Table S2.
Data-driven nodes that were predicted as HYPs by RCR on the GSE6206, E-MEXP-1968, GSE13330 RS, GSE13330 SIPS, and GSE19018 building data sets.
| Data-Driven Nodes Added to DACS Network | Expected Direction | DNA Damage Data Sets | Senescence Data Sets | Submode I | |||
|---|---|---|---|---|---|---|---|
| GSE6206 | E-MEXP-1968 | GSE13330 RS | GSE13330 SIPS | GSE19018 | |||
| ATF2 | DNA Damage—Double—strand break response | ||||||
| BACH1 | Senescence—Stress—induced premature senescence | ||||||
| BIRC5 | Apoptosis—NFKB signaling | ||||||
| BNIP3L | Senescence—Oncogene—induced senescence | ||||||
| catof(proteasome complex (sensu Eukarya) Hs) | Senescence—Stress—induced premature senescence | ||||||
| catof(PTGS2) | Senescence—Stress—induced premature senescence | ||||||
| CCL5 | Senescence—Transcriptional regulation of the SASP | ||||||
| CCND1 | DNA Damage—Double—strand break response | ||||||
| CTNNB1 | Senescence—Regulation by tumor suppressors | ||||||
| DDIT3 | Apoptosis—ER stress—induced apoptosis | ||||||
| DNMT3A | Senescence—Replicative senescence | ||||||
| ENO1 | Senescence—Regulation by tumor suppressors | ||||||
| EP300 | Apoptosis—MAPK signaling | ||||||
| ETS2 | Senescence—Oncogene—induced senescence | ||||||
| FHIT | DNA Damagee—single—strand break response | ||||||
| gtpof(RAC1) | Apoptosis—MAPK signaling | ||||||
| gtpof(RHOA) | DNA Damagee—single—strand break response | ||||||
| gtpof(RHOB) | DNA Damagee—single—strand break response | ||||||
| HDAC1 | Senescence—Regulation by tumor suppressors | ||||||
| HDAC3 | Senescence—Regulation of p16INK expression | ||||||
| IFNA1 | Senescence—Regulation by tumor suppressors | ||||||
| IL1A | Senescence—Transcriptional regulation of the SASP | ||||||
| IRF1 | Senescence—Regulation by tumor suppressors | ||||||
| IRF3 | Senescence—Regulation by tumor suppressors | ||||||
| IRF5 | Senescence—Replicative senescence | ||||||
| kaof(MAP2K1) | Senescence—Oncogene—induced senescence | ||||||
| kaof(PKC Family Hs) | Apoptosis—PKC signaling | ||||||
| kaof(RAF1) | Senescence—Oncogene—induced senescence | ||||||
| MAP2K1 | Senescence—Oncogene—induced senescence | ||||||
| MYC | DNA Damage—Double—strand break response | ||||||
| PKC Family Hs | Apoptosis—PKC signaling | ||||||
| PPARG | Senescence—Regulation of p16INK expression | ||||||
| proteasome complex (sensu Eukarya) Hs | Senescence—Stress—induced premature senescence | ||||||
| PTGS2 | Senescence—Stress—induced premature senescence | ||||||
| RAC1 | Apoptosis—MAPK signaling | ||||||
| RAF1 | Senescence—Oncogene—induced senescence | ||||||
| RASSF1 | DNA Damage—Double—strand break response | ||||||
| RHOA | DNA Damage—Double—strand break response | ||||||
| RHOB | DNA Damage—Double—strand break response | ||||||
| SMARCB1 | Senescence—Regulation of p16INK expression | ||||||
| SP1 | Senescence—Regulation of p16INK expression | ||||||
| taof(ATF2) | DNA Damage—Double—strand break response | ||||||
| taof(BACH1) | Senescence—Stress—induced premature senescence | ||||||
| taof(CTNNB1) | Senescence—Regulation by tumor suppressors | ||||||
| taof(EP300) | Apoptosis—MAPK signaling | ||||||
| taof(ETS2) | Senescence—Oncogene—induced senescence | ||||||
| taof(IRF1) | Senescence—Regulation by tumor suppressors | ||||||
| taof(IRF3) | Senescence—Regulation by tumor suppressors | ||||||
| taof(IRF5) | Senescence—Replicative senescence | ||||||
| taof(PPARG) | Senescence—Regulation of p16INK expression | ||||||
| taof(SP1) | Senescence—Regulation of p16INK expression | ||||||
| taof(TFDP1) | Senescence—Regulation by tumor suppressors | ||||||
| taof(TP63) | DNA Damage—Componenets affecting TP63 activity | ||||||
| taof(TP73) | DNA Damage—Componenets affecting TP73 activity | ||||||
| taof(XBP1) | Apoptosis—ER stress—induced apoptosis | ||||||
| taof(YY1) | DNA Damage—Componenets affecting TP53 activity | ||||||
| TFDP1 | Senescence—Regulation by tumor suppressors | ||||||
| TP63 | DNA Damage—Componenets affecting TP63 activity | ||||||
| TP73 | DNA Damage—Componenets affecting TP73 activity | ||||||
| TWIST1 | Senescence—Stress—induced premature senescence | ||||||
| VHL | Senescence—Stress—induced premature senescence | ||||||
| XBP1 | Apoptosis—ER stress—induced apoptosis | ||||||
| YY1 | DNA Damage—Componenets affecting TP53 activity | ||||||
Notes: These data-driven nodes were added to the indicated submodels of the DACS Network based on their mechanistic connections to the processes reflected by the submodels. Expected direction is based on internal causality of the indicated submodels. Yellow = predicted increase in abundance or activity, blue = predicted decrease in abundance or activity.
Abbreviations: catof(X), catalytic activity of X; gtpof(X), GTP-bound activity of X; kaof(X), kinase activity of X; taof(X), transcriptional activity of X.