Details for: CL0000187

Cell ID: CL0000187

Cell Name: muscle cell

Description: A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.

Synonyms: muscle fiber, myocyte

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

Image representation

Depiction of muscle cell
Courtesy of SwissBioPics

Significant Genes List

Genes with the highest and lowest Percentile Rank Scores (PRS) for muscle cell 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 muscle cell. 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 muscle cell. 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 muscle cell. 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:  muscle cell (CL0000187)

 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 [muscle cell](/details-cell/CL0000187), or myocyte, is a mature contractile cell defined by its organized myofibrillar cytoplasm. Based on its gene significance profile, the identity of this cell type is overwhelmingly characterized by a highly specialized and constitutively active bioenergetic infrastructure. The top marker genes are dominated by components of the mitochondrial electron transport chain and ATP synthesis machinery, such as [NDUFA4](/details-gene/4697), [ATP5F1E](/details-gene/514), and [COX7C](/details-gene/1350). This suggests that the defining feature of a [muscle cell](/details-cell/CL0000187) at the transcriptomic level is its immense and unique capacity for aerobic respiration to fuel its primary function of contraction. ## Key Characteristics and Function **Overall**, the gene expression landscape of the [muscle cell](/details-cell/CL0000187) points towards a cell exquisitely optimized for high energy expenditure and the maintenance of a complex protein-based contractile apparatus. * **Mitochondrial Bioenergetics as a Core Identity:** The most striking characteristic is the high specificity score (`csi_z`) for a large cluster of genes involved in oxidative phosphorylation. This includes numerous subunits of the NADH:ubiquinone oxidoreductase complex ([NDUFA4](/details-gene/4697)), ATP synthase ([ATP5F1E](/details-gene/514), [ATP5MC2](/details-gene/517), [ATP5F1B](/details-gene/506), [ATP5MG](/details-gene/10632), [ATP5ME](/details-gene/521)), and cytochrome c oxidase ([COX7C](/details-gene/1350), [COX4I1](/details-gene/1327), [COX6C](/details-gene/1345)). The high specificity of these genes suggests that the particular composition and regulation of the mitochondrial machinery is a unique identifier for myocytes compared to other cell types. * **Primed for High Glycolytic Flux:** The high rank of glyceraldehyde-3-phosphate dehydrogenase ([GAPDH](/details-gene/2597)), a key enzyme in glycolysis, is significant. While often considered a ubiquitous housekeeping gene, its status as a top specific marker indicates that muscle cells maintain an exceptionally high and specific capacity for glycolysis to provide pyruvate for the Krebs cycle and subsequent oxidative phosphorylation. * **Sarcomeric Structure and Protein Maintenance:** The cell's contractile function is directly represented by the high specificity of [TCAP](/details-gene/8557) (Telethonin), a protein integral to the sarcomere's Z-disc where it interacts with titin ([Link](https://pubmed.ncbi.nlm.nih.gov/9350988/)). Furthermore, the prominence of genes involved in protein synthesis and degradation, such as the ubiquitin gene [UBB](/details-gene/7314) and translation elongation factors ([EEF1D](/details-gene/1936), [EEF1B2](/details-gene/1933)), underscores the constant turnover and maintenance required for the complex myofibrillar protein structures. * **Distinction from Other Lineages:** The analysis of anti-markers helps to define what a [muscle cell](/details-cell/CL0000187) is not. The low specificity score for the MHC class I gene [HLA E](/details-gene/3133) is consistent with muscle cells having a relatively low immune surveillance profile compared to professional immune cells. Similarly, a low score for [COL3A1](/details-gene/1281), a key collagen gene, distinguishes the myocyte from surrounding fibroblasts that produce the extracellular matrix. ## Clinical Significance and Contextual Roles The gene signature of the [muscle cell](/details-cell/CL0000187) provides direct insights into its potential roles in disease. The profound reliance on a specific set of mitochondrial and structural proteins makes it particularly vulnerable to genetic and metabolic