Table 1. Relevant gene sets grouped in functional modules.
| Functional module | Gene set name | Collection | Size | NES | NOM P-value | FDR q-value |
|---|---|---|---|---|---|---|
| MDM4 p53 target |
MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP |
C2 |
83 |
1.952 |
0.000 |
0.042 |
| |
MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_UP |
C2 |
79 |
1.676 |
0.000 |
0.131 |
| Response to growth factor |
AMIT_EGF_RESPONSE_40_HELA |
C2 |
40 |
1.879 |
0.000 |
0.064 |
| |
AMIT_EGF_RESPONSE_480_MCF10A |
C2 |
35 |
1.781 |
0.000 |
0.126 |
| |
ST_ERK1_ERK2_MAPK_PATHWAY |
C2 |
26 |
1.775 |
0.000 |
0.121 |
| |
AMIT_SERUM_RESPONSE_40_MCF10A |
C2 |
27 |
1.749 |
0.000 |
0.116 |
| |
AMIT_EGF_RESPONSE_60_MCF10A |
C2 |
34 |
1.740 |
0.000 |
0.122 |
| |
REACTOME_MAPK_TARGETS_NUCLEAR_EVENTS_MEDIATED_BY_MAP_KINASES |
C2 |
24 |
1.722 |
0.000 |
0.110 |
| Cytokine stimulation |
CYTOKINE_METABOLIC_PROCESS |
C5 |
17 |
1.693 |
0.000 |
0.121 |
| |
CYTOKINE_BIOSYNTHETIC_PROCESS |
C5 |
16 |
1.686 |
0.000 |
0.112 |
| |
CYTOKINE_ACTIVITY |
C5 |
31 |
1.749 |
0.000 |
0.097 |
| Angiogenesis |
VASCULATURE_DEVELOPMENT |
C5 |
31 |
1.813 |
0.000 |
0.079 |
| |
ANGIOGENESIS |
C5 |
26 |
1.666 |
0.000 |
0.132 |
| |
REGULATION_OF_ANGIOGENESIS |
C5 |
15 |
1.748 |
0.000 |
0.083 |
| Hypoxia |
WINTER_HYPOXIA_UP |
C2 |
80 |
1.813 |
0.000 |
0.117 |
| |
MANALO_HYPOXIA_UP |
C2 |
142 |
1.751 |
0.000 |
0.124 |
| |
JIANG_HYPOXIA_NORMAL |
C2 |
184 |
1.734 |
0.000 |
0.107 |
| |
HARRIS_HYPOXIA |
C2 |
61 |
1.731 |
0.000 |
0.106 |
| |
WINTER_HYPOXIA_METAGENE |
C2 |
172 |
1.718 |
0.000 |
0.112 |
| ATM target |
RASHI_RESPONSE_TO_IONIZING_RADIATION_1 |
C2 |
31 |
1.897 |
0.000 |
0.074 |
| Histone |
REACTOME_TELOMERE_MAINTENANCE |
C2 |
55 |
1.710 |
0.000 |
0.115 |
| Chemotaxis |
LOCOMOTORY_BEHAVIOR |
C5 |
31 |
1.595 |
0.000 |
0.176 |
| |
BEHAVIOR |
C5 |
45 |
1.599 |
0.000 |
0.178 |
| |
THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_UP |
C2 |
59 |
1.735 |
0.000 |
0.119 |
| Stat3 |
DAUER_STAT3_TARGETS_UP |
C2 |
31 |
1.714 |
0.000 |
0.114 |
| Acid-base balance |
CARBON_OXYGEN_LYASE_ACTIVITY |
C5 |
22 |
1.647 |
0.000 |
0.147 |
| HYDRO_LYASE_ACTIVITY | C5 | 18 | 1.637 | 0.000 | 0.136 |
Abbreviations: C2=curated gene collection; C5=gene ontology collection; FDR=false discovery rate; NES=normalised enrichment score.
The table reports the most relevant upregulated gene sets (P-value<0.01 and FDR<0.25) connected with bone metastatic process.