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{"sheet":"Sheet1","index":0,"n_rows":140,"n_cols":7,"rows_kept":140,"merged":[[0,1,4,6],[5,1,6,2],[5,3,6,3],[5,4,6,4],[5,5,6,5],[5,6,6,6],[7,1,11,2],[7,3,9,3],[10,3,11,3],[10,4,11,5],[10,6,11,6],[12,1,14,2],[13,3,14,3],[13,4,14,5],[13,6,14,6],[15,1,17,2],[16,3,17,3],[16,4,17,5],[16,6,17,6],[18,1,23,2],[18,3,20,3],[21,3,23,3],[21,4,23,5],[21,6,23,6],[24,1,29,2],[24,3,26,3],[27,3,29,3],[27,4,29,5],[27,6,29,6],[30,1,36,2],[30,3,33,3],[34,3,36,3],[34,4,36,5],[34,6,36,6],[37,1,43,2],[37,3,40,3],[41,3,43,3],[41,4,43,5],[41,6,43,6],[44,1,51,2],[44,3,48,3],[49,3,51,3],[49,4,51,5],[49,6,51,6],[52,1,58,2],[52,3,55,3],[56,3,58,3],[56,4,58,5],[56,6,58,6],[59,1,65,2],[59,3,62,3],[63,3,65,3],[63,4,65,5],[63,6,65,6],[66,1,70,2],[66,3,68,3],[69,3,70,3],[69,4,70,5],[69,6,70,6],[71,1,74,2],[71,3,72,3],[73,3,74,3],[73,4,74,5],[73,6,74,6],[75,1,77,2],[76,3,77,3],[76,4,77,5],[76,6,77,6],[78,1,86,2],[78,3,82,3],[83,3,86,3],[83,4,86,5],[83,6,86,6],[87,1,93,2],[87,3,90,3],[91,3,93,3],[91,4,93,5],[91,6,93,6],[94,1,100,2],[94,3,96,3],[98,3,100,3],[98,4,100,5],[98,6,100,6],[101,1,106,2],[101,3,103,3],[104,3,106,3],[104,4,106,5],[104,6,106,6],[107,1,112,2],[107,3,110,3],[111,3,112,3],[111,4,112,5],[111,6,112,6],[113,1,116,2],[113,3,114,3],[115,3,116,3],[115,4,116,5],[115,6,116,6],[117,1,120,2],[117,3,118,3],[119,3,120,3],[119,4,120,5],[119,6,120,6],[121,1,126,2],[121,3,123,3],[124,3,126,3],[124,4,126,5],[124,6,126,6],[127,1,131,2],[127,3,129,3],[130,3,131,3],[130,4,131,5],[130,6,131,6],[132,1,134,2],[133,3,134,3],[133,4,134,5],[133,6,134,6],[135,1,137,2],[136,3,137,3],[136,4,137,5],[136,6,137,6],[138,1,140,2],[139,3,140,3],[139,4,140,5],[139,6,140,6]]}
[null," Logical rules that control node states of the model in Fig. 1 (highlighted in green) in terms of the state of its regulators.  The left-hand side lists the official names of the molecules (target node) (highlighted in cream color), while the right-hand side lists the references of each upcoming interaction to the target node."]
[]
[]
[]
[]
[null," Oﬃcial names of the molecules ",null,"Target node","Interactions","Descriptions ","PuBMed References"]
[]
[null,"ATM serine/threonine kinase ",null,"ATM","DNA_Damage","DNA damage directly activates ATM","PMID: 31210753"]
[{"$nulls":4},"HDAC1","HDAC1 directly inhibits ATM","PMID: 23939379"]
[{"$nulls":4},"Wip1","Wip1 directly inhibits ATM","PMID: 17685927"]
[{"$nulls":3},"Rule","DNA_damage AND (NOT Wip1 OR NOT HDAC1)",null,"ATM can be activated in the occupation of DNA damage while in the absence of Wip1 and HDAC1."]
