TABLE 1.
Results of a Gene Set Enrichment Analysis on 32 colon adenomas vs. 32 normal colon samples from GSE8671, using 1,502 canonical pathways from the curated pathway database from MSigDB (c2/cp).
| Up in | Position | Name | nom.p | fdr.q | fwer.q |
| A | |||||
| Adenoma | 1 | PID_FOXM1_PATHWAY | 0.000 | 0.224 | 0.133 |
| Adenoma | 2 | PID_AURORA_A_PATHWAY | 0.000 | 0.211 | 0.222 |
| Adenoma | 3 | REACTOME_CHROMOSOME_MAINTENANCE | 0.000 | 0.193 | 0.262 |
| Adenoma | 4 | KEGG_CELL_CYCLE | 0.002 | 0.151 | 0.271 |
| Adenoma | 5 | REACTOME_G2_M_CHECKPOINTS | 0.002 | 0.141 | 0.303 |
| Adenoma | 6 | REACTOME_CELLULAR_RESPONSE_TO_HEAT_STRESS | 0.002 | 0.121 | 0.306 |
| Adenoma | 7 | REACTOME_REGULATION_OF_TP53_ACTIVITY_THROUGH_PHOSPHORYLATION | 0.000 | 0.105 | 0.312 |
| Adenoma | 8 | PID_MYC_ACTIV_PATHWAY | 0.000 | 0.093 | 0.314 |
| Adenoma | 9 | REACTOME_CELL_CYCLE_CHECKPOINTS | 0.002 | 0.083 | 0.314 |
| Adenoma | 10 | REACTOME_REGULATION_OF_HSF1_MEDIATED_HEAT_SHOCK_RESPONSE | 0.002 | 0.088 | 0.352 |
| Adenoma | 11 | REACTOME_BASE_EXCISION_REPAIR | 0.000 | 0.085 | 0.364 |
| Adenoma | 12 | BIOCARTA_G2_PATHWAY | 0.000 | 0.081 | 0.374 |
| Adenoma | 13 | REACTOME_DNA_REPAIR | 0.000 | 0.079 | 0.384 |
| Adenoma | 14 | REACTOME_RHO_GTPASES_ACTIVATE_FORMINS | 0.014 | 0.077 | 0.397 |
| Adenoma | 15 | REACTOME_METABOLISM_OF_NUCLEOTIDES | 0.000 | 0.072 | 0.397 |
| Adenoma | 16 | REACTOME_REGULATION_OF_RAS_BY_GAPS | 0.002 | 0.068 | 0.403 |
| Adenoma | 17 | REACTOME_PROTEIN_FOLDING | 0.002 | 0.065 | 0.409 |
| Adenoma | 18 | SA_G1_AND_S_PHASES | 0.002 | 0.063 | 0.412 |
| Adenoma | 19 | REACTOME_TELOMERE_MAINTENANCE | 0.000 | 0.061 | 0.419 |
| Adenoma | 20 | REACTOME_TP53_REGULATES_TRANSCRIPTION_OF_GENES_INVOLVED_IN_G2_CELL_CYCLE_ARREST | 0.000 | 0.059 | 0.421 |
| B | |||||
| Adenoma | 125 | REACTOME_DEGRADATION_OF_BETA_CATENIN_BY_THE_DESTRUCTION_COMPLEX | 0.018 | 0.036 | 0.724 |
| Adenoma | 257 | REACTOME_TCF_DEPENDENT_SIGNALING_IN_RESPONSE_TO_WNT | 0.015 | 0.046 | 0.914 |
| Adenoma | 387 | REACTOME_SIGNALING_BY_WNT | 0.055 | 0.179 | 1.000 |
| Adenoma | 482 | PID_BETA_CATENIN_DEG_PATHWAY | 0.227 | 0.363 | 1.000 |
| Adenoma | 496 | PID_BETA_CATENIN_NUC_PATHWAY | 0.244 | 0.393 | 1.000 |
| Adenoma | 507 | REACTOME_FORMATION_OF_THE_BETA_CATENIN_TCF_TRANSACTIVATING_COMPLEX | 0.324 | 0.420 | 1.000 |
| Adenoma | 540 | WNT_SIGNALING | 0.330 | 0.463 | 1.000 |
| Adenoma | 546 | KEGG_WNT_SIGNALING_PATHWAY | 0.334 | 0.475 | 1.000 |
| Adenoma | 561 | REACTOME_DEACTIVATION_OF_THE_BETA_CATENIN_TRANSACTIVATING_COMPLEX | 0.405 | 0.483 | 1.000 |
| Adenoma | 568 | BIOCARTA_WNT_PATHWAY | 0.425 | 0.487 | 1.000 |
