Details for: CL0000188

Cell ID: CL0000188

Cell Name: cell of skeletal muscle

Description: A somatic cell located in skeletal muscle.

Synonyms: skeletal muscle cell

Selected Context(s): Overall

Gene Significance Landscape

Display Options
Score:
Display
Genes

Contexts:

Cell Significance Index (CSI) is uniquely calculated to reveal cell-specific gene markers. More info here

Significant Genes List

Genes with the highest and lowest Percentile Rank Scores (PRS) for cell of skeletal muscle within the selected context(s).

Gene ID: A unique numerical identifier for this specific gene.
Symbol: Shortened abbreviation or name that represents this gene.
Ensembl Gene ID: A unique identifier assigned by Ensembl for genomic data mapping.
CSI Score: A combined effect size and statistical significance measure for cell of skeletal muscle. Higher scores indicate a stronger, more significant difference in expression.
(Previously described as "Fold Change", but now represents Cliff's Delta × –log10(p).)

Gene ID: A unique numerical identifier for this specific gene.
Symbol: Shortened abbreviation or name that represents this gene.
Ensembl Gene ID: A unique identifier assigned by Ensembl for genomic data mapping.
CSI Score: A combined effect size and statistical significance measure for cell of skeletal muscle. Higher scores indicate a stronger, more significant difference in expression.
Average CSI: csi sum / gene count
Cell network configuration

This network visualizes key genes for cell of skeletal muscle. It primarily includes:
1. Top genes highly significant for this cell (Num. Top Cell Genes - based on the 'Min. CSI' setting).
2. Any additional specific 'Context Genes' you add below.
The final network is a combined view. Choose an Interaction Source (pathways or protein interactions) and optionally compare CSI scores with a Baseline Cell Type.

Maximum number of selected genes.
Select a context for the baseline cell.
Select a context for the target cell.
Target Cell for CSI:  cell of skeletal muscle (CL0000188)

 Legend
Nodes (Genes):
 Query Gene
Node size also reflects Target Cell CSI magnitude.
Node Color (Target Cell CSI in specific network):
 Very High
 High
 Medium
 Low
 Very Low
 N/A or Not Sig.
Edges (Interactions):
 STRING (Protein-Protein)
 ONTOLOGY (Shared Pathway)
 Colors vary by pathway category; default arrow applies.

Loading network (please wait)...