[]
[null,"\nMitogen-activated protein kinase 14",null,"p38 MAPK","ATM","ATM directly activates p38MAPK","PMID: 12970909"]
[{"$nulls":3},"Rule","ATM",null,"p38 MAPK can be activated in the presence of ATM."]
[]
[null,"Growth arrest-specific transcript",null,"lncRNA GAS5","DNA_damage","DNA damage can activates lncRNA GAS5","PMID: 32945519"]
[{"$nulls":3},"Rule","DNA damage",null,"lncRNA GAS5 can be activated upon DNA damage."]
[]
[null,"microRNA-34c",null,"miR-34c","ATM","ATM can activate miR-34c expression","PMID: 26996824"]
[{"$nulls":4},"p38 MAPK","p38 MAPK pathway can induces miR-34c","PMID: 20212154"]
[{"$nulls":4},"E2F1","E2F1 directly inhibits miR-34c expression","PMID: 32089626"]
[{"$nulls":3},"Rule","(ATM OR p38MAPK) AND NOT E2F1",null,"ATM and p38 MAPK can trigger the activation of miR-34c whereas E2F1 directly inhibits miR-34c expression."]
[]
[]
[null,"Histone deacetylase 1",null,"HDAC1","miR-34c","HDAC1 is a direct target of miR-34c","PMID: 23836017"]
[{"$nulls":4},"Sirt1","SIRT1  inhibits HDAC1 expression","PMID: 25950477"]
[{"$nulls":4},"DNA damage","DNA Damage directly inhibits HDAC1","PMID: 23088869"]
[{"$nulls":3},"Rule","(NOT miR-34c AND NOT Sirt1) OR NOT DNA_damage",null,"HDAC1 can be activated only in the absence of miR-34c or in the absence of Sirt1 and  in the absence of DNA Damage."]
[]
[]
[null,"Myc proto-oncogene protein",null,"Myc","miR-34c","Myc is a direct target of miR-34c","PMID: 20603603"]
[{"$nulls":4},"RB1","RB1 directly inhibits Myc expression","PMID: 28280720"]
[{"$nulls":4},"p21","p21 directly inhibits Myc ","PMID: 19440234"]
[{"$nulls":4},"p38MAPK","p38MAPK can activates Myc","PMID: 16365184"]
[{"$nulls":3},"Rule","(p38MAPK OR NOT miR_34c) AND NOT RB1 AND NOT p21",null,"Myc can be activated in the presence of p38 MAPK or the lack of miR-34c and the deficiency of RB1 and the lack of p21."]
[]
[]
[null,"Tumor supressor p53 protein",null,"p53","ATM","ATM activates p53 transcription","PMID: 27612029"]
[{"$nulls":4},"p38MAPK","p38MAPK activates p53","PMID: 29751559"]
[{"$nulls":4},"GAS5","lncRNA GAS5 induces p53 expression","PMID: 31530437"]
[{"$nulls":4},"Mdm2","Mdm2 inhibits p53","PMID: 20020415"]
[{"$nulls":3},"Rule","(ATM OR GAS5) AND NOT Mdm2 AND p38MAPK",null,"p53 activated in the presence of ATM or GAS5 and the presence of p388MAPK and the absence of Mdm2."]
[]
[]
[null,"E3 ubiquitin protein ligase homolog protein",null,"Mdm2","Wip1","Wip1 negatively regulates Mdm2","PMID: 17936559"]
[{"$nulls":4},"p53","p53 activates Mdm2","PMID: 12563309"]
[{"$nulls":4},"ATM","ATM inhibits Mdm2","PMID: 16082221"]
[{"$nulls":4},"RB1","RB1 directly inhibits Mdm2 expression","PMID: 10618708"]
[{"$nulls":4},"miR-34c","Mdm2 is direct target of miR-34c","PMID: 18451145"]
[{"$nulls":3},"Rule","(NOT Wip1 OR p53) AND NOT ATM AND NOT RB1 AND NOT miR_34c",null,"Mdm2 activated in the presence of p53 or the absence of Wip1 and the absence of ATM and the absence of RB1 and miR-34c."]
