Single cell type - SCN5A - The Human Protein Atlas

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.	SCN5A
Gene descriptionⁱ Full gene name according to HGNC.	Sodium voltage-gated channel alpha subunit 5
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes FDA approved drug targets Human disease related genes Metabolic proteins Plasma proteins 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, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	8

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.	Cardiomyocytes - Cardiac muscle contraction & structure (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 (Cardiomyocytes)
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.	0.87
Brain cell type 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 type

Cell type summary (DVP)

Cell type enrichment

Expression clustering

SINGLE CELL TYPESⁱ A summary of normalized single cell RNA (nCPM) from all single cell types. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. * Single nuclei
Single cell type groups RNA single cell type group specificity: Cell type enriched (Myocytes)

DVP - RNA AND PROTEIN ABUNDANCE COMPARISON

RNA cell type specificity:	Group enriched (Cardiomyocytes, Neutrophils)	Agreement detection:	Yes (0.70)
Protein cell type specificity:	Group enriched (Capillaries, Cardiomyocytes)	Agreement expression:	Yes (0.87)
RNA tau score:	0.84	Overlap:	Elevated - Partial overlap
Protein tau score:	0.96

BULK RNA DECONVOLUTIONⁱ 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.

EXPRESSION CLUSTERING & CORRELATIONⁱ

SCN5A is part of cluster 55 Cardiomyocytes - Cardiac muscle contraction & structure with confidenceⁱ 1
227 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.
RBM20	RNA binding motif protein 20	0.8393	55
TMEM182	Transmembrane protein 182	0.8161	55
MYH6	Myosin heavy chain 6	0.7721	55
MYBPC3	Myosin binding protein C3	0.7655	55
TNNT2	Troponin T2, cardiac type	0.7562	55
RYR2	Ryanodine receptor 2	0.7468	55
FPGT-TNNI3K	FPGT-TNNI3K readthrough	0.7462	55
LRRC10	Leucine rich repeat containing 10	0.7448	55
NKX2-5	NK2 homeobox 5	0.7427	55
LMAN1L	Lectin, mannose binding 1 like	0.7415	55
PXDNL	Peroxidasin like	0.7345	55
GRXCR2	Glutaredoxin and cysteine rich domain containing 2	0.7331	55
PCDHGC5	Protocadherin gamma subfamily C, 5	0.7325	55
C14orf180	Chromosome 14 open reading frame 180	0.7295	55
MYOZ2	Myozenin 2	0.7267	55