomach	8.0 nTPM
PBMC	7.4 nTPM
Tongue	6.9 nTPM
Lymph node	6.8 nTPM
Bone marrow	6.8 nTPM
Endometrium	6.5 nTPM
Salivary gland	6.5 nTPM
Skeletal muscle	6.0 nTPM
Vascular	6.0 nTPM
Thymus	5.9 nTPM
Esophagus	4.9 nTPM
Lung	4.7 nTPM
Breast	4.5 nTPM
Spleen	4.3 nTPM
Prostate	4.0 nTPM
Colon	3.9 nTPM
Fallopian tube	3.4 nTPM
Liver	3.3 nTPM
Skin	3.2 nTPM
Adipose tissue	2.9 nTPM
Kidney	2.7 nTPM

Undifferentiated cells	6.3 nTPM
Colon	8.3 nTPM
Small intestine	6.1 nTPM
Rectum	4.4 nTPM

Amygdala excitatory	54.0 nTPM
Hypothalamus	67.2 nTPM
Basal ganglia	58.6 nTPM
Thalamus	56.3 nTPM
Amygdala	54.6 nTPM
Cerebral cortex	43.9 nTPM
Hippocampus	43.3 nTPM

Astrocyte	26.7 nTPM
Amygdala	37.9 nTPM
Hypothalamus	30.7 nTPM
Hippocampus	30.5 nTPM
Cerebral cortex	29.3 nTPM
Thalamus	28.5 nTPM
Basal ganglia	26.1 nTPM
Midbrain	25.9 nTPM
Cerebellum	23.1 nTPM
Pons	22.8 nTPM
Medulla oblongata	22.3 nTPM
Spinal cord	16.8 nTPM

Bergmann glia	70.6 nTPM
Cerebellum	84.6 nTPM
Pons	67.6 nTPM
Medulla oblongata	59.7 nTPM

Central nervous system macrophage	55.1 nTPM
Hypothalamus	70.0 nTPM
Amygdala	69.0 nTPM
Thalamus	58.1 nTPM
Midbrain	55.9 nTPM
Cerebellum	55.4 nTPM
Basal ganglia	52.9 nTPM
Hippocampus	52.2 nTPM
Spinal cord	51.5 nTPM
Pons	50.4 nTPM
Medulla oblongata	46.4 nTPM
Cerebral cortex	44.7 nTPM

Cerebellar inhibitory	39.9 nTPM
Cerebellum	46.2 nTPM
Midbrain	43.5 nTPM
Spinal cord	38.5 nTPM
Medulla oblongata	37.7 nTPM
Pons	33.7 nTPM

Cge interneuron	61.5 nTPM
Hypothalamus	88.8 nTPM
Amygdala	65.2 nTPM
Cerebral cortex	61.4 nTPM
Basal ganglia	59.1 nTPM
Hippocampus	55.8 nTPM
Midbrain	50.9 nTPM
Thalamus	48.9 nTPM

Choroid plexus epithelial cell	61.7 nTPM
Basal ganglia	103.3 nTPM
Medulla oblongata	69.0 nTPM
Thalamus	46.6 nTPM
Hippocampus	27.7 nTPM

Committed oligodendrocyte precursor	31.6 nTPM
Hippocampus	41.1 nTPM
Spinal cord	36.8 nTPM
Medulla oblongata	36.1 nTPM
Cerebral cortex	35.5 nTPM
Basal ganglia	32.3 nTPM
Amygdala	31.6 nTPM
Hypothalamus	29.4 nTPM
Midbrain	29.4 nTPM
Pons	26.6 nTPM
Thalamus	25.2 nTPM
Cerebellum	23.8 nTPM

Deep-layer corticothalamic and 6b	47.7 nTPM
Hypothalamus	62.9 nTPM
Cerebral cortex	46.5 nTPM
Midbrain	45.5 nTPM
Amygdala	45.2 nTPM
Basal ganglia	43.6 nTPM
Hippocampus	42.7 nTPM

Deep-layer intratelencephalic	50.6 nTPM
Hypothalamus	71.8 nTPM
Hippocampus	46.6 nTPM
Amygdala	46.4 nTPM
Basal ganglia	45.5 nTPM
Cerebral cortex	42.5 nTPM

Deep-layer near-projecting	47.6 nTPM
Hypothalamus	62.1 nTPM
Amygdala	47.3 nTPM
Hippocampus	44.9 nTPM
Cerebral cortex	44.3 nTPM
Basal ganglia	39.3 nTPM

Eccentric medium spiny neuron	46.5 nTPM
Hypothalamus	55.1 nTPM
Amygdala	50.3 nTPM
Cerebral cortex	46.8 nTPM
Basal ganglia	46.2 nTPM
Thalamus	45.0 nTPM
Hippocampus	35.6 nTPM

Endothelial cell	73.0 nTPM
Amygdala	96.1 nTPM
Pons	84.3 nTPM
Thalamus	81.3 nTPM
Cerebellum	75.1 nTPM
Hippocampus	74.4 nTPM
Midbrain	70.9 nTPM
Medulla oblongata	68.7 nTPM
Basal ganglia	65.2 nTPM
Cerebral cortex	64.6 nTPM
Hypothalamus	62.0 nTPM
Spinal cord	60.4 nTPM