Single cell type - SYNDIG1 - The Human Protein Atlas

SYNDIG1

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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.	SYNDIG1
Gene descriptionⁱ Full gene name according to HGNC.	Synapse differentiation inducing 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Transporters
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
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.	Oligodendrocytes - Unknown function (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 (Microglial cells, Oligodendrocytes, Excitatory 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.	0.91
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.	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.	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 (Microglial cells, Oligodendrocytes, Excitatory 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: 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: 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

SYNDIG1 is part of cluster 51 Oligodendrocytes - Unknown function with confidenceⁱ 1
302 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.
FMNL2	Formin like 2	0.7167	51
SGMS1	Sphingomyelin synthase 1	0.6959	76
PCDH9	Protocadherin 9	0.6656	51
CACNA2D1	Calcium voltage-gated channel auxiliary subunit alpha2delta 1	0.6548	65
PVALEF	Parvalbumin like EF-hand containing	0.6432	51
JAKMIP3	Janus kinase and microtubule interacting protein 3	0.6385	51
TPTEP2-CSNK1E	TPTEP2-CSNK1E readthrough	0.6341	47
GTDC1	Glycosyltransferase like domain containing 1	0.6301	34
INVS	Inversin	0.6237	8
NKAIN2	Sodium/potassium transporting ATPase interacting 2	0.6232	51
NRG1	Neuregulin 1	0.6214	34
ELMO1	Engulfment and cell motility 1	0.6162	51
LY75-CD302	LY75-CD302 readthrough	0.6149	34
DEFB109B	Defensin beta 109B	0.6148	51
PKP4	Plakophilin 4	0.6131	51

Adipocytes	0.0 nTPM
Adipose tissue	0.0 nTPM
Breast	0.0 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	0.0 nTPM
Lung	0.0 nTPM

Astrocytes	4.3 nTPM
Brain	4.3 nTPM

B-cells	0.0 nTPM
Lymph node	0.1 nTPM
Thymus	0.1 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
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
Fallopian tube	0.9 nTPM
Endometrium	0.2 nTPM
Bronchus	0.0 nTPM
Lung	0.0 nTPM

Club cells	0.0 nTPM
Bronchus	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM

Endothelial cells	0.2 nTPM
Prostate	0.7 nTPM
Vascular	0.6 nTPM
Heart muscle	0.5 nTPM
Esophagus	0.5 nTPM
Fallopian tube	0.3 nTPM
Salivary gland	0.2 nTPM
Thymus	0.2 nTPM
Tongue	0.1 nTPM
Ovary	0.1 nTPM
Testis	0.0 nTPM
Liver	0.0 nTPM
Placenta	0.0 nTPM
Endometrium	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Lung	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	2.2 nTPM
Prostate	7.9 nTPM
Pancreas	7.0 nTPM
Heart muscle	4.8 nTPM
Vascular	4.2 nTPM
Fallopian tube	2.4 nTPM
Thymus	2.2 nTPM
Lung	2.0 nTPM
Skin	1.1 nTPM
Salivary gland	1.0 nTPM
Skeletal muscle	0.8 nTPM
Esophagus	0.5 nTPM
Placenta	0.4 nTPM
Adipose tissue	0.1 nTPM
Breast	0.1 nTPM
Liver	0.0 nTPM
Stomach	0.0 nTPM

Granulocytes	0.1 nTPM
Fallopian tube	0.2 nTPM
Lung	0.0 nTPM
Tongue	0.0 nTPM

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

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

Macrophages	0.4 nTPM
Pancreas	2.1 nTPM
Prostate	1.4 nTPM
Breast	1.3 nTPM
Salivary gland	1.2 nTPM
Fallopian tube	1.1 nTPM
Lung	0.1 nTPM
Vascular	0.1 nTPM
Testis	0.0 nTPM
Kidney	0.0 nTPM
Endometrium	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
Thymus	0.0 nTPM
Tongue	0.0 nTPM

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

Bipolar cells	5.4 nTPM
Eye	5.4 nTPM

Distal tubular cells	9.2 nTPM
Kidney	9.2 nTPM

Plasma cells	0.0 nTPM
Liver	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM
Fallopian tube	0.0 nTPM

Schwann cells	0.5 nTPM
Vascular	1.6 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM

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

Smooth muscle cells	1.0 nTPM
Thymus	6.1 nTPM
Vascular	3.5 nTPM
Fallopian tube	2.0 nTPM
Liver	1.3 nTPM
Placenta	1.0 nTPM
Tongue	0.6 nTPM
Breast	0.6 nTPM
Endometrium	0.5 nTPM
Adipose tissue	0.2 nTPM
Ovary	0.1 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Salivary gland	0.0 nTPM

T-cells	0.1 nTPM
Kidney	0.9 nTPM
Endometrium	0.5 nTPM
Vascular	0.4 nTPM
Prostate	0.2 nTPM
Fallopian tube	0.1 nTPM
Colon	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	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
Thymus	0.0 nTPM
Tongue	0.0 nTPM
Breast	0.0 nTPM

