Single cell type - SCN11A - The Human Protein Atlas

SCN11A

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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.	SCN11A
Gene descriptionⁱ Full gene name according to HGNC.	Sodium voltage-gated channel alpha subunit 11
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes FDA approved drug targets Human disease related genes Transporters Voltage-gated ion channels
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.	6

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.	Spermatogonia - Spermatogenesis (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 (Spermatocytes, Spermatogonia, Early spermatids, Astrocytes, Adipocytes, Late spermatids)
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.	0.85
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 (Bergmann glia)
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 (Spermatocytes, Spermatogonia, Early spermatids, Astrocytes, Adipocytes, Late spermatids)

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 (Bergmann glia)

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

SCN11A is part of cluster 67 Spermatogonia - Spermatogenesis with confidenceⁱ 1
123 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.
ZNF722	Zinc finger protein 722	0.6462	67
TSPYL6	TSPY like 6	0.5898	67
DCAF4L1	DDB1 and CUL4 associated factor 4 like 1	0.5796	67
MORC1	MORC family CW-type zinc finger 1	0.5737	31
PAGE2B	PAGE family member 2B	0.5543	67
XAGE1B	X antigen family member 1B	0.5481	67
KRT26	Keratin 26	0.5267	67
PAGE5	PAGE family member 5	0.5239	67
XAGE1A	X antigen family member 1A	0.5124	67
DMRT1	Doublesex and mab-3 related transcription factor 1	0.5093	67
PAGE2	PAGE family member 2	0.5068	67
ZNF729	Zinc finger protein 729	0.5058	79
TRIM43	Tripartite motif containing 43	0.5056	67
CSAG1	Chondrosarcoma associated gene 1	0.5046	67
LUZP4	Leucine zipper protein 4	0.4945	67

Adipocytes	6.0 nTPM
Adipose tissue	10.1 nTPM
Breast	1.9 nTPM

Alveolar cells type 1	0.1 nTPM
Lung	0.1 nTPM

Alveolar cells type 2	0.3 nTPM
Lung	0.3 nTPM

B-cells	0.8 nTPM
Skin	6.8 nTPM
Stomach	1.3 nTPM
Lymph node	0.9 nTPM
Bone marrow	0.7 nTPM
Salivary gland	0.6 nTPM
Thymus	0.5 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Spleen	0.0 nTPM
Lung	0.0 nTPM

Basal keratinocytes	0.4 nTPM
Tongue	0.7 nTPM
Skin	0.2 nTPM

Ciliated cells	1.5 nTPM
Lung	3.5 nTPM
Fallopian tube	1.0 nTPM
Endometrium	0.9 nTPM
Bronchus	0.7 nTPM

Club cells	0.8 nTPM
Prostate	2.2 nTPM
Bronchus	0.2 nTPM
Lung	0.0 nTPM

Endothelial cells	1.5 nTPM
Skin	8.2 nTPM
Breast	4.4 nTPM
Skeletal muscle	2.6 nTPM
Esophagus	2.2 nTPM
Thymus	2.0 nTPM
Liver	1.3 nTPM
Salivary gland	1.2 nTPM
Placenta	1.1 nTPM
Testis	0.9 nTPM
Ovary	0.8 nTPM
Heart muscle	0.7 nTPM
Endometrium	0.7 nTPM
Vascular	0.5 nTPM
Lung	0.2 nTPM
Tongue	0.2 nTPM
Fallopian tube	0.1 nTPM
Pancreas	0.0 nTPM
Prostate	0.0 nTPM

Enteroendocrine cells	0.0 nTPM
Colon	0.1 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Fibroblasts	0.6 nTPM
Liver	3.6 nTPM
Skeletal muscle	1.0 nTPM
Esophagus	1.0 nTPM
Skin	0.6 nTPM
Breast	0.6 nTPM
Placenta	0.4 nTPM
Salivary gland	0.4 nTPM
Thymus	0.4 nTPM
Vascular	0.4 nTPM
Adipose tissue	0.3 nTPM
Fallopian tube	0.2 nTPM
Heart muscle	0.0 nTPM
Pancreas	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM

Granulocytes	0.0 nTPM
Lung	0.0 nTPM
Tongue	0.0 nTPM
Fallopian tube	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	2.8 nTPM
Ovary	5.5 nTPM
Fallopian tube	0.2 nTPM

Macrophages	0.2 nTPM
Tongue	0.9 nTPM
Adipose tissue	0.5 nTPM
Thymus	0.4 nTPM
Breast	0.4 nTPM
Skeletal muscle	0.3 nTPM
Lung	0.3 nTPM
Salivary gland	0.3 nTPM
Vascular	0.1 nTPM
Fallopian tube	0.1 nTPM
Testis	0.0 nTPM
Kidney	0.0 nTPM
Endometrium	0.0 nTPM
Pancreas	0.0 nTPM
Skin	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

Astrocytes	7.4 nTPM
Brain	7.4 nTPM

Excitatory neurons	1.6 nTPM
Brain	1.6 nTPM

Plasma cells	0.5 nTPM
Fallopian tube	1.9 nTPM
Salivary gland	0.9 nTPM
Liver	0.5 nTPM
Thymus	0.5 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	0.0 nTPM
Salivary gland	0.1 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	0.4 nTPM
Endometrium	1.4 nTPM
Placenta	1.3 nTPM
Esophagus	1.2 nTPM
Skeletal muscle	0.8 nTPM
Adipose tissue	0.4 nTPM
Ovary	0.4 nTPM
Tongue	0.3 nTPM
Vascular	0.3 nTPM
Breast	0.2 nTPM
Thymus	0.1 nTPM
Liver	0.0 nTPM
Skin	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Salivary gland	0.0 nTPM
Fallopian tube	0.0 nTPM

