Single cell type - CHSY3 - The Human Protein Atlas

CHSY3

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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.	CHSY3
Gene descriptionⁱ Full gene name according to HGNC.	Chondroitin sulfate synthase 3
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.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	1

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 (Excitatory neurons, 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.	0.90
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.	Not detected in immune cells
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: Group enriched (Excitatory neurons, 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: Not detected in immune cells
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

CHSY3 is part of cluster 34 Neurons - Neuronal signaling with confidenceⁱ 1
518 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.
ADAMTS19	ADAM metallopeptidase with thrombospondin type 1 motif 19	0.8912	34
OR2AG2	Olfactory receptor family 2 subfamily AG member 2	0.8433	34
KCNB2	Potassium voltage-gated channel subfamily B member 2	0.8159	69
DYNC1I1	Dynein cytoplasmic 1 intermediate chain 1	0.8144	34
EPHA5	EPH receptor A5	0.8107	69
CACNA1B	Calcium voltage-gated channel subunit alpha1 B	0.8098	34
PTPRR	Protein tyrosine phosphatase receptor type R	0.8057	34
RGPD6	RANBP2 like and GRIP domain containing 6	0.7893	65
GABRA5	Gamma-aminobutyric acid type A receptor subunit alpha5	0.7726	34
LINC02210-CRHR1	LINC02210-CRHR1 readthrough	0.7673	34
HTR1F	5-hydroxytryptamine receptor 1F	0.7621	34
GLIS1	GLIS family zinc finger 1	0.7609	34
PRR16	Proline rich 16	0.7591	69
CLSTN2	Calsyntenin 2	0.7527	34
LINGO2	Leucine rich repeat and Ig domain containing 2	0.7488	34

Adipocytes	1.8 nTPM
Breast	2.1 nTPM
Adipose tissue	1.6 nTPM

Alveolar cells type 1	1.6 nTPM
Lung	1.6 nTPM

Alveolar cells type 2	1.2 nTPM
Lung	1.2 nTPM

Astrocytes	19.2 nTPM
Brain	19.2 nTPM

B-cells	0.0 nTPM
Thymus	0.2 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Salivary gland	0.0 nTPM

Ciliated cells	0.3 nTPM
Endometrium	0.6 nTPM
Lung	0.4 nTPM
Fallopian tube	0.1 nTPM
Bronchus	0.0 nTPM

Club cells	0.3 nTPM
Lung	0.7 nTPM
Bronchus	0.1 nTPM
Prostate	0.0 nTPM

Endothelial cells	1.6 nTPM
Liver	6.3 nTPM
Placenta	4.5 nTPM
Skeletal muscle	3.8 nTPM
Endometrium	2.5 nTPM
Skin	2.0 nTPM
Esophagus	1.8 nTPM
Thymus	1.7 nTPM
Vascular	1.3 nTPM
Ovary	1.2 nTPM
Salivary gland	1.0 nTPM
Testis	0.9 nTPM
Lung	0.9 nTPM
Tongue	0.4 nTPM
Prostate	0.3 nTPM
Fallopian tube	0.3 nTPM
Heart muscle	0.0 nTPM
Pancreas	0.0 nTPM
Breast	0.0 nTPM

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

Fibroblasts	4.2 nTPM
Placenta	22.8 nTPM
Fallopian tube	7.3 nTPM
Pancreas	5.8 nTPM
Esophagus	4.8 nTPM
Liver	4.7 nTPM
Lung	4.4 nTPM
Thymus	2.6 nTPM
Vascular	2.6 nTPM
Adipose tissue	2.4 nTPM
Skin	2.3 nTPM
Skeletal muscle	2.3 nTPM
Stomach	1.4 nTPM
Salivary gland	1.4 nTPM
Breast	0.9 nTPM
Prostate	0.7 nTPM
Heart muscle	0.0 nTPM

Granulocytes	0.3 nTPM
Fallopian tube	1.0 nTPM
Lung	0.0 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	0.1 nTPM
Rectum	0.2 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Lymphatic endothelial cells	9.7 nTPM
Ovary	10.9 nTPM
Fallopian tube	8.5 nTPM

Macrophages	0.2 nTPM
Vascular	1.4 nTPM
Salivary gland	0.7 nTPM
Thymus	0.6 nTPM
Breast	0.6 nTPM
Tongue	0.2 nTPM
Fallopian tube	0.2 nTPM
Lung	0.1 nTPM
Testis	0.0 nTPM
Kidney	0.0 nTPM
Endometrium	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Prostate	0.0 nTPM

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

Endometrial stromal cells	14.2 nTPM
Endometrium	14.2 nTPM

Excitatory neurons	491.2 nTPM
Brain	491.2 nTPM

Plasma cells	0.8 nTPM
Esophagus	5.2 nTPM
Salivary gland	0.4 nTPM
Fallopian tube	0.3 nTPM
Spleen	0.2 nTPM
Thymus	0.1 nTPM
Liver	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM

Schwann cells	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Vascular	0.0 nTPM

Serous glandular cells	0.1 nTPM
Salivary gland	0.2 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	7.5 nTPM
Tongue	21.3 nTPM
Esophagus	19.2 nTPM
Adipose tissue	12.7 nTPM
Placenta	11.4 nTPM
Thymus	10.8 nTPM
Vascular	8.8 nTPM
Prostate	7.3 nTPM
Skeletal muscle	7.0 nTPM
Endometrium	6.4 nTPM
Skin	5.7 nTPM
Breast	4.1 nTPM
Salivary gland	2.8 nTPM
Lung	1.2 nTPM
Liver	0.8 nTPM
Ovary	0.6 nTPM
Fallopian tube	0.3 nTPM

