Single cell type - ST3GAL4 - The Human Protein Atlas

ST3GAL4

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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.	ST3GAL4
Gene descriptionⁱ Full gene name according to HGNC.	ST3 beta-galactoside alpha-2,3-sialyltransferase 4
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Enzymes Metabolic proteins
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, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	17

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.	Syncytiotrophoblasts - Pregnancy (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 (Syncytiotrophoblasts)
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.	0.62
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 (Oligodendrocyte)
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.	Group enriched (basophil, plasmacytoid DC, neutrophil)
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 enriched (Syncytiotrophoblasts)

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 (Oligodendrocyte)

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: Group enriched (basophil, plasmacytoid DC, neutrophil)
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

ST3GAL4 is part of cluster 27 Syncytiotrophoblasts - Pregnancy with confidenceⁱ 1
142 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.
INHA	Inhibin subunit alpha	0.8160	27
LGALS14	Galectin 14	0.8128	27
PSG7	Pregnancy specific beta-1-glycoprotein 7	0.8126	27
ERVFRD-1	Endogenous retrovirus group FRD member 1, envelope	0.8124	27
CYP19A1	Cytochrome P450 family 19 subfamily A member 1	0.8119	27
PSG6	Pregnancy specific beta-1-glycoprotein 6	0.8112	27
PSG9	Pregnancy specific beta-1-glycoprotein 9	0.8111	27
INSL4	Insulin like 4	0.8109	27
ERVV-2	Endogenous retrovirus group V member 2, envelope	0.8109	27
LGALS16	Galectin 16	0.8108	27
CGB1	Chorionic gonadotropin subunit beta 1	0.8106	27
ERVV-1	Endogenous retrovirus group V member 1, envelope	0.8100	27
LGALS13	Galectin 13	0.8100	27
PSG11	Pregnancy specific beta-1-glycoprotein 11	0.8096	27
PSG1	Pregnancy specific beta-1-glycoprotein 1	0.8084	27

IMMUNE CELLS

ST3GAL4 is part of cluster 41 Basophils - Unknown function with confidenceⁱ 0.65
293 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.
PRR14L	Proline rich 14 like	0.9762	41
PPP1R15A	Protein phosphatase 1 regulatory subunit 15A	0.9762	41
ITPRID2	ITPR interacting domain containing 2	0.9762	10
NEK4	NIMA related kinase 4	0.9524	41
DDX17	DEAD-box helicase 17	0.9286	35
CSF2RB	Colony stimulating factor 2 receptor subunit beta	0.9286	41
BLTP3B	Bridge-like lipid transfer protein family member 3B	0.9286	41
ARF4	ADP ribosylation factor 4	0.9286	10
GAS8	Growth arrest specific 8	0.9048	10
TNRC18	Trinucleotide repeat containing 18	0.9048	41
GET1	Guided entry of tail-anchored proteins factor 1	0.9048	35
TRIM8	Tripartite motif containing 8	0.9048	35
TMUB2	Transmembrane and ubiquitin like domain containing 2	0.9048	41
NFIL3	Nuclear factor, interleukin 3 regulated	0.9048	41
DYNC1I1	Dynein cytoplasmic 1 intermediate chain 1	0.9048	35

Adipocytes	9.6 nTPM
Breast	10.5 nTPM
Adipose tissue	8.7 nTPM

Alveolar cells type 1	24.2 nTPM
Lung	24.2 nTPM

Alveolar cells type 2	1.7 nTPM
Lung	1.7 nTPM

Astrocytes	16.1 nTPM
Brain	16.1 nTPM

B-cells	3.5 nTPM
Lung	14.8 nTPM
Skin	13.6 nTPM
Kidney	5.2 nTPM
Liver	4.8 nTPM
Adipose tissue	2.9 nTPM
Thymus	1.5 nTPM
Stomach	0.8 nTPM
Lymph node	0.5 nTPM
Salivary gland	0.4 nTPM
Spleen	0.3 nTPM
Bone marrow	0.2 nTPM
PBMC	0.0 nTPM
Esophagus	0.0 nTPM

Ciliated cells	5.8 nTPM
Bronchus	11.2 nTPM
Lung	5.5 nTPM
Endometrium	3.5 nTPM
Fallopian tube	3.1 nTPM

