Table 1.
Gene ontology-based analyses of epithelial ovarian cancer (EOC)-related RUNX3 core and transcript variant (TV)-specific pathways.
| Gene Category a | Affected Pathways | n genes | % | p-Value | FDR | Genes b |
|---|---|---|---|---|---|---|
| I RUNX3 core (46 genes) |
GO:0001764~neuron migration | 4 | 9.09 | 0.0018 | >0.05 | GATA2, TUBB2B, NAV1, DDIT4 |
| GO:0030574~collagen catabolic process | 3 | 6.82 | 0.0097 | >0.05 | COL6A2, COL15A1, COL5A1 | |
| GO:0030198~extracellular matrix organization | 4 | 9.09 | 0.0105 | >0.05 | ITGA5, SERPINE1, COL6A2, COL5A1 | |
| GO:0001525~angiogenesis | 4 | 9.09 | 0.0149 | >0.05 | NRP2, ITGA5, SERPINE1, COL15A1 | |
| GO:0035313~wound healing | 2 | 4.55 | 0.0207 | >0.05 | ITGA5, COL5A1 | |
| GO:0007155~cell adhesion | 5 | 11.36 | 0.0213 | >0.05 | NRP2, ITGA5, COL6A2, COL15A1, COL5A1 | |
| GO:0031589~cell–substrate adhesion | 2 | 4.55 | 0.0388 | >0.05 | CORO1A, ITGA5 | |
| I TV1-regulated (core+6 genes) |
GO:0007165~signal transduction | 8 | 16.33 | 0.0238 | >0.05 | PSD, ARRB1, TLR1, PDE5A, SRGAP3, COL15A1, GDF15, DAPK1 |
| I TV2-regulated (core+7 genes) |
GO:0030198~extracellular matrix organization | 5 | 9.8 | 0.0018 | >0.05 | ITGA5, SERPINE1, COL6A2, CDH1, COL5A1 |
| GO:0048565~digestive tract development | 3 | 5.88 | 0.0039 | >0.05 | GATA2, FAT4, DCHS1 | |
| GO:0007157~heterophilic cell–cell adhesion | 3 | 5.88 | 0.0079 | >0.05 | FAT4, ITGA5, DCHS1 | |
| GO:0072137~mesenchymal cell proliferation | 2 | 3.92 | 0.0080 | >0.05 | FAT4, DCHS1 | |
| GO:0007156~homophilic cell adhesion | 4 | 7.84 | 0.0087 | >0.05 | DCHS2, FAT4, CDH1, DCHS1 | |
| GO:0043931~ossification in bone maturation | 2 | 3.92 | 0.0186 | >0.05 | FAT4, DCHS1 | |
| II TV1/2 DEG (1070 genes) |
GO:0043062~extracellular structure organization | 91 | 8.50 | 0 | 0 | CDH1, FN1, PDGFB, PECAM1, TNXB |
| GO:0050673~epithelial cell proliferation | 73 | 6.82 | 2.22 × 10−15 | 9.43 × 10−13 | CCL2, FGF1, GATA2, NGFR. WNT5A | |
| GO:0001525~angiogenesis | 84 | 7.85 | 3.99 × 10−14 | 1.05 × 10−11 | ANGPT1, EGF, GJA5, THBS2, VEGFC | |
| GO:0002009~morphogenesis of an epithelium | 83 | 7.76 | 4.95 × 10−14 | 1.05 × 10−11 | AREG, DLG3, ESRP2, VDR, WT1 | |
| GO:0001667~ameboidal-type cell migration | 71 | 6.64 | 8.37 × 10−14 | 1.42 × 10−11 | ANXA6, DPP4, MEF2C, TACSTD2, TWIST1 | |
| GO:0043588~skin development | 73 | 6.82 | 3.53 × 10−13 | 5.00 × 10−11 | BCL2, CDH3, DSC2, KDF1, KRT | |
| GO:0061564~axon development | 81 | 7.57 | 1.21 × 10−12 | 1.47 × 10−10 | APOE,CRABP2, CXCL12, GDNF, NCAM1 | |
| GO:0090130~tissue migration | 56 | 5.23 | 3.12 × 10−12 | 3.31 × 10−10 | ADAMTS9, CDH13, SEMA5A, SLIT2, ZEB2 | |
| GO:0001655~urogenital system development | 60 | 5.61 | 1.27 × 10−11 | 1.16 × 10−9 | ACE, AR, ESR1, FOXB1, IRX3 | |
| GO:0034330~cell junction organization | 55 | 5.14 | 1.37 × 10−11 | 1.16 × 10−9 | CADM1, GJA1, JUP, OCLN, PKP1 |
a Category I: Genes dysregulated in both cell-lines, RUNX3 core genes are affected by both TV, whereas the TV-specific pathways are dysregulated by a specific TV, Category II: All differentially expressed genes (DEG) between cells overexpressing RUNX3 TV1 or TV2 in A2780 or A13-2-12, b Genes specifically regulated by TV1 or TV2 are marked in bold, For category II only 5 genes of each pathway are named exemplarily (complete lists in Supplementary Table S7).