T-cells	0.4 nTPM
Colon	1.9 nTPM
Stomach	1.2 nTPM
Kidney	0.9 nTPM
Lung	0.7 nTPM
Lymph node	0.6 nTPM
Endometrium	0.4 nTPM
Skin	0.4 nTPM
Vascular	0.4 nTPM
Bone marrow	0.3 nTPM
Spleen	0.3 nTPM
Tongue	0.2 nTPM
Thymus	0.1 nTPM
Breast	0.1 nTPM
Fallopian tube	0.1 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skeletal muscle	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Prostate	0.0 nTPM
Salivary gland	0.0 nTPM

Undifferentiated cells	0.1 nTPM
Colon	0.3 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Amygdala excitatory	778.9 nTPM
Amygdala	1008.4 nTPM
Hypothalamus	935.5 nTPM
Basal ganglia	811.4 nTPM
Cerebral cortex	714.4 nTPM
Hippocampus	671.3 nTPM
Thalamus	532.7 nTPM

Astrocyte	18.6 nTPM
Hypothalamus	43.9 nTPM
Medulla oblongata	23.3 nTPM
Amygdala	23.2 nTPM
Pons	19.7 nTPM
Basal ganglia	18.5 nTPM
Cerebral cortex	17.2 nTPM
Hippocampus	15.9 nTPM
Thalamus	15.4 nTPM
Midbrain	11.9 nTPM
Spinal cord	9.0 nTPM
Cerebellum	6.4 nTPM

Bergmann glia	4.1 nTPM
Cerebellum	5.7 nTPM
Pons	4.3 nTPM
Medulla oblongata	2.1 nTPM

Central nervous system macrophage	362.2 nTPM
Hypothalamus	671.8 nTPM
Thalamus	400.3 nTPM
Pons	389.3 nTPM
Medulla oblongata	375.4 nTPM
Basal ganglia	372.6 nTPM
Amygdala	356.6 nTPM
Midbrain	310.9 nTPM
Hippocampus	299.5 nTPM
Spinal cord	292.9 nTPM
Cerebellum	267.5 nTPM
Cerebral cortex	247.5 nTPM

Cerebellar inhibitory	18.9 nTPM
Pons	48.5 nTPM
Medulla oblongata	21.4 nTPM
Midbrain	16.2 nTPM
Cerebellum	8.6 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	704.3 nTPM
Hypothalamus	830.7 nTPM
Thalamus	785.4 nTPM
Amygdala	745.4 nTPM
Basal ganglia	707.0 nTPM
Midbrain	661.2 nTPM
Cerebral cortex	606.2 nTPM
Hippocampus	594.1 nTPM

Choroid plexus epithelial cell	131.6 nTPM
Medulla oblongata	355.4 nTPM
Thalamus	87.7 nTPM
Basal ganglia	58.3 nTPM
Hippocampus	25.0 nTPM

Committed oligodendrocyte precursor	78.6 nTPM
Thalamus	125.8 nTPM
Amygdala	123.5 nTPM
Hypothalamus	116.1 nTPM
Basal ganglia	104.6 nTPM
Medulla oblongata	91.7 nTPM
Hippocampus	69.3 nTPM
Midbrain	63.0 nTPM
Cerebral cortex	58.9 nTPM
Spinal cord	58.9 nTPM
Pons	31.9 nTPM
Cerebellum	20.6 nTPM

Deep-layer corticothalamic and 6b	918.3 nTPM
Hypothalamus	1103.4 nTPM
Hippocampus	1090.7 nTPM
Amygdala	926.9 nTPM
Midbrain	830.9 nTPM
Basal ganglia	784.7 nTPM
Cerebral cortex	773.1 nTPM

Deep-layer intratelencephalic	1054.9 nTPM
Hypothalamus	1244.2 nTPM
Hippocampus	1090.3 nTPM
Amygdala	1076.2 nTPM
Basal ganglia	955.5 nTPM
Cerebral cortex	908.2 nTPM

Deep-layer near-projecting	1206.2 nTPM
Hypothalamus	1602.3 nTPM
Amygdala	1392.6 nTPM
Cerebral cortex	1150.3 nTPM
Hippocampus	950.0 nTPM
Basal ganglia	935.7 nTPM

Eccentric medium spiny neuron	266.5 nTPM
Basal ganglia	325.8 nTPM
Thalamus	323.4 nTPM
Amygdala	304.6 nTPM
Cerebral cortex	259.2 nTPM
Hypothalamus	237.1 nTPM
Hippocampus	149.2 nTPM

Endothelial cell	22.7 nTPM
Basal ganglia	80.2 nTPM
Hypothalamus	50.9 nTPM
Amygdala	23.5 nTPM
Hippocampus	19.9 nTPM
Cerebral cortex	17.9 nTPM
Medulla oblongata	15.4 nTPM
Thalamus	15.2 nTPM
Pons	10.0 nTPM
Midbrain	8.5 nTPM
Cerebellum	4.6 nTPM
Spinal cord	3.5 nTPM

Ependymal cell	18.8 nTPM
Thalamus	25.9 nTPM
Basal ganglia	24.0 nTPM
Amygdala	23.9 nTPM
Midbrain	21.0 nTPM
Hypothalamus	19.6 nTPM
Pons	16.9 nTPM
Hippocampus	13.9 nTPM
Medulla oblongata	12.5 nTPM
Spinal cord	11.5 nTPM