1. Ajani, J. A. et al. Gastric adenocarcinoma. Nat Rev Dis Primers 3, 1–19 (2017).
2. Smith, M.-G., Hold, G.-L., Tahara, E. & El-Omar, E.-M. Cellular and molecular aspects of gastric cancer. World J Gastroenterol 12, 2979–2990 (2006).
3. Zheng, H., Wang, J.-J., Yang, X.-R. & Yu, Y.-L. Upregulation of miR-34c after silencing E2F transcription factor 1 inhibits paclitaxel combined with cisplatin resistance in gastric cancer cells. World J Gastroenterol 26, 499–513 (2020).
4. Salzman, D. W. et al. miR-34 activity is modulated through 5’-end phosphorylation in response to DNA damage. Nat Commun 7, 10954 (2016).
5. Cannell, I. G. et al. p38 MAPK/MK2-mediated induction of miR-34c following DNA damage prevents Myc-dependent DNA replication. PNAS 107, 5375–5380 (2010).
6. Suzuki, H. et al. Methylation-associated silencing of microRNA-34b/c in gastric cancer and its involvement in an epigenetic field defect. Carcinogenesis 31, 2066–2073 (2010).
7. Liu, Z.-M. et al. Upregulation of heme oxygenase-1 and p21 confers resistance to apoptosis in human gastric cancer cells. Oncogene 23, 503–513 (2004).
8. Subhash, V. V. et al. ATM Expression Predicts Veliparib and Irinotecan Sensitivity in Gastric Cancer by Mediating P53-Independent Regulation of Cell Cycle and Apoptosis. Mol Cancer Ther 15, 3087–3096 (2016).
9. Zhao, J., Lammers, P., Torrance, C. J. & Bader, A. G. TP53-independent function of miR-34a via HDAC1 and p21(CIP1/WAF1.). Mol Ther 21, 1678–1686 (2013).
10. Birney, E. et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816 (2007).
11. Guttman, M. et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223–227 (2009).
12. Cui, L. et al. Gastric juice MicroRNAs as potential biomarkers for the screening of gastric cancer. Cancer 119, 1618–1626 (2013).
13. Gu, Y. et al. LncRNAs: emerging biomarkers in gastric cancer. Future Oncol 11, 2427–2441 (2015).
14. Liu, Y. et al. lncRNA GAS5 enhances G1 cell cycle arrest via binding to YBX1 to regulate p21 expression in stomach cancer. Sci Rep 5, 10159 (2015).
15. Sun, M. et al. Decreased expression of long noncoding RNA GAS5 indicates a poor prognosis and promotes cell proliferation in gastric cancer. BMC Cancer 14, 319 (2014).
16. Schwab, J. D., Kühlwein, S. D., Ikonomi, N., Kühl, M. & Kestler, H. A. Concepts in Boolean network modeling: What do they all mean? Computational and Structural Biotechnology Journal 18, 571–582 (2020).
17. Rozum, J. C., Gómez Tejeda Zañudo, J., Gan, X., Deritei, D. & Albert, R. Parity and time reversal elucidate both decision-making in empirical models and attractor scaling in critical Boolean networks. Sci Adv 7, eabf8124 (2021).
18. Thomas, R., Thieffry, D. & Kaufman, M. Dynamical behaviour of biological regulatory networks--I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state. Bull Math Biol 57, 247–276 (1995).
19. Deritei, D., Rozum, J., Ravasz Regan, E. & Albert, R. A feedback loop of conditionally stable circuits drives the cell cycle from checkpoint to checkpoint. Sci Rep 9, 16430 (2019).
20. Silveira, D. A., Gupta, S. & Mombach, J. C. M. Systems biology approach suggests new miRNAs as phenotypic stability factors in the epithelial-mesenchymal transition. J R Soc Interface 17, 20200693 (2020).