T-cells	0.3 nTPM
Kidney	0.9 nTPM
Thymus	0.9 nTPM
Tongue	0.9 nTPM
Vascular	0.8 nTPM
Liver	0.6 nTPM
PBMC	0.6 nTPM
Skeletal muscle	0.4 nTPM
Lymph node	0.4 nTPM
Prostate	0.4 nTPM
Salivary gland	0.4 nTPM
Breast	0.4 nTPM
Adipose tissue	0.3 nTPM
Fallopian tube	0.2 nTPM
Stomach	0.1 nTPM
Colon	0.0 nTPM
Endometrium	0.0 nTPM
Skin	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Lung	0.0 nTPM

Undifferentiated cells	0.1 nTPM
Rectum	0.2 nTPM
Colon	0.1 nTPM
Small intestine	0.1 nTPM

Amygdala excitatory	20.4 nTPM
Amygdala	40.0 nTPM
Hippocampus	22.5 nTPM
Basal ganglia	16.0 nTPM
Thalamus	15.9 nTPM
Cerebral cortex	15.1 nTPM
Hypothalamus	13.2 nTPM

Astrocyte	54.9 nTPM
Amygdala	70.2 nTPM
Hypothalamus	60.9 nTPM
Basal ganglia	60.4 nTPM
Midbrain	58.3 nTPM
Pons	56.0 nTPM
Thalamus	55.1 nTPM
Cerebral cortex	53.7 nTPM
Hippocampus	49.6 nTPM
Medulla oblongata	47.3 nTPM
Cerebellum	46.8 nTPM
Spinal cord	45.5 nTPM

Bergmann glia	60.4 nTPM
Medulla oblongata	70.3 nTPM
Cerebellum	56.2 nTPM
Pons	54.7 nTPM

Central nervous system macrophage	2.1 nTPM
Amygdala	2.6 nTPM
Cerebral cortex	2.5 nTPM
Midbrain	2.5 nTPM
Basal ganglia	2.3 nTPM
Hippocampus	2.1 nTPM
Hypothalamus	2.1 nTPM
Thalamus	2.0 nTPM
Cerebellum	1.8 nTPM
Spinal cord	1.8 nTPM
Pons	1.7 nTPM
Medulla oblongata	1.2 nTPM

Cerebellar inhibitory	5.6 nTPM
Medulla oblongata	8.3 nTPM
Cerebellum	7.2 nTPM
Pons	6.3 nTPM
Midbrain	3.4 nTPM
Spinal cord	2.7 nTPM

Cge interneuron	5.2 nTPM
Hippocampus	6.2 nTPM
Amygdala	6.1 nTPM
Midbrain	6.0 nTPM
Hypothalamus	5.3 nTPM
Basal ganglia	4.9 nTPM
Cerebral cortex	4.3 nTPM
Thalamus	3.4 nTPM

Choroid plexus epithelial cell	10.6 nTPM
Thalamus	19.2 nTPM
Medulla oblongata	10.8 nTPM
Basal ganglia	9.5 nTPM
Hippocampus	2.8 nTPM

Committed oligodendrocyte precursor	10.3 nTPM
Amygdala	14.1 nTPM
Cerebral cortex	12.7 nTPM
Thalamus	11.9 nTPM
Hippocampus	11.6 nTPM
Hypothalamus	11.6 nTPM
Spinal cord	11.0 nTPM
Basal ganglia	10.4 nTPM
Cerebellum	9.5 nTPM
Pons	8.0 nTPM
Midbrain	7.6 nTPM
Medulla oblongata	5.2 nTPM

Deep-layer corticothalamic and 6b	14.1 nTPM
Amygdala	18.2 nTPM
Hippocampus	16.0 nTPM
Hypothalamus	14.6 nTPM
Midbrain	13.3 nTPM
Cerebral cortex	12.0 nTPM
Basal ganglia	10.5 nTPM

Deep-layer intratelencephalic	12.3 nTPM
Hypothalamus	14.8 nTPM
Hippocampus	14.3 nTPM
Amygdala	12.2 nTPM
Basal ganglia	10.1 nTPM
Cerebral cortex	9.9 nTPM

Deep-layer near-projecting	11.0 nTPM
Hypothalamus	13.5 nTPM
Amygdala	12.8 nTPM
Basal ganglia	11.1 nTPM
Cerebral cortex	9.0 nTPM
Hippocampus	8.5 nTPM

Eccentric medium spiny neuron	10.3 nTPM
Thalamus	11.9 nTPM
Cerebral cortex	11.8 nTPM
Amygdala	11.3 nTPM
Basal ganglia	10.1 nTPM
Hypothalamus	9.7 nTPM
Hippocampus	7.0 nTPM

Endothelial cell	7.5 nTPM
Hypothalamus	17.4 nTPM
Amygdala	11.2 nTPM
Basal ganglia	10.3 nTPM
Medulla oblongata	9.2 nTPM
Thalamus	6.8 nTPM
Spinal cord	5.2 nTPM
Cerebral cortex	5.1 nTPM
Hippocampus	4.8 nTPM
Cerebellum	4.6 nTPM
Midbrain	3.8 nTPM
Pons	3.7 nTPM

Ependymal cell	34.6 nTPM
Amygdala	42.1 nTPM
Basal ganglia	41.7 nTPM
Hypothalamus	40.2 nTPM
Thalamus	36.8 nTPM
Hippocampus	35.8 nTPM
Pons	31.0 nTPM
Medulla oblongata	30.3 nTPM
Spinal cord	28.7 nTPM
Midbrain	24.8 nTPM