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

Amygdala excitatory	198.9 nTPM
Amygdala	332.8 nTPM
Hypothalamus	231.3 nTPM
Cerebral cortex	216.3 nTPM
Hippocampus	181.1 nTPM
Basal ganglia	135.7 nTPM
Thalamus	96.2 nTPM

Astrocyte	43.9 nTPM
Spinal cord	102.2 nTPM
Hypothalamus	90.0 nTPM
Medulla oblongata	71.8 nTPM
Cerebellum	62.7 nTPM
Pons	39.4 nTPM
Hippocampus	24.6 nTPM
Thalamus	23.2 nTPM
Midbrain	22.5 nTPM
Amygdala	19.4 nTPM
Basal ganglia	16.2 nTPM
Cerebral cortex	10.9 nTPM

Bergmann glia	57.5 nTPM
Medulla oblongata	57.5 nTPM
Pons	57.5 nTPM
Cerebellum	57.3 nTPM

Central nervous system macrophage	2747.7 nTPM
Hypothalamus	3908.9 nTPM
Basal ganglia	3120.7 nTPM
Hippocampus	3080.4 nTPM
Amygdala	3062.4 nTPM
Midbrain	2876.7 nTPM
Pons	2698.5 nTPM
Medulla oblongata	2680.8 nTPM
Thalamus	2655.3 nTPM
Cerebral cortex	2345.0 nTPM
Cerebellum	2287.0 nTPM
Spinal cord	1509.0 nTPM

Cerebellar inhibitory	360.4 nTPM
Cerebellum	481.9 nTPM
Medulla oblongata	368.5 nTPM
Midbrain	353.0 nTPM
Spinal cord	346.5 nTPM
Pons	252.1 nTPM

Cge interneuron	83.8 nTPM
Hypothalamus	100.7 nTPM
Amygdala	93.2 nTPM
Hippocampus	84.6 nTPM
Thalamus	82.3 nTPM
Cerebral cortex	77.4 nTPM
Midbrain	75.2 nTPM
Basal ganglia	73.3 nTPM

Choroid plexus epithelial cell	14.3 nTPM
Thalamus	30.1 nTPM
Basal ganglia	17.2 nTPM
Medulla oblongata	9.8 nTPM
Hippocampus	0.0 nTPM

Committed oligodendrocyte precursor	173.6 nTPM
Hypothalamus	310.7 nTPM
Amygdala	259.4 nTPM
Thalamus	242.9 nTPM
Hippocampus	167.4 nTPM
Cerebral cortex	165.3 nTPM
Basal ganglia	159.9 nTPM
Cerebellum	142.7 nTPM
Spinal cord	139.8 nTPM
Pons	115.1 nTPM
Midbrain	106.7 nTPM
Medulla oblongata	99.4 nTPM

Deep-layer corticothalamic and 6b	134.4 nTPM
Hypothalamus	171.1 nTPM
Hippocampus	162.8 nTPM
Cerebral cortex	157.2 nTPM
Midbrain	124.3 nTPM
Basal ganglia	98.7 nTPM
Amygdala	92.1 nTPM

Deep-layer intratelencephalic	281.4 nTPM
Hypothalamus	430.7 nTPM
Cerebral cortex	270.8 nTPM
Amygdala	242.0 nTPM
Basal ganglia	237.3 nTPM
Hippocampus	226.0 nTPM

Deep-layer near-projecting	196.0 nTPM
Amygdala	248.7 nTPM
Hypothalamus	240.8 nTPM
Cerebral cortex	213.2 nTPM
Hippocampus	154.2 nTPM
Basal ganglia	122.9 nTPM

Eccentric medium spiny neuron	57.7 nTPM
Thalamus	88.0 nTPM
Hippocampus	77.5 nTPM
Basal ganglia	74.1 nTPM
Cerebral cortex	48.0 nTPM
Amygdala	39.3 nTPM
Hypothalamus	19.4 nTPM

Endothelial cell	8.3 nTPM
Pons	13.1 nTPM
Spinal cord	12.1 nTPM
Medulla oblongata	11.3 nTPM
Cerebral cortex	9.6 nTPM
Basal ganglia	9.3 nTPM
Hippocampus	8.7 nTPM
Hypothalamus	8.7 nTPM
Midbrain	5.7 nTPM
Thalamus	5.6 nTPM
Cerebellum	3.9 nTPM
Amygdala	3.4 nTPM

Ependymal cell	50.0 nTPM
Medulla oblongata	88.5 nTPM
Pons	84.9 nTPM
Amygdala	52.3 nTPM
Basal ganglia	52.0 nTPM
Midbrain	51.4 nTPM
Thalamus	41.7 nTPM
Spinal cord	30.7 nTPM
Hippocampus	24.1 nTPM
Hypothalamus	24.1 nTPM