Single cell type - SOX17 - The Human Protein Atlas

SOX17

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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.	SOX17
Gene descriptionⁱ Full gene name according to HGNC.	SRY-box transcription factor 17
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Cancer-related genes Disease related genes Human disease related genes Transcription factors
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.	Glandular & Luminal cells - 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.	Cell type enhanced (Glandular and luminal cells, Adipocytes, Endothelial cells, Ciliated cells, Secretory cells)
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.	0.86
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 (Endothelial cell)
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: Cell type enhanced (Glandular and luminal cells, Adipocytes, Endothelial cells, Ciliated cells, Secretory cells)

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 (Endothelial cell)

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

SOX17 is part of cluster 37 Glandular & Luminal cells - Unknown function with confidenceⁱ 1
334 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.
MSX1	Msh homeobox 1	0.8678	37
NEDD9	Neural precursor cell expressed, developmentally down-regulated 9	0.7977	37
CLDN22	Claudin 22	0.7561	37
POU5F1B	POU class 5 homeobox 1B	0.7512	37
RCAN1	Regulator of calcineurin 1	0.7453	37
PAX2	Paired box 2	0.7352	37
C2CD4B	C2 calcium dependent domain containing 4B	0.7204	41
TMEM101	Transmembrane protein 101	0.7004	37
MMP26	Matrix metallopeptidase 26	0.6971	37
SCGB2A1	Secretoglobin family 2A member 1	0.6943	37
STC1	Stanniocalcin 1	0.6899	37
UGCG	UDP-glucose ceramide glucosyltransferase	0.6893	37
SCGB1D2	Secretoglobin family 1D member 2	0.6786	37
DIPK1B	Divergent protein kinase domain 1B	0.6775	41
LRATD2	LRAT domain containing 2	0.6733	37

Adipocytes	466.9 nTPM
Adipose tissue	828.0 nTPM
Breast	105.7 nTPM

Alveolar cells type 1	0.1 nTPM
Lung	0.1 nTPM

Alveolar cells type 2	0.3 nTPM
Lung	0.3 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	1.5 nTPM
Skin	11.9 nTPM
Kidney	5.2 nTPM
Thymus	2.2 nTPM
Lymph node	0.2 nTPM
Salivary gland	0.1 nTPM
Liver	0.0 nTPM
PBMC	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

Ciliated cells	118.3 nTPM
Endometrium	365.0 nTPM
Fallopian tube	107.6 nTPM
Lung	0.5 nTPM
Bronchus	0.0 nTPM

Club cells	0.4 nTPM
Prostate	1.3 nTPM
Bronchus	0.0 nTPM
Lung	0.0 nTPM

Endothelial cells	214.9 nTPM
Skeletal muscle	772.4 nTPM
Fallopian tube	759.0 nTPM
Skin	636.9 nTPM
Thymus	394.6 nTPM
Testis	216.4 nTPM
Esophagus	148.8 nTPM
Ovary	141.9 nTPM
Vascular	117.0 nTPM
Placenta	112.4 nTPM
Salivary gland	105.0 nTPM
Tongue	92.3 nTPM
Prostate	85.1 nTPM
Endometrium	79.6 nTPM
Lung	71.9 nTPM
Pancreas	64.6 nTPM
Heart muscle	36.8 nTPM
Liver	32.8 nTPM
Breast	0.0 nTPM

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

Fibroblasts	8.7 nTPM
Stomach	63.4 nTPM
Liver	51.0 nTPM
Thymus	12.0 nTPM
Skin	3.6 nTPM
Skeletal muscle	2.6 nTPM
Fallopian tube	2.5 nTPM
Vascular	1.0 nTPM
Heart muscle	0.8 nTPM
Esophagus	0.8 nTPM
Breast	0.8 nTPM
Adipose tissue	0.6 nTPM
Lung	0.3 nTPM
Salivary gland	0.2 nTPM
Placenta	0.0 nTPM
Pancreas	0.0 nTPM
Prostate	0.0 nTPM

