Table 3 Gene set enrichment analysis table for the 20 most significant gene sets based on the 0.4 cut-off analysis
Gene Set Name (All hypomethylated) | Description | # Genes in Overlap | FDR q-value |
|---|---|---|---|
GOBP_ACTIN_FILAMENT_BASED_PROCESS (1) | Hypomethylation of these genes suggests increased cytoskeletal organization, rearrangement, and actin filament dynamics, leading to enhanced cell motility, structural adaptability, and migration. | 20 | 1.84 × 10− 6 |
GOBP_CELL_MOTILITY (1) | 29 | 1.84 × 10− 6 | |
GOCC_ACTIN_CYTOSKELETON (1) | 13 | 1.4 × 10− 4 | |
GOMF_CYTOSKELETAL_PROTEIN_BINDING (1) | Enhanced expression of genes encoding cytoskeletal-binding proteins is linked to improved cell shape maintenance, intracellular transport, and mechanical stress response. | 18 | 9.99 × 10− 5 |
GOBP_RESPONSE_TO_WOUNDING (2) | Hypomethylation highlights the activation of genes driving tissue repair and ECM remodeling, facilitating rapid responses to damage and improved regenerative capacity and maintaining intercellular interactions in both normal and pathological conditions | 16 | 4.86 × 10− 6 |
GOBP_WOUND_HEALING (2) | 13 | 4.17 × 10− 5 | |
GOBP_POSITIVE_REGULATION_OF_EXTRACELLULAR_ MATRIX_ORGANIZATION (2) | 5 | 1.27 × 10− 4 | |
GOBP_POSITIVE_REGULATION_OF_CELL_PROJECTION_ ORGANIZATION | Hypomethylation promotes the formation of cellular projections such as filopodia and lamellipodia, enhancing cell motility and migration, critical in processes like metastasis and wound healing. | 11 | 4.16 × 10− 6 |
GOBP_CELL_JUNCTION_ORGANIZATION (3) | Hypomethylation of genes involved in cell junction formation supports enhanced adhesion and structural coordination, important for tissue stability and function. Upregulation of genes facilitating the assembly of cellular components could strengthen structural stability and adaptability in dynamic environments like 3D cultures. | 17 | 3.28 × 10− 5 |
GOCC_ANCHORING_JUNCTION (3) | 18 | 4.17 × 10− 5 | |
GOBP_POSITIVE_REGULATION_OF_CELLULAR_ COMPONENT_ORGANIZATION (3/6) | 22 | 1.66 × 10− 4 | |
GOBP_MUSCLE_STRUCTURE_DEVELOPMENT (4) | Hypomethylation activates genes required for muscle structure development and differentiation, suggesting a shift towards tissue-specific functional states or increased plasticity in response to environmental (in vitro conditions) or physiological demands. | 16 | 4.7 × 10− 5 |
GOBP_POSITIVE_REGULATION_OF_DEVELOPMENTAL_ PROCESS (4) | Hypomethylation-driven upregulation may indicate enhanced epithelial tissue development, contributing to epithelial-mesenchymal transitions or remodeling processes (plasticity) | 21 | 1.37 × 10− 4 |
GOBP_EPITHELIUM_DEVELOPMENT (4) | 20 | 1.04 × 10− 4 | |
GOBP_POSITIVE_REGULATION_OF_TRANSCRIPTION_ BY_RNA_POLYMERASE_II (5) | Hypomethylation might lead to increased transcriptional activity and RNA metabolism. This aligns with the observation that hypomethylation often removes repressive marks, enabling more active transcription of genes. | 22 | 1.35 × 10− 5 |
GOBP_POSITIVE_REGULATION_OF_RNA_METABOLIC_ PROCESS (5) | 26 | 5.83 × 10− 5 | |
GOBP_LOCOMOTION (1) | Hypomethylation of genes regulating locomotion suggests increased cellular movement and migration, playing a significant role in tissue repair, immune responses, and cancer progression | 21 | 1.04 × 10− 4 |
GOBP_REGULATION_OF_LOCOMOTION (1) | 20 | 5.83 × 10− 5 | |
GOCC_NEURON_PROJECTION (6) | This indicates that genes involved in the formation, structure, or function of neuron projections (such as axons, dendrites, or other cellular protrusions) are likely upregulated in the 3D cell model. | 21 | 9.85 × 10− 5 |
REACTOME_SIGNALING_BY_RHO_GTPASES_ MIRO_GTPASES_AND_RHOBTB3 (6) | Suggests that hypomethylation activates Rho GTPase-related signaling, which is a key regulator of cytoskeletal dynamics, cell migration, and intracellular trafficking. This pathway likely plays a central role in the structural and motility-related changes observed. | 15 | 1.53 × 10− 4 |