Details for: CL0000189

Cell ID: CL0000189

Cell Name: slow muscle cell

Description: A muscle cell that develops tension more slowly than a fast-twitch fiber.

Synonyms: slow muscle fiber

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 slow 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 slow 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 slow 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 slow 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:  slow muscle cell (CL0000189)

 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 A [slow muscle cell](/details-cell/CL0000189), also known as a slow-twitch or type I muscle fiber, is a highly specialized contractile cell designed for sustained, low-intensity contractions and resistance to fatigue. Analysis of its gene expression landscape reveals a distinct molecular signature centered on three core functional pillars: a unique contractile apparatus, a high capacity for aerobic respiration, and specialized structural and signaling proteins that maintain cellular integrity. The high expression specificity (csi_z) of genes like the LIM-domain protein [FHL1](/details-gene/2273), the sarcomeric protein [TCAP](/details-gene/8557), and the slow-twitch specific beta-myosin heavy chain [MYH7](/details-gene/4625) underscore its unique identity and function within the musculoskeletal system. ## Key Characteristics and Function The defining features of the [slow muscle cell](/details-cell/CL0000189) are evident from its most specific gene markers, which can be grouped into distinct functional clusters. * **Sarcomeric and Contractile Machinery:** The **Overall** identity of this cell is dominated by genes encoding components of the sarcomere, the fundamental unit of muscle contraction. The most notable is [MYH7](/details-gene/4625), which encodes the beta-myosin heavy chain characteristic of slow-twitch fibers and is critical for the slow, efficient ATPase activity of these cells. This is complemented by a suite of other structural proteins with highly specific expression, including skeletal alpha-actin ([ACTA1](/details-gene/58)), titin ([TTN](/details-gene/7273)), nebulin ([NEB](/details-gene/4703)), telethonin ([TCAP](/details-gene/8557)), and various troponin and tropomyosin isoforms ([TNNC1](/details-gene/7134), [TPM2](/details-gene/7169)). The specific expression of LIM-domain proteins that associate with the actin cytoskeleton, such as [PDLIM3](/details-gene/27295) and [FHL1](/details-gene/2273), further suggests a sophisticated system for maintaining Z-disc integrity and transducing mechanical stress. * **Aerobic Metabolism and Oxygen Supply:** Consistent with its endurance function, the [slow muscle cell](/details-cell/CL0000189) shows specific expression of genes essential for oxidative phosphorylation. The high specificity of the mitochondrial ADP/ATP translocator ([SLC25A4](/details-gene/291)), which facilitates the transport of ATP out of the mitochondria, highlights the cell's reliance on aerobic energy production. This is strongly supported by the specific expression of myoglobin ([MB](/details-gene/4151)), which functions as an intracellular oxygen reservoir, and muscle-specific isoforms of cytochrome c oxidase subunits ([COX6A2](/details-gene/1339), [COX7A1](/details-gene/1346)), a key enzyme complex in the electron transport chain. The expression of carbonic anhydrase 3 ([CA3](/details-gene/761) also points to a specialized role in managing metabolic byproducts. * **Protein Turnover and Stress Response:** A high specificity score for [FBXO32](/details-gene/114907), an E3 ubiquitin ligase also known as Atrogin-1, is particularly noteworthy. While well-known for its role in muscle atrophy ([Link](https://doi.org/10.1126/science.1065874)), its status as a defining marker in a general context suggests a crucial homeostatic role in protein quality control, likely necessary to manage the wear and tear from continuous activity. Additionally, the ankyrin repeat protein [ANKRD2](/details-gene/26287) is a known stress-response molecule in muscle, reinforcing the idea that these cells are equipped with mechanisms to handle mechanical and metabolic stress. * **Anti-Markers:** The lack of specificity for several core mitochondrial NADH dehydrogenase subunits ([ND4L](/details-gene/4539), [ND5](/details-gene/4540)) and cytochrome c oxidase subunit 3 ([COX3](/details-gene/4514)) is informative. It suggests that while mitochondrial respiration is central, the cell's unique identity is conferred by muscle-specific isoforms of metabolic machinery (e.g., [COX6A2](/details-gene/1339), [COX7A1](/details-gene/1346)) rather than the universally expressed core components. Similarly, the negative or low specificity for broadly expressed transcription and ubiquitination factors like [HMGB1](/details-gene/3146), [SUB1](/details-gene/10923), and [RBX1](/details-gene/9978) reinforces that this is a terminally differentiated cell whose identity is primarily defined by its specialized structural and metabolic proteome, not by general housekeeping genes. ## Clinical Significance and Contextual Roles The gene signature of the [slow muscle cell](/details-cell/CL0000189) directly implicates it in a variety of inherited muscle diseases (myopathies). Mutations in many of its top marker genes are known causes of debilitating conditions. **Overall**, the integrity of this cell type is paramount for posture, endurance, and basic motor function. Disruptions in its key genes often lead to severe pathology: * Mutations in [MYH7](/details-gene/4625) are a well-established cause of familial hypertrophic and dilated cardiomyopathies, as well as specific skeletal myopathies. * Defects in the giant structural protein titin, encoded by [TTN](/details-gene/7273), are one of the most common causes of inherited cardiomyopathies and are also linked to limb-girdle muscular dystrophies. * Mutations in skeletal alpha-actin ([ACTA1](/details-gene/58)) lead to a group of disorders including actin myopathy and nemaline myopathy ([Link](https://doi.org/10.1038/13837)). * Similarly, mutations in [NEXN](/details-gene/91624), which encodes the Z-disc protein nexilin, have been shown to destabilize the sarcomere and result in dilated cardiomyopathy ([Link](https://doi.org/10.1038/nm.2037)). The prominent expression of [FBXO32](/details-gene/114907) also highlights the cell's potential role in muscle wasting conditions (cachexia and sarcopenia), where this gene is a key mediator of protein degradation. Understanding the regulation of these highly specific genes in [slow muscle cells](/details-cell/CL0000189) is therefore critical for developing therapies for a wide range of neuromuscular diseases. ## Potential Mechanisms and Research Directions The data suggest several avenues for future investigation into the unique biology of the [slow muscle cell](/details-cell/CL0000189). 1. **Hypothesis:** The LIM-domain protein [FHL1](/details-gene/2273) acts as a master organizational hub that functionally couples the mechanical stress-sensing apparatus of the sarcomere with the metabolic machinery to maintain the endurance phenotype. Its position as the single most specific gene marker suggests a role beyond simple structural support, potentially acting as a scaffold that coordinates signals between the Z-disc and mitochondria. * **Surprising Findings:** It is striking that a signaling and scaffolding protein like [FHL1](/details-gene/2273) exhibits greater expression specificity (CSI=7.51) than the canonical slow-twitch motor protein [MYH7](/details-gene/4625) (CSI=6.76). This may indicate that the regulatory and sensing network is an even more unique feature of this cell's identity than its contractile isoform. * **Testable Questions:** Does targeted disruption of [FHL1](/details-gene/2273) in adult slow muscle fibers alter mitochondrial function, localization, or the expression of key metabolic genes like [SLC25A4](/details-gene/291) and [MB](/details-gene/4151), independent of immediate effects on sarcomeric integrity? 2. **Hypothesis:** The high constitutive specificity of the E3 ubiquitin ligase [FBXO32](/details-gene/114907) reflects a critical homeostatic role in protein quality control that is essential for the long-term function and fatigue resistance of slow-twitch fibers. Rather than being solely a catabolic factor in disease, its primary function may be the continuous, selective removal of damaged or misfolded contractile and mitochondrial proteins generated during sustained activity. * **Surprising Findings:** The common understanding of [FBXO32](/details-gene/114907) (Atrogin-1) is as a primary driver of muscle atrophy. Its identification as a top-three defining marker in a general, non-diseased context suggests its homeostatic, surveillance role is a fundamental and highly specific aspect of slow muscle biology. * **Testable Questions:** What is the basal ubiquitome profile of [slow muscle cells](/details-cell/CL0000189) compared to fast-twitch fibers, and are the primary targets of [FBXO32](/details-gene/114907) under resting conditions enriched for specific sarcomeric or mitochondrial proteins known to have high turnover rates?