Granulocytes	2.5 nTPM
Tongue	4.9 nTPM
Fallopian tube	2.7 nTPM
Lung	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	0.9 nTPM
Fallopian tube	1.7 nTPM
Ovary	0.0 nTPM

Macrophages	4.7 nTPM
Endometrium	52.3 nTPM
Thymus	13.0 nTPM
Skeletal muscle	9.1 nTPM
Esophagus	3.9 nTPM
Skin	3.3 nTPM
Fallopian tube	3.3 nTPM
Breast	1.5 nTPM
Vascular	1.1 nTPM
Adipose tissue	0.9 nTPM
Testis	0.6 nTPM
Tongue	0.5 nTPM
Lung	0.3 nTPM
Prostate	0.3 nTPM
Salivary gland	0.1 nTPM
Kidney	0.0 nTPM
Pancreas	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

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

Collecting duct cells	1.9 nTPM
Kidney	1.9 nTPM

Early spermatids	1.9 nTPM
Testis	1.9 nTPM

Endometrial stromal cells	43.6 nTPM
Endometrium	43.6 nTPM

Plasma cells	0.5 nTPM
Thymus	1.6 nTPM
Fallopian tube	1.3 nTPM
Liver	1.0 nTPM
Salivary gland	0.4 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	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	0.1 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	18.2 nTPM
Skeletal muscle	222.4 nTPM
Liver	27.6 nTPM
Endometrium	12.8 nTPM
Fallopian tube	11.6 nTPM
Breast	3.7 nTPM
Thymus	3.3 nTPM
Skin	2.6 nTPM
Prostate	2.4 nTPM
Adipose tissue	1.8 nTPM
Lung	1.2 nTPM
Salivary gland	0.9 nTPM
Vascular	0.8 nTPM
Ovary	0.5 nTPM
Tongue	0.3 nTPM
Placenta	0.1 nTPM
Esophagus	0.0 nTPM

T-cells	3.1 nTPM
Endometrium	50.7 nTPM
Skin	6.3 nTPM
Fallopian tube	3.3 nTPM
Skeletal muscle	2.6 nTPM
Breast	1.1 nTPM
Liver	0.4 nTPM
Prostate	0.4 nTPM
Lung	0.3 nTPM
Adipose tissue	0.1 nTPM
Thymus	0.1 nTPM
Tongue	0.1 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
PBMC	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
Salivary gland	0.0 nTPM
Vascular	0.0 nTPM

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

Amygdala excitatory	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Thalamus	0.0 nTPM

Astrocyte	0.0 nTPM
Medulla oblongata	0.1 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebellum	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM
Thalamus	0.0 nTPM

Bergmann glia	0.0 nTPM
Cerebellum	0.1 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	0.0 nTPM
Cerebral cortex	0.1 nTPM
Medulla oblongata	0.1 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebellum	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM
Thalamus	0.0 nTPM

Cerebellar inhibitory	0.0 nTPM
Cerebellum	0.0 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM
Thalamus	0.0 nTPM

Choroid plexus epithelial cell	0.0 nTPM
Thalamus	0.0 nTPM
Basal ganglia	0.0 nTPM
Hippocampus	0.0 nTPM
Medulla oblongata	0.0 nTPM

Committed oligodendrocyte precursor	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebellum	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM
Thalamus	0.0 nTPM

Deep-layer corticothalamic and 6b	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM

Deep-layer near-projecting	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM

Eccentric medium spiny neuron	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Thalamus	0.0 nTPM

Endothelial cell	52.6 nTPM
Medulla oblongata	81.0 nTPM
Cerebellum	79.8 nTPM
Pons	64.3 nTPM
Cerebral cortex	56.9 nTPM
Hypothalamus	48.4 nTPM
Spinal cord	46.6 nTPM
Hippocampus	44.9 nTPM
Basal ganglia	44.7 nTPM
Midbrain	39.7 nTPM
Amygdala	36.9 nTPM
Thalamus	35.0 nTPM

Ependymal cell	0.0 nTPM
Thalamus	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM