Table 1 Connections between three layers (processes–transcription factors (TF)–physiological parameters) for 5 days and 12 weeks. The relationship indicates between which layers the edge occurs, and the size of overlap shows the amount of genes overlapping. Similarly, coefficient is a measurement of similarity between the two gene set of the two nodes connected by an edge
Edge ID | Relationship | Size of overlap | Similarity coefficient |
|---|---|---|---|
5 days | |||
BM gain—HMGA1 | Physiology–TF | 1 | 0.5 |
BM gain—OSR2 | Physiology–TF | 1 | 1 |
ESR1—regulation_of_biological_quality | TF–processes | 3 | 0.6 |
FANK 1—Chromosome | TF–processes | 1 | 1 |
FANK1—nucleus | TF–processes | 1 | 1 |
FANK1—RNA_polymerase_II_transcription_factor_activity | TF–processes | 1 | 1 |
HMGA1—cytoskeletal_protein_binding | TF–processes | 1 | 0.5 |
HMGA1—extracellular_region | TF–processes | 1 | 0.5 |
HMGA1—kinase_regulator_activity | TF–processes | 1 | 0.5 |
HMGA1—pattern_binding | TF–processes | 1 | 0.5 |
HMGA1—polysaccharide_binding | TF–processes | 1 | 0.5 |
HMGA1—signal_transduction | TF–processes | 1 | 0.5 |
ING2—negative_regulation_of_biological_process | TF–processes | 1 | 1 |
ING2—regulation_of_biological_quality | TF–processes | 1 | 1 |
ING2—regulation_of_multicellular_organismal_process | TF–processes | 1 | 1 |
ING2—response_to_external_stimulus | TF–processes | 1 | 1 |
ING2—response_to_stress | TF–processes | 1 | 1 |
ING2—response_to_wounding | TF–processes | 1 | 1 |
MECOM—biopolymer_metabolic_process | TF–processes | 1 | 1 |
MECOM—nucleobasenucleosidenucleotide_and_nucleic_acid_metabolic_process | TF–processes | 1 | 1 |
MECOM—RNA_biosynthetic_process | TF–processes | 1 | 1 |
MECOM—signal_transduction | TF–processes | 1 | 1 |
MECOM—transcription | TF–processes | 1 | 1 |
MTPN—regulation_of_biological_quality | TF–processes | 2 | 0.5 |
NCOA6—negative_regulation_of_biological_process | TF–processes | 1 | 0.5 |
NCOA6—regulation_of_biological_quality | TF–processes | 1 | 0.5 |
NCOA6—response_to_external_stimulus | TF–processes | 1 | 0.5 |
NCOA6—response_to_stress | TF–processes | 1 | 0.5 |
NCOA6—response_to_wounding | TF–processes | 1 | 0.5 |
ORS2—receptor_binding | TF–processes | 1 | 1 |
OSR2—anatomical_structure_development | TF–processes | 1 | 1 |
OSR2—multicellular_organismal_development | TF–processes | 1 | 1 |
OSR2—signal_transduction | TF–processes | 1 | 1 |
PPARD—oxidoreductase_activity | TF–processes | 2 | 0.666666667 |
SLC2A4RG—carbohydrate_metabolic_process | TF–processes | 1 | 1 |
SLC2A4RG—cell_surface | TF–processes | 1 | 1 |
SLC2A4RG—integral_to_membrane | TF–processes | 1 | 1 |
SLC2A4RG—membrane_part | TF–processes | 1 | 1 |
SLC2A4RG—organelle_membrane | TF–processes | 1 | 1 |
SLC2A4RG—plasma_membrane | TF–processes | 1 | 1 |
SLC2A4RG—plasma_membrane_part | TF–processes | 1 | 1 |
SLC2A4RG—regulation_of_biological_quality | TF–processes | 1 | 1 |
TAF6—chromosome | TF–processes | 1 | 0.5 |
TAF6—nucleus | TF–processes | 1 | 0.5 |
TAF6—RNA_polymerase_II_transcription_factor_activity | TF–processes | 1 | 0.5 |
NCOA6—regulation_of_multicellular_organismal_process | TF–processes | 1 | 0.5 |
12 weeks | 0.4 | ||
Energy intake (KJ/D)(whole intervention period)—cellular_respiration | Physiology–processes | 6 | 0.333333333 |
eWAT weight (g)—cellular_respiration | Physiology–processes | 5 | 0.315789474 |
eWAT weight (g)—cofactor_biosynthetic_process | Physiology–processes | 6 | 0.388888889 |
eWAT weight (g)—proteasome_complex | Physiology–processes | 7 | 0.5 |
ETS2—energy intake (KJ/D)(whole intervention period) | TF–physiology | 7 | 0.571428571 |
FOSL1—energy intake (KJ/D)(first 3 days after diet switch) | TF–physiology | 8 | 0.615384615 |
FOXO4—eWAT weight (g) | TF–physiology | 8 | 0.583333333 |
MLXIPL—eWAT weight (g) | TF–physiology | 7 | 0.6 |
NCOA6—eWAT weight (g) | TF–physiology | 3 | 0.5 |
NFYA—eWAT weight (g) | TF–physiology | 8 | 0.5 |
PDE—energy intake (KJ/D)(whole intervention period) | TF–physiology | 2 | 0.5 |
RCOR1—energy intake (KJ/D)(first 3 days after diet switch) | TF–physiology | 1 | 0.5 |
SMAD5—energy intake (KJ/D)(first 3 days after diet switch) | TF–physiology | 3 | 0.666666667 |
SMAD5—eWAT weight (g) | TF–physiology | 4 | 0.5 |
SOX10—energy intake (KJ/D)(whole intervention period) | TF–physiology | 4 | 0.53125 |
SREBF2—eWAT weight (g) | TF–physiology | 17 | 0.5 |
DEK—membrane_part | TF–processes | 2 | 0.625 |
FXR—lipid_metabolic_process | TF–processes | 5 | 0.666666667 |
HNRNPD—biopolymer_metabolic_process | TF–processes | 2 | 0.666666667 |
KDM3A—extracellular_region | TF–processes | 4 | 0.5 |
KDM3A—response_to_external_stimulus | TF–processes | 3 | 0.666666667 |
KDM3A—signal_transduction | TF–processes | 4 | 0.6 |
NCOA6—response_to_external_stimulus | TF–processes | 3 | 0.4 |