disorders. * **Muscular Dystrophies and Cardiomyopathies:** The high significance of structural proteins like [TCAP](/details-gene/8557) is clinically relevant, as mutations in this gene are known to cause limb-girdle muscular dystrophy and cardiomyopathies by disrupting the integrity of the sarcomere ([Link](https://pubmed.ncbi.nlm.nih.gov/9350988/)). This highlights how disruption of even a single highly specific component can lead to catastrophic failure of the entire cell's function. * **Mitochondrial Diseases:** Given that the cell's identity is defined by a large suite of mitochondrial protein-encoding genes ([NDUFA4](/details-gene/4697), [COX7C](/details-gene/1350), etc.), it is a primary target for diseases of mitochondrial origin (mitochondriopathies). Deficiencies in any of these components would likely lead to severe myopathies characterized by energy deprivation, muscle weakness, and exercise intolerance. * **Metabolic Syndrome and Diabetes:** The prominent role of [GAPDH](/details-gene/2597) and the overall bioenergetic signature suggest that muscle cell function is tightly linked to systemic glucose metabolism. In conditions like insulin resistance and type 2 diabetes, the inability to efficiently utilize glucose would severely compromise the energy supply chain that is so central to this cell's identity and function. ## Potential Mechanisms and Research Directions The data provides a clear picture of the [muscle cell](/details-cell/CL0000187) as a metabolic powerhouse, but it also raises intriguing questions about the hierarchy of genes that define its identity. 1. **Hypothesis: The defining transcriptomic signature of a [muscle cell](/details-cell/CL0000187) is its bioenergetic support system, rather than its core contractile machinery.** This model posits that while contractile proteins are essential for function, it is the uniquely configured and exceptionally high expression of the metabolic engine that most distinguishes myocytes from other cell types at the mRNA level. * **Surprising Findings:** It is highly unexpected that cornerstone genes for excitation-contraction coupling, such as the ryanodine receptor ([RYR1](/details-gene/6261)) and the sarcoplasmic reticulum Ca2+-ATPase ([ATP2A1](/details-gene/487)), are found among the anti-markers with low specificity scores. These proteins are fundamentally critical to muscle function and are often considered definitive markers. Their low `csi_z` score suggests their mRNA expression may not be as unique to muscle cells as previously assumed, or that post-transcriptional mechanisms are more critical for establishing their functional protein levels. * **Testable Questions:** Is there a significant divergence between transcript and protein abundance for [RYR1](/details-gene/6261) and [ATP2A1](/details-gene/487) specifically in [muscle cells](/details-cell/CL0000187) compared to other cell types? A comparative proteomic and transcriptomic study across multiple cell types could determine if muscle cells achieve high protein levels of these components through enhanced translational efficiency or protein stability rather than through uniquely high transcription. 2. **Hypothesis: Genes traditionally classified as "housekeeping," such as [GAPDH](/details-gene/2597), have adopted highly specialized, rate-limiting roles in [muscle cells](/details-cell/CL0000187) that are critical to their identity.** This suggests that to meet extreme metabolic demands, muscle cells have co-opted and uniquely regulate ubiquitous metabolic enzymes to a degree that they become defining features of the cell's phenotype. * **Surprising Findings:** The classification of [GAPDH](/details-gene/2597), a canonical housekeeping gene used as a loading control in many experiments, as the third most specific marker for a highly specialized cell is counterintuitive. This challenges the context-independent view of such genes and implies a muscle-specific regulatory layer that elevates its expression and importance beyond a simple basal level. * **Testable Questions:** Do muscle-specific transcription factors or enhancers bind to the [GAPDH](/details-gene/2597) gene locus to drive its exceptionally high expression in myocytes? Chromatin immunoprecipitation sequencing (ChIP-seq) for muscle-specific transcription factors (e.g., MYOD1) could reveal unique binding sites at the [GAPDH](/details-gene/2597) promoter or enhancer regions in myocyte lineages.