| Adenoma | 652 | REACTOME_SIGNALING_BY_WNT_IN_CANCER | 0.792 | 0.764 | 1.000 |
| C | |||||
| Normal | 1 | KEGG_NITROGEN_METABOLISM | 0.000 | 0.178 | 0.095 |
| Normal | 2 | KEGG_ALDOSTERONE_REGULATED_SODIUM_REABSORPTION | 0.000 | 0.242 | 0.209 |
| Normal | 3 | KEGG_PROXIMAL_TUBULE_BICARBONATE_RECLAMATION | 0.006 | 0.216 | 0.263 |
| Normal | 4 | KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION | 0.002 | 0.260 | 0.351 |
| Normal | 5 | REACTOME_NITRIC_OXIDE_STIMULATES_GUANYLATE_CYCLASE | 0.000 | 0.241 | 0.380 |
| Normal | 6 | REACTOME_PLATELET_HOMEOSTASIS | 0.000 | 0.206 | 0.383 |
| Normal | 7 | KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION | 0.000 | 0.183 | 0.391 |
| Normal | 8 | REACTOME_DIGESTION | 0.000 | 0.181 | 0.412 |
| Normal | 9 | REACTOME_GLUCAGON_LIKE_PEPTIDE_1_GLP1_REGULATES_INSULIN_SECRETION | 0.000 | 0.163 | 0.415 |
| Normal | 10 | REACTOME_DIGESTION_AND_ABSORPTION | 0.000 | 0.148 | 0.418 |
| Normal | 11 | REACTOME_GLUCAGON_SIGNALING_IN_METABOLIC_REGULATION | 0.000 | 0.147 | 0.433 |
| Normal | 12 | REACTOME_SUMOYLATION_OF_INTRACELLULAR_RECEPTORS | 0.000 | 0.144 | 0.444 |
| Normal | 13 | REACTOME_FCGR3A_MEDIATED_IL10_SYNTHESIS | 0.004 | 0.137 | 0.451 |
| Normal | 14 | REACTOME_AQUAPORIN_MEDIATED_TRANSPORT | 0.000 | 0.131 | 0.455 |
| Normal | 15 | REACTOME_STIMULI_SENSING_CHANNELS | 0.000 | 0.131 | 0.470 |
| Normal | 16 | REACTOME_FOXO_MEDIATED_TRANSCRIPTION | 0.004 | 0.140 | 0.495 |
| Normal | 17 | REACTOME_RHO_GTPASES_ACTIVATE_PAKS | 0.002 | 0.151 | 0.533 |
| Normal | 18 | NABA_ECM_GLYCOPROTEINS | 0.006 | 0.154 | 0.547 |
| Normal | 19 | REACTOME_BINDING_AND_UPTAKE_OF_LIGANDS_BY_SCAVENGER_RECEPTORS | 0.002 | 0.152 | 0.558 |
| Normal | 20 | REACTOME_CREATION_OF_C4_AND_C2_ACTIVATORS | 0.006 | 0.151 | 0.573 |
| D | |||||
| Normal | 406 | PID_WNT_CANONICAL_PATHWAY | 0.200 | 0.401 | 1.000 |
| Normal | 672 | PID_WNT_SIGNALING_PATHWAY | 0.534 | 0.619 | 1.000 |
| Normal | 783 | REACTOME_BETA_CATENIN_PHOSPHORYLATION_CASCADE | 0.777 | 0.804 | 1.000 |
| Normal | 791 | REACTOME_WNT_LIGAND_BIOGENESIS_AND_TRAFFICKING | 0.852 | 0.837 | 1.000 |
| Normal | 792 | REACTOME_WNT5A_DEPENDENT_INTERNALIZATION_OF_FZD4 | 0.829 | 0.836 | 1.000 |
(A) 20 most upregulated pathways in colonadenomas. (B) Canonical Wnt-related pathways upregulated in colon adenomas. (C) 20 most upregulated pathways in normal colon samples. (D) Canonical Wnt-related pathways upregulated in normal colon samples. Per pathway the rank is given in the list of upregulated pathways (position), the nominal p-value (nom.p), false-discovery-rate corrected p-value (fdr.q), and the family-wise error corrected p-value (fwer.q).