Table 2.
Top 20 pathways in the 500 signatures of ER-positive and ER-negative tumors evaluated by Global Test
| Pathways | GO_ID | P | Frequency |
| ER-positive tumors | |||
| Apoptosis | 6915 | 3.06E-7 | 250 |
| Regulation of cell cycle | 74 | 2.46E-5 | 203 |
| Protein amino acid phosphorylation | 6468 | 2.48E-5 | 114 |
| Cytokinesis | 910 | 6.13E-5 | 165 |
| Cell motility | 6928 | 0.00015 | 93 |
| Cell cycle | 7049 | 0.00028 | 138 |
| Cell surface receptor-linked signal transd. | 7166 | 0.00033 | 172 |
| Mitosis | 7067 | 0.00036 | 256 |
| Intracellular protein transport | 6886 | 0.00054 | 141 |
| Mitotic chromosome segregation | 70 | 0.00057 | 98 |
| Ubiquitin-dependent protein catabolism | 6511 | 0.00074 | 158 |
| DNA repair | 6281 | 0.00079 | 156 |
| Induction of apoptosis | 6917 | 0.00083 | 115 |
| Immune response | 6955 | 0.00094 | 167 |
| Protein biosynthesis | 6412 | 0.0010 | 145 |
| DNA replication | 6260 | 0.0015 | 92 |
| Oncogenesis | 7048 | 0.0020 | 228 |
| Metabolism | 8152 | 0.0021 | 83 |
| Cellular defense response | 6968 | 0.0025 | 131 |
| Chemotaxis | 6935 | 0.0027 | 89 |
| ER-negative tumors | |||
| Regulation of cell growth | 1558 | 0.00012 | 136 |
| Regul. of G-coupled receptor signaling | 8277 | 0.00013 | 153 |
| Skeletal development | 1501 | 0.00024 | 160 |
| Protein amino acid phosphorylation | 6468 | 0.0051 | 151 |
| Cell adhesion | 7155 | 0.0065 | 110 |
| Carbohydrate metabolism | 5975 | 0.0066 | 86 |
| Nuclear mRNA splicing, via spliceosome | 398 | 0.0067 | 203 |
| Signal transduction | 7165 | 0.0078 | 160 |
| Cation transport | 6812 | 0.0098 | 160 |
| Calciumion transport | 6816 | 0.010 | 93 |
| Protein modification | 6464 | 0.011 | 132 |
| Intracellular signaling cascade | 7242 | 0.012 | 135 |
| mRNA processing | 6397 | 0.012 | 81 |
| RNA splicing | 8380 | 0.014 | 192 |
| Endocytosis | 6897 | 0.026 | 166 |
| Regul. of transcription from PolII promoter | 6357 | 0.031 | 109 |
| Regulation of cell cycle | 74 | 0.043 | 88 |
| Protein complex assembly | 6461 | 0.048 | 183 |
| Protein biosynthesis | 6412 | 0.063 | 99 |
| Cell cycle | 7049 | 0.084 | 72 |
Each of the top 20 over-represented pathways that have the highest frequencies in the 500 signatures of ER-positive and ER-negative tumors were subjected to Global Test program [12, 14]. The Global Test examines the association of a group of genes as a whole to a specific clinical parameter, in this case DMFS, and generates an asymptotic theory p value for the pathway. The pathways are ranked by their p value in the respective ER-subgroup of tumors.