21. Gupta, S. & Hashimoto, R. F. Dynamical Analysis of a Boolean Network Model of the Oncogene Role of lncRNA ANRIL and lncRNA UFC1 in Non-Small Cell Lung Cancer. Biomolecules 12, 420 (2022).
22. Gupta, S., Silveira, D. A. & Mombach, J. C. M. Towards DNA-damage induced autophagy: A Boolean model of p53-induced cell fate mechanisms. DNA Repair 96, 102971 (2020).
23. Guberman, E., Sherief, H. & Regan, E. R. Boolean model of anchorage dependence and contact inhibition points to coordinated inhibition but semi-independent induction of proliferation and migration. Computational and Structural Biotechnology Journal 18, 2145–2165 (2020).
24. Wooten, D. J. et al. Mathematical modeling of the Candida albicans yeast to hyphal transition reveals novel control strategies. PLOS Computational Biology 17, e1008690 (2021).
25. Gupta, S., Silveira, D. A., Hashimoto, R. F. & Mombach, J. C. M. A Boolean Model of the Proliferative Role of the lncRNA XIST in Non-Small Cell Lung Cancer Cells. Biology 11, 480 (2022).
26. Gupta, S. et al. Dynamical modeling of miR-34a, miR-449a, and miR-16 reveals numerous DDR signaling pathways regulating senescence, autophagy, and apoptosis in HeLa cells. Sci Rep 12, 4911 (2022).
27. Zhang, Q. et al. By recruiting HDAC1, MORC2 suppresses p21Waf1/Cip1 in gastric cancer. Oncotarget 6, 16461–16470 (2015).
28. Wisnieski, F. et al. Differential expression of histone deacetylase and acetyltransferase genes in gastric cancer and their modulation by trichostatin A. Tumour Biol 35, 6373–6381 (2014).
29. Li, Y. et al. Long non-coding RNA growth arrest specific transcript 5 acts as a tumour suppressor in colorectal cancer by inhibiting interleukin-10 and vascular endothelial growth factor expression. Oncotarget 8, 13690–13702 (2017).
30. Liu, S.-D. et al. GAS5 promotes myocardial apoptosis in myocardial ischemia-reperfusion injury via upregulating LAS1 expression. Eur Rev Med Pharmacol Sci 22, 8447–8453 (2018).
31. Long, X. et al. Long non-coding RNA GAS5 inhibits DDP-resistance and tumor progression of epithelial ovarian cancer via GAS5-E2F4-PARP1-MAPK axis. J Exp Clin Cancer Res 38, 345 (2019).
32. Ke, K., Sun, Z. & Wang, Z. Downregulation of long non-coding RNA GAS5 promotes cell proliferation, migration and invasion in esophageal squamous cell carcinoma. Oncol Lett 16, 1801–1808 (2018).
33. Guo, X. et al. GAS5 Inhibits Gastric Cancer Cell Proliferation Partly by Modulating CDK6. Oncol Res Treat 38, 362–366 (2015).
34. Liu, X. & Hu, C. Novel Potential Therapeutic Target for E2F1 and Prognostic Factors of E2F1/2/3/5/7/8 in Human Gastric Cancer. Mol Ther Methods Clin Dev 18, 824–838 (2020).
35. Li, W. et al. The Long Noncoding RNA, Growth Arrest-Specific 5, Suppresses Gastric Cancer by Downregulating miR-21 Expression. Pharmacology 105, 434–444 (2020).
36. Dong, S., Zhang, X. & Liu, D. Overexpression of long noncoding RNA GAS5 suppresses tumorigenesis and development of gastric cancer by sponging miR-106a-5p through the Akt/mTOR pathway. Biol Open 8, bio041343 (2019).
37. Liu, Y., Yin, L., Chen, C., Zhang, X. & Wang, S. Long non-coding RNA GAS5 inhibits migration and invasion in gastric cancer via interacting with p53 protein. Dig Liver Dis 52, 331–338 (2020).
