Table 2.
Top pathway-centric supermodules with at least 3 pathway overlapping genes (with 10 repeats with different initial modules)
| (A) Pathway name (ER+ versus ER-) | Pathway size | Module size | # pathway genes | q-value | P-value | Module |
|---|---|---|---|---|---|---|
| REACTOME_COMPLEMENT_CASCADE | 32 | 25 | 4 | 2.14E-05 | 1.93E-07 | H7,H8 |
| GO_IMMUNE_RESPONSE | 235 | 28 | 7 | 5.63E-05 | 1.33E-06 | H9,L1,L2 |
| REACTOME_REGULATION_OF_COMPLEMENT_CASCADE | 14 | 25 | 3 | 5.63E-05 | 2.47E-06 | H7,H8 |
| GO_ORGAN_MORPHOGENESIS | 144 | 35 | 6 | 5.63E-05 | 2.80E-06 | H3,H5,L9 |
| BIOCARTA_TCYTOTOXIC_PATHWAY | 14 | 23 | 3 | 5.63E-05 | 2.85E-06 | H3,L5 |
| (B) Pathway name (ILC versus IDC) |
Pathway size | Module size | # pathway genes | q-value | P-value | Module |
|---|---|---|---|---|---|---|
| GO_PROTEASE_INHIBITOR_ACTIVITY | 41 | 27 | 3 | 0.003 | 6.13E-05 | L2,L4,L8 |
| GO_PROTEINACEOUS_EXTRACELLULAR_MATRIX | 98 | 15 | 3 | 0.003 | 0.00085 | L5,L7 |
| GO_EXTRACELLULAR_MATRIX | 100 | 15 | 3 | 0.003 | 0.00085 | L5,L7 |
Module starts with H indicates it is more densely connected in ER+ or ILC network, while module starts with L indicates it is more densely connected in ER- or IDC network.