Club cells	39.8 nTPM
Prostate	73.7 nTPM
Bronchus	35.1 nTPM
Lung	10.6 nTPM

Dendritic cells	41.1 nTPM
PBMC	43.2 nTPM
Adipose tissue	38.9 nTPM

Endothelial cells	8.7 nTPM
Liver	34.0 nTPM
Pancreas	15.5 nTPM
Ovary	14.7 nTPM
Skeletal muscle	10.4 nTPM
Placenta	10.2 nTPM
Skin	8.7 nTPM
Lung	8.2 nTPM
Testis	7.9 nTPM
Salivary gland	6.7 nTPM
Endometrium	6.2 nTPM
Thymus	5.7 nTPM
Tongue	5.6 nTPM
Vascular	5.4 nTPM
Esophagus	4.3 nTPM
Prostate	3.9 nTPM
Breast	3.5 nTPM
Heart muscle	3.0 nTPM
Fallopian tube	2.8 nTPM

Enteroendocrine cells	6.8 nTPM
Colon	13.6 nTPM
Rectum	6.7 nTPM
Small intestine	0.0 nTPM

Fibroblasts	37.7 nTPM
Lung	68.9 nTPM
Skin	57.5 nTPM
Esophagus	55.4 nTPM
Breast	47.8 nTPM
Liver	43.9 nTPM
Thymus	43.1 nTPM
Pancreas	36.2 nTPM
Vascular	34.2 nTPM
Adipose tissue	33.8 nTPM
Stomach	31.7 nTPM
Skeletal muscle	30.9 nTPM
Heart muscle	28.8 nTPM
Fallopian tube	28.2 nTPM
Prostate	25.1 nTPM
Salivary gland	21.4 nTPM
Placenta	16.5 nTPM

Granulocytes	66.1 nTPM
Lung	88.7 nTPM
Tongue	82.5 nTPM
Fallopian tube	27.1 nTPM

Intestinal goblet cells	68.5 nTPM
Colon	108.8 nTPM
Rectum	94.8 nTPM
Small intestine	1.9 nTPM

Lymphatic endothelial cells	5.3 nTPM
Ovary	5.5 nTPM
Fallopian tube	5.1 nTPM

Macrophages	6.7 nTPM
Bone marrow	13.2 nTPM
Endometrium	11.7 nTPM
Adipose tissue	10.0 nTPM
Breast	8.6 nTPM
Testis	8.1 nTPM
Kidney	8.0 nTPM
Skin	7.8 nTPM
Stomach	7.7 nTPM
Skeletal muscle	6.3 nTPM
Pancreas	6.2 nTPM
Spleen	6.0 nTPM
Fallopian tube	5.4 nTPM
Salivary gland	5.0 nTPM
Tongue	4.9 nTPM
Thymus	4.5 nTPM
Vascular	4.3 nTPM
Esophagus	3.9 nTPM
Prostate	3.4 nTPM
Lung	2.6 nTPM

Basal prostatic cells	2.4 nTPM
Prostate	2.4 nTPM

Basal respiratory cells	23.0 nTPM
Bronchus	23.0 nTPM

Basal squamous epithelial cells	1.3 nTPM
Esophagus	1.3 nTPM

Cholangiocytes	7.6 nTPM
Liver	7.6 nTPM

Paneth cells	153.7 nTPM
Colon	358.2 nTPM
Rectum	102.7 nTPM
Small intestine	0.0 nTPM

Plasma cells	4.8 nTPM
Esophagus	10.4 nTPM
Bone marrow	7.6 nTPM
Liver	6.0 nTPM
Salivary gland	4.5 nTPM
Fallopian tube	3.9 nTPM
Thymus	3.1 nTPM
Spleen	2.9 nTPM
Stomach	0.4 nTPM

Schwann cells	16.6 nTPM
Vascular	39.2 nTPM
Adipose tissue	10.5 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	12.8 nTPM
Tongue	22.1 nTPM
Salivary gland	3.6 nTPM

Smooth muscle cells	21.3 nTPM
Liver	50.1 nTPM
Ovary	34.7 nTPM
Vascular	27.8 nTPM
Thymus	27.7 nTPM
Placenta	25.4 nTPM
Lung	23.5 nTPM
Breast	23.5 nTPM
Skin	20.8 nTPM
Tongue	19.2 nTPM
Adipose tissue	17.8 nTPM
Fallopian tube	16.9 nTPM
Esophagus	14.4 nTPM
Skeletal muscle	12.9 nTPM
Prostate	9.7 nTPM
Endometrium	9.2 nTPM
Salivary gland	6.9 nTPM

Suprabasal keratinocytes	10.5 nTPM
Tongue	18.2 nTPM
Skin	2.8 nTPM

T-cells	6.7 nTPM
Liver	13.9 nTPM
Vascular	12.1 nTPM
Colon	11.7 nTPM
Bone marrow	10.6 nTPM
Spleen	9.2 nTPM
Skeletal muscle	9.1 nTPM
Lung	8.3 nTPM
Breast	8.3 nTPM
Adipose tissue	8.0 nTPM
Endometrium	7.6 nTPM
Esophagus	7.3 nTPM
Skin	6.0 nTPM
Stomach	4.6 nTPM
Kidney	4.4 nTPM
PBMC	4.2 nTPM
Fallopian tube	4.1 nTPM
Tongue	3.0 nTPM
Prostate	2.7 nTPM
Thymus	2.5 nTPM
Salivary gland	1.7 nTPM
Lymph node	1.1 nTPM

Undifferentiated cells	4.4 nTPM
Rectum	7.3 nTPM
Colon	6.1 nTPM
Small intestine	0.0 nTPM

Amygdala excitatory	13.3 nTPM
Amygdala	17.0 nTPM
Cerebral cortex	16.5 nTPM
Hippocampus	15.3 nTPM
Hypothalamus	11.6 nTPM
Basal ganglia	10.9 nTPM
Thalamus	8.6 nTPM

Astrocyte	24.5 nTPM
Cerebellum	35.9 nTPM
Thalamus	30.8 nTPM
Cerebral cortex	27.6 nTPM
Hippocampus	27.6 nTPM
Medulla oblongata	23.1 nTPM
Midbrain	22.6 nTPM
Amygdala	22.1 nTPM
Basal ganglia	21.9 nTPM
Pons	19.9 nTPM
Hypothalamus	19.8 nTPM
Spinal cord	18.2 nTPM

Bergmann glia	55.3 nTPM
Cerebellum	64.6 nTPM
Medulla oblongata	55.4 nTPM
Pons	46.0 nTPM

Central nervous system macrophage	3.1 nTPM
Medulla oblongata	4.8 nTPM
Hypothalamus	4.2 nTPM
Spinal cord	4.1 nTPM
Cerebellum	3.6 nTPM
Midbrain	3.5 nTPM
Pons	2.9 nTPM
Hippocampus	2.8 nTPM
Cerebral cortex	2.4 nTPM
Basal ganglia	2.2 nTPM
Thalamus	2.2 nTPM
Amygdala	1.7 nTPM

Cerebellar inhibitory	7.5 nTPM
Midbrain	8.7 nTPM
Cerebellum	8.6 nTPM
Medulla oblongata	7.7 nTPM
Pons	7.1 nTPM
Spinal cord	5.5 nTPM

Cge interneuron	15.1 nTPM
Hypothalamus	18.9 nTPM
Amygdala	17.5 nTPM
Thalamus	15.6 nTPM
Basal ganglia	15.2 nTPM
Cerebral cortex	14.2 nTPM
Hippocampus	12.3 nTPM
Midbrain	11.7 nTPM

Choroid plexus epithelial cell	61.0 nTPM
Basal ganglia	71.8 nTPM
Hippocampus	66.6 nTPM
Medulla oblongata	59.3 nTPM
Thalamus	46.6 nTPM

Committed oligodendrocyte precursor	36.4 nTPM
Thalamus	95.9 nTPM
Hypothalamus	62.8 nTPM
Amygdala	50.7 nTPM
Hippocampus	34.9 nTPM
Basal ganglia	32.9 nTPM
Medulla oblongata	27.1 nTPM
Cerebellum	27.0 nTPM
Cerebral cortex	22.8 nTPM
Pons	19.5 nTPM
Midbrain	16.0 nTPM
Spinal cord	11.0 nTPM

Deep-layer corticothalamic and 6b	9.8 nTPM
Hypothalamus	11.8 nTPM
Basal ganglia	10.0 nTPM
Midbrain	10.0 nTPM
Amygdala	9.9 nTPM
Cerebral cortex	9.7 nTPM
Hippocampus	7.6 nTPM

Deep-layer intratelencephalic	17.4 nTPM
Hypothalamus	21.3 nTPM
Cerebral cortex	17.7 nTPM
Hippocampus	17.3 nTPM
Basal ganglia	15.9 nTPM
Amygdala	14.9 nTPM

Deep-layer near-projecting	6.5 nTPM
Hippocampus	8.1 nTPM
Amygdala	6.4 nTPM
Hypothalamus	6.4 nTPM
Basal ganglia	6.1 nTPM
Cerebral cortex	5.2 nTPM

Eccentric medium spiny neuron	6.8 nTPM
Hippocampus	8.7 nTPM
Cerebral cortex	8.4 nTPM
Amygdala	8.0 nTPM
Thalamus	5.9 nTPM
Hypothalamus	5.3 nTPM
Basal ganglia	4.3 nTPM