38. Frank, F. et al. The lncRNA Growth Arrest Specific 5 Regulates Cell Survival via Distinct Structural Modules with Independent Functions. Cell Rep 32, 107933 (2020).
39. Purvis, J. E. et al. p53 dynamics control cell fate. Science 336, 1440–1444 (2012).
40. Blanchet, A., Bourgmayer, A., Kurtz, J.-E., Mellitzer, G. & Gaiddon, C. Isoforms of the p53 Family and Gastric Cancer: A Ménage à Trois for an Unfinished Affair. Cancers (Basel) 13, 916 (2021).
41. Zhu, Q. et al. Irinotecan Induces Autophagy-Dependent Apoptosis and Positively Regulates ROS-Related JNK- and P38-MAPK Pathways in Gastric Cancer Cells. Onco Targets Ther 13, 2807–2817 (2020).
42. Shi, T., van Soest, D. M. K., Polderman, P. E., Burgering, B. M. T. & Dansen, T. B. DNA damage and oxidant stress activate p53 through differential upstream signaling pathways. Free Radic Biol Med 172, 298–311 (2021).
43. Cheng, Q. & Chen, J. Mechanism of p53 stabilization by ATM after DNA damage. Cell Cycle 9, 472–478 (2010).
44. Hu, H. & Gatti, R. A. MicroRNAs: new players in the DNA damage response. J Mol Cell Biol 3, 151–158 (2011).
45. NCBI Resource Coordinators. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 44, D7-19 (2016).
46. Oughtred, R. et al. The BioGRID interaction database: 2019 update. Nucleic Acids Res 47, D529–D541 (2019).
47. Hamberg, M. et al. MiRTargetLink--miRNAs, Genes and Interaction Networks. Int J Mol Sci 17, 564 (2016).
48. Agarwal, V., Bell, G. W., Nam, J.-W. & Bartel, D. P. Predicting effective microRNA target sites in mammalian mRNAs. Elife 4, (2015).
49. Naldi, A. et al. Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0. Front Physiol 9, 646 (2018).
50. Abou-Jaoudé, W. et al. Logical Modeling and Dynamical Analysis of Cellular Networks. Front Genet 7, 94 (2016).
51. Gupta, S., Silveira, D. A. & Mombach, J. C. M. Modeling the role of microRNA-449a in the regulation of the G2/M cell cycle checkpoint in prostate LNCaP cells under ionizing radiation. PLoS One 13, e0200768 (2018).
52. Gupta, S., Silveira, D. A. & Mombach, J. C. M. ATM/miR-34a-5p axis regulates a p21-dependent senescence-apoptosis switch in non-small cell lung cancer: a Boolean model of G1/S checkpoint regulation. FEBS Lett 594, 227–239 (2020).
53. Zhou, Y. & Chen, B. GAS5‑mediated regulation of cell signaling (Review). Mol Med Rep 22, 3049–3056 (2020).
54. Sancar, A., Lindsey-Boltz, L. A., Unsal-Kaçmaz, K. & Linn, S. Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. Annu Rev Biochem 73, 39–85 (2004).
55. Bakkenist, C. J. & Kastan, M. B. DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation. Nature 421, 499–506 (2003).
56. Zhang, X.-P., Liu, F. & Wang, W. Two-phase dynamics of p53 in the DNA damage response. Proc Natl Acad Sci U S A 108, 8990–8995 (2011).
57. Hermeking, H. The miR-34 family in cancer and apoptosis. Cell Death Differ 17, 193–199 (2010).
58. Xiong, S., Hu, M., Li, C., Zhou, X. & Chen, H. Role of miR‑34 in gastric cancer: From bench to bedside (Review). Oncol Rep 42, 1635–1646 (2019).
59. Bi, E. et al. Oridonin induces growth inhibition and apoptosis in human gastric carcinoma cells by enhancement of p53 expression and function. Braz J Med Biol Res 51, e7599 (2018).