Table 4.
Top 20 candidate gene sets selected from gene-set analysis for all patients.
| Model | Rank | Gene set name | nGenes | Beta | SE | P | P a |
|---|---|---|---|---|---|---|---|
| Trend | 1 | go_transmembrane_receptor_protein_tyrosine_kinase_signaling_pathway | 490 | 0.14 | 0.0377 | 0.00010183 | 1 |
| Trend | 2 | go_morphogenesis_of_a_polarized_epithelium | 27 | 0.521 | 0.146 | 0.00018275 | 1 |
| Trend | 3 | chang_pou5f1_targets_up | 15 | 0.697 | 0.201 | 0.00027201 | 1 |
| Trend | 4 | pid_fanconi_pathway | 46 | 0.421 | 0.122 | 0.00028575 | 1 |
| Trend | 5 | go_oxidoreductase_activity_acting_on_paired_donors_with_incorporation_or_reduction_of_molecular_oxygen_reduced_flavin_or_flavoprotein_as_one_donor_and_incorporation_of_one_atom_of_oxygen | 24 | 0.613 | 0.184 | 0.00043085 | 1 |
| Trend | 6 | go_apical_protein_localization | 12 | 0.825 | 0.25 | 0.00048715 | 1 |
| Trend | 7 | delaserna_myod_targets_dn | 56 | 0.375 | 0.115 | 0.0005732 | 1 |
| Trend | 8 | go_execution_phase_of_apoptosis | 53 | 0.379 | 0.117 | 0.00059648 | 1 |
| Trend | 9 | go_atpase_activity_coupled | 299 | 0.149 | 0.0462 | 0.00064486 | 1 |
| Trend | 10 | liu_sox4_targets_dn | 299 | 0.152 | 0.0472 | 0.00066145 | 1 |
| Trend | 11 | firestein_ctnnb1_pathway | 32 | 0.475 | 0.149 | 0.00070207 | 1 |
| Trend | 12 | ning_chronic_obstructive_pulmonary_disease_dn | 117 | 0.23 | 0.0722 | 0.00072694 | 1 |
| Trend | 13 | mariadason_response_to_butyrate_curcumin_sulindac_tsa_1 | 9 | 1.11 | 0.349 | 0.00074306 | 1 |
| Trend | 14 | ross_aml_with_pml_rara_fusion | 72 | 0.316 | 0.1 | 0.00082081 | 1 |
| Trend | 15 | go_establishment_of_tissue_polarity | 17 | 0.57 | 0.181 | 0.00083939 | 1 |
| Trend | 16 | kondo_colon_cancer_hcp_with_h3k27me1 | 26 | 0.521 | 0.168 | 0.00098707 | 1 |
| Trend | 17 | go_enzyme_linked_receptor_protein_signaling_pathway | 675 | 0.1 | 0.0327 | 0.0010865 | 1 |
| Trend | 18 | go_atp_dependent_dna_helicase_activity | 33 | 0.411 | 0.135 | 0.0011325 | 1 |
| Trend | 19 | ikeda_mir30_targets_up | 115 | 0.232 | 0.0772 | 0.0013186 | 1 |
| Trend | 20 | go_gamma_tubulin_binding | 24 | 0.498 | 0.166 | 0.0013693 | 1 |
| Dominant | 1 | go_arachidonic_acid_monooxygenase_activity | 15 | 1.14 | 0.263 | 0.0000075774 | 0.08072962 |
| Dominant | 2 | go_oxidoreductase_activity_acting_on_paired_donors_with_incorporation_or_reduction_of_molecular_oxygen_reduced_flavin_or_flavoprotein_as_one_donor_and_incorporation_of_one_atom_of_oxygen | 24 | 0.75 | 0.188 | 0.000032941 | 0.350953414 |
| Dominant | 3 | pid_fanconi_pathway | 46 | 0.453 | 0.125 | 0.00013871 | 1 |
| Dominant | 4 | go_positive_regulation_of_receptor_recycling | 11 | 0.767 | 0.215 | 0.00018422 | 1 |
| Dominant | 5 | go_dna_double_strand_break_processing | 19 | 0.624 | 0.175 | 0.00018853 | 1 |
| Dominant | 6 | lenaour_dendritic_cell_maturation_up | 111 | 0.252 | 0.0754 | 0.00042167 | 1 |
| Dominant | 7 | kondo_colon_cancer_hcp_with_h3k27me1 | 26 | 0.574 | 0.172 | 0.00042761 | 1 |
| Dominant | 8 | go_apical_protein_localization | 12 | 0.842 | 0.255 | 0.00048821 | 1 |
| Dominant | 9 | reactome_xenobiotics | 15 | 0.874 | 0.266 | 0.00051506 | 1 |
| Dominant | 10 | delaserna_myod_targets_dn | 56 | 0.379 | 0.118 | 0.0006494 | 1 |