## Summary The [cell of skeletal muscle](/details-cell/CL0000188), also known as a skeletal muscle cell, is a somatic cell type responsible for voluntary movement. The gene significance profile suggests that its identity is defined not only by its core contractile machinery but also by a highly active metabolic state and complex regulatory networks. The top marker based on expression specificity (`csi_z`) is the long non-coding RNA [GAS5](/details-gene/60674), indicating that post-transcriptional regulation plays a crucial role in maintaining the specialized state of this cell. This is complemented by the high significance of genes involved in energy production, protein synthesis, and chromatin organization, painting a picture of a cell constantly maintaining structural integrity while being primed for high energy expenditure. ## Key Characteristics and Function **Overall**, the gene expression profile of the [cell of skeletal muscle](/details-cell/CL0000188) highlights its specialization in electromechanical coupling, contraction, and metabolic activity. The top marker genes can be grouped into several key functional clusters: * **Muscle Contraction and Structure:** As expected, genes encoding core components of the sarcomere are highly significant. These include [TNNT2](/details-gene/7139) (Troponin T2, cardiac type), a key component of the troponin complex that regulates muscle contraction, and [MYOZ2](/details-gene/51778), which links the calcineurin signaling pathway to the Z-disc of the sarcomere. The presence of [MYL12B](/details-gene/103910) (Myosin Light Chain 12B) and [ARPC3](/details-gene/10094) (Actin Related Protein 2/3 Complex Subunit 3) further underscores the cell's reliance on a highly organized actin cytoskeleton for both structure and force generation. * **Energy Metabolism:** A prominent signature is the high significance of multiple subunits of the mitochondrial ATP synthase complex, including [ATP5ME](/details-gene/521), [ATP5PF](/details-gene/522), and [ATP5F1B](/details-gene/506). This points to the critical role of oxidative phosphorylation in meeting the high energy demands of muscle contraction. The significance of [LDHB](/details-gene/3945) (Lactate Dehydrogenase B) also suggests a well-developed capacity for anaerobic glycolysis, which is essential during intense bursts of activity. * **Gene Expression and Protein Turnover:** The profile reveals a complex system for regulating gene expression and maintaining protein homeostasis. The top marker, [GAS5](/details-gene/60674), and another highly-ranked non-coding RNA, [MEG3](/details-gene/55384), suggest that non-coding RNAs are central to skeletal muscle identity. Transcriptional regulation is highlighted by factors like [SUB1](/details-gene/10923) and [TCF4](/details-gene/6925). Furthermore, the significance of the proteasome subunit [PSMB1](/details-gene/5689) and numerous ribosomal protein pseudogenes (e.g., [RPL13AP5](/details-gene/728658), [RPL36AP37](/details-gene/729362)) suggests a high and precisely controlled rate of protein turnover, which is essential for muscle repair and adaptation. * **Chromatin and Nuclear Organization:** Genes such as [H2AZ1](/details-gene/3015) (a histone variant) and [SET](/details-gene/6418) (a histone chaperone) are significant, indicating that epigenetic and chromatin-level regulation are important for maintaining the specific gene expression programs of this terminally differentiated cell type. The anti-marker profile is also informative. The low significance of immediate early genes like [FOS](/details-gene/2353) and [JUN](/details-gene/3725) is consistent with the post-mitotic, quiescent state of mature muscle fibers. Similarly, the strong negative significance of genes involved in iron storage ([FTH1](/details-gene/2495)) and general RNA processing ([DDX5](/details-gene/1655), [HNRNPA2B1](/details-gene/3181)) may suggest that skeletal muscle employs highly specialized pathways for these processes that are distinct from those in other cell types. ## Clinical Significance and Contextual Roles The gene profile of the [cell of skeletal muscle](/details-cell/CL0000188) provides direct links to several well-characterized human diseases, highlighting its central role in neuromuscular health. * **Cardiomyopathies and Muscular Dystrophies:** The high significance of [TNNT2](/details-gene/7139) is clinically relevant, as mutations in this gene are a known cause of familial hypertrophic and dilated cardiomyopathies ([Link](https://pubmed.ncbi.nlm.nih.gov/8576938/)). Although the data pertains to skeletal muscle, the shared protein machinery means that insights may be transferable. * **Neuromuscular Disorders:** [SOD1](/details-gene/6647) (Superoxide Dismutase 1) is a significant marker whose mutations are famously associated with familial Amyotrophic Lateral Sclerosis (ALS), a fatal neurodegenerative disease that leads to the loss of motor neurons and subsequent skeletal muscle atrophy. The ion channel [KCNMA1](/details-gene/3778) is linked to a spectrum of neurological disorders, including paroxysmal nonkinesigenic dyskinesia and epilepsy, which can involve muscle dysfunction. * **Developmental Syndromes:** The transcription factor [TCF4](/details-gene/6925) is associated with Pitt-Hopkins syndrome, a neurodevelopmental disorder characterized by severe intellectual disability and physical features that include muscular hypotonia. This underscores the importance of precise transcriptional control for proper muscle development and function. The overall profile suggests that the health of skeletal muscle cells depends on a delicate balance between structural protein integrity, robust energy supply, and stringent regulatory control. Disruptions in any of these core functional areas can lead to significant pathology. ## Potential Mechanisms and Research Directions 1. **Hypothesis: Long non-coding RNAs, particularly [GAS5](/details-gene/60674), function as critical hubs in skeletal muscle for integrating metabolic state with gene expression programs governing contractile and mitochondrial proteins.** * **Surprising Findings:** The most specific gene marker for a cell type defined physically by its contractile apparatus is not a structural protein but a long non-coding RNA, [GAS5](/details-gene/60674). This suggests that post-transcriptional regulation may be a primary layer of control that defines and maintains the unique phenotype of skeletal muscle cells. * **Testable Questions:** Does targeted degradation of [GAS5](/details-gene/60674) in cultured myotubes or in vivo mouse models alter the expression of mitochondrial ATP synthase subunits or sarcomeric proteins like [TNNT2](/details-gene/7139)? Does [GAS5](/details-gene/60674) expression change in response to metabolic stressors like glucose deprivation or stimuli mimicking exercise? 2. **Hypothesis: The high and specific expression of numerous ribosomal protein (RP) pseudogenes (e.g., [RPL13AP5](/details-gene/728658), [RPL36AP37](/details-gene/729362)) in skeletal muscle cells indicates they are not inert genomic relics but functional regulatory transcripts, possibly acting as competing endogenous RNAs (ceRNAs) to modulate the translation of canonical RP genes and other key mRNAs.** * **Surprising Findings:** It is highly unusual for multiple pseudogenes to rank among the most specific markers for a cell type. Their high expression specificity strongly implies a functional, rather than vestigial, role. This challenges the conventional view of pseudogenes as non-functional. * **Testable Questions:** Can transcripts from [RPL13AP5](/details-gene/728658) or [RPL36AP37](/details-gene/729362) be detected in association with RNA-induced silencing complexes (RISC) in skeletal muscle lysates? Does the overexpression or knockdown of these pseudogene transcripts alter the rate of protein synthesis or the stability of specific mRNAs in skeletal muscle cells, particularly under conditions of hypertrophy or atrophy?