Table 6.
EDDY Analysis of the PAH Transcriptome
| Pathway | DB | No. Genes | P Value | JS | New Dependency | Rewiring | Essentiality Mediators | Specificity Mediators |
|---|---|---|---|---|---|---|---|---|
| Formation of ATP by chemiosmotic coupling | R | 16 | 0.0053 | 0.9675 | 0 | 0.62 | ATP5H ATP5A1 ATP5C1 ATP5B | — |
| Mitochondrial tRNA aminoacylation | R | 21 | 0.0084 | 0.9882 | 0.47 | 0.8 | VARS2 CARS2 HARS2 | — |
| TGF-β receptor signaling in EMT | R | 16 | 0.0104 | 0.9441 | 0 | 0.79 | ARHGEF18 CGN | — |
| Translocation of ZAP70 to immunological synapse | R | 14 | 0.0164 | 0.922 | 0 | 0.46 | HLA-DQA1 ZAP70 | CD3E CD4 |
| RNA Pol I transcription initiation | R | 25 | 0.0231 | 0.9705 | 0.08 | 0.72 | GTF2H3 CDK7 GTF2H4 | RRN3 |
| CDC6 association with the ORC origin complex | R | 11 | 0.0268 | 0.9471 | 0.14 | 0.75 | ORC1 | — |
| DCC-mediated attractive signaling | R | 13 | 0.0296 | 0.9604 | 0.04 | 0.67 | DOCK1 WASL NTN1 | — |
| Amino acid synthesis and interconversion transamination | R | 17 | 0.0337 | 0.9196 | 0.65 | 0.68 | PYCR1 PHGDH | — |
| Activation of IRF3/IRF7 mediated by TBK1 IKKϵ | R | 14 | 0.0341 | 0.9647 | 0.05 | 0.89 | TLR3 TICAM1 RPS27A | — |
| tRNA aminoacylation | R | 42 | 0.0342 | 0.9669 | 0.42 | 0.57 | DARS MARS VARS2 YARS YARS2 EPRS | CARS2 MARS2 TARS2 VARS2 SARS2 NARS2 FARS2 PARS2 IARS2 LARS2 WARS2 AARS2 QARS |
| Resolution of AP sites via the single nucleotide replacement | R | 12 | 0.0348 | 0.9819 | 0.43 | 1 | MPG LIG3 | — |
| mRNA decay by 3 to 5 exornase | R | 11 | 0.0382 | 0.938 | 0.06 | 0.71 | EXOSC6 | — |
| Regulation of hypoxia inducible factor HIF by oxygen | R | 25 | 0.0383 | 0.9864 | 0.14 | 0.78 | RBX1 CREBBP HIF3A | — |
| Phosphorylation of CD3 and TCRζ chains | R | 16 | 0.0421 | 0.8915 | 0 | 0.57 | LCK CD4 | CD3E |
| Activated TAK1 mediates p38 MAPK activation | R | 18 | 0.0482 | 0.9482 | 0.16 | 0.75 | RIPK2 MAP3K7 IRAK2 | — |
| mTORC1-mediated signaling | R | 11 | 0.0489 | 0.9736 | 0.12 | 0.81 | EIF4E |
Definition of abbreviations: AP = apurinic/apyrimidinic; DB = database; DCC = deleted in colorectal cancer; EDDY = Evaluation of Differential DependencY; EMT = epithelial-to-mesenchymal transition; HIF = hypoxia-inducible factor; IRF = IFN-regulatory factor; JS = Jensen-Shannon divergence estimate; MAPK = mitogen-activated protein kinase; mTORC = mTOR complex; ORC = origin complex; Pol = polymerase; TAK = mitogen-activated protein kinase kinase kinase 7 (MAP3K7/TAK1); TBK = TANK binding kinase; TCRζ = T-cell receptor; ZAP = Zeta chain of T cell receptor associated protein kinase 70.