| Dominant | 11 | go_cytoplasmic_dynein_complex | 15 | 0.62 | 0.195 | 0.00072543 | 1 |
| Dominant | 12 | go_execution_phase_of_apoptosis | 53 | 0.373 | 0.12 | 0.0008959 | 1 |
| Dominant | 13 | go_cellular_response_to_exogenous_dsrna | 12 | 0.79 | 0.253 | 0.00091276 | 1 |
| Dominant | 14 | jechlinger_epithelial_to_mesenchymal_transition_up | 69 | 0.315 | 0.101 | 0.0009394 | 1 |
| Dominant | 15 | go_dna_metabolic_process | 728 | 0.0982 | 0.0317 | 0.00098413 | 1 |
| Dominant | 16 | taylor_methylated_in_acute_lymphoblastic_leukemia | 72 | 0.306 | 0.099 | 0.00099275 | 1 |
| Dominant | 17 | reactome_heparan_sulfate_heparin_hs_gag_metabolism | 52 | 0.385 | 0.126 | 0.0011419 | 1 |
| Dominant | 18 | go_dna_repair | 461 | 0.119 | 0.0391 | 0.0011488 | 1 |
| Dominant | 19 | go_poly_a_binding | 13 | 0.58 | 0.19 | 0.0011566 | 1 |
| Dominant | 20 | go_asymmetric_protein_localization | 19 | 0.594 | 0.195 | 0.0011843 | 1 |
| Recessive | 1 | go_fructose_metabolic_process | 14 | 1.24 | 0.25 | 0.00000036488 | 0.00388743152* |
| Recessive | 2 | kang_immortalized_by_tert_up | 86 | 0.349 | 0.0873 | 0.000032117 | 0.342174518 |
| Recessive | 3 | go_translation_factor_activity_rna_binding | 79 | 0.363 | 0.0956 | 0.000072849 | 0.776133246 |
| Recessive | 4 | go_regulation_of_hexokinase_activity | 11 | 0.886 | 0.238 | 0.00010025 | 1 |
| Recessive | 5 | haddad_t_lymphocyte_and_nk_progenitor_up | 75 | 0.344 | 0.0928 | 0.00010685 | 1 |
| Recessive | 6 | go_regulation_of_attachment_of_spindle_microtubules_to_kinetochore | 11 | 1.04 | 0.296 | 0.00022662 | 1 |
| Recessive | 7 | go_regulation_of_cell_projection_assembly | 148 | 0.247 | 0.0703 | 0.00022671 | 1 |
| Recessive | 8 | go_regulation_of_t_cell_tolerance_induction | 12 | 0.712 | 0.215 | 0.00045907 | 1 |
| Recessive | 9 | zwang_down_by_2nd_egf_pulse | 217 | 0.186 | 0.0564 | 0.00049442 | 1 |
| Recessive | 10 | go_regulation_of_membrane_lipid_metabolic_process | 13 | 0.782 | 0.238 | 0.00051065 | 1 |
| Recessive | 11 | kenny_ctnnb1_targets_up | 50 | 0.396 | 0.122 | 0.00056843 | 1 |
| Recessive | 12 | go_immunoglobulin_binding | 18 | 0.581 | 0.182 | 0.00068753 | 1 |
| Recessive | 13 | reactome_tca_cycle_and_respiratory_electron_transport | 115 | 0.26 | 0.0822 | 0.00076392 | 1 |
| Recessive | 14 | nielsen_synovial_sarcoma_dn | 19 | 0.791 | 0.25 | 0.00076547 | 1 |
| Recessive | 15 | doane_breast_cancer_esr1_dn | 48 | 0.376 | 0.119 | 0.00078823 | 1 |
| Recessive | 16 | go_dna_replication_dependent_nucleosome_organization | 31 | 0.839 | 0.267 | 0.0008361 | 1 |
| Recessive | 17 | go_t_cell_apoptotic_process | 15 | 0.651 | 0.207 | 0.00084519 | 1 |
| Recessive | 18 | go_lymphocyte_apoptotic_process | 18 | 0.605 | 0.193 | 0.0008619 | 1 |
| Recessive | 19 | go_regulation_of_pseudopodium_assembly | 13 | 0.735 | 0.237 | 0.00098328 | 1 |
| Recessive | 20 | lee_aging_cerebellum_dn | 80 | 0.292 | 0.0946 | 0.0010161 | 1 |
Model, the genetic model in which candidate gene sets were selected by analysis; nGenes, the number of genes in the data that are in the gene set; Beta, the regression coefficient of the gene set; SE, the standard error of the regression coefficient; P a , adjusted P-value for multiple testing; *, Significant association after the conservative Bonferroni correction.