[]
[]
[null,"Tumor supressor p53 protein (Ser-15 and Ser-20)",null,"p53_A","Sirt1","Sirt1 inhibits p53","PMID: 20471503"]
[{"$nulls":4},"p53","p53 phosphorylated at Ser-15 and Ser-20","PMID: 21576488"]
[{"$nulls":4},"p53_K","p53 phosphorylated at Ser-46 inhibits Ser-15 and Ser-20","PMID: 21576488"]
[{"$nulls":4},"p53INP1","Control of p53 accumulation","PMID: 21576488"]
[{"$nulls":3},"Rule","NOT Sirt1 AND NOT p53K AND  (p53 OR NOT p53INP1)",null,"p53-A can be activated in the absence of Sirt1 and in the absence of p53-K or in the presence of p53-INP1 or in the presence of p53."]
[]
[]
[null,"Tumor supressor p53 protein (Ser-46)",null,"p53_K","Sirt1","Sirt1 inhibits p53","PMID: 20471503"]
[{"$nulls":4},"p53_A","p53 phosphorylated at Ser-46 ","PMID: 21576488"]
[{"$nulls":4},"p53","p53 phosphorylated at Ser-15 and Ser-20 inhibits Ser-46","PMID: 21576488"]
[{"$nulls":4},"Wip1","Wip1 inhibits p53","PMID: 27959454"]
[{"$nulls":3},"Rule","NOT p53_A AND (NOT Sirt_1 OR NOT Wip1) AND p53",null,"p53-K can be activated in the absence of p53-A and in the absence of Sirt1 or in the absence of Wip1 and in the presence of p53."]
[]
[]
[null,"Sirtuin 1",null,"Sirt1","E2F1","E2F1 activates Sirt1","PMID: 24020005"]
[{"$nulls":4},"miR-34c","Sirt1 is a directly target of miR-34c","PMID: 21946562"]
[{"$nulls":4},"HDAC1","HDAC1 inhibits Sirt1","PMID: 18193082"]
[{"$nulls":3},"Rule","E2F1 AND NOT (miR_34c AND HDAC1)",null,"Sirt1 can be activated in the presence of E2F1 and in the absence of miR-34c and in the absence of HDAC1."]
[]
[null,"Tumor protein p53 inducible nuclear protein 1",null,"p53INP1","p53_A","p53 Ser-15 and Ser-20 activate p53-INP1","PMID: 21576488"]
[{"$nulls":4},"p53_K","p53 Ser-46 activates p53-INP1","PMID: 21576488"]
[{"$nulls":3},"Rule","p53_A OR p53_K",null,"p53INP1 can be activated in the presence of p53-A or in the presence of p53-K."]
[]
[null,"Protein Phosphatase 1D",null,"Wip1","p53_A","p53 activates Wip1","PMID: 26883196"]
[{"$nulls":3},"Rule","p53_A ",null,"Wip1 can be activated in the presence of p53-A."]
[]
[null,"Cyclin-dependent kinase inhibitor 1A ",null,"p21","p53_A","p53 activates p21","PMID: 31416295"]
[{"$nulls":4},"HDAC1","Repression of HDAC1 activates p21 expression","PMID: 26794658"]
[{"$nulls":4},"Myc","Repression of Myc activates p21 expression","PMID: 27105536"]
[{"$nulls":4},"p38MAPK","p38MAPK can activates p21","PMID: 19528229"]
[{"$nulls":4},"Caspase","Caspase3 inhibits p21","PMID: 10022118"]
[{"$nulls":3},"Rule","p53_A OR  ((NOT HDAC1 OR NOT Myc) AND NOT Caspase AND p38MAPK)",null,"p21 can be activated in the presence of p53-A or in the absence of HDAC1 or in the absence of Myc and in the absence of Caspase3 and in the presence of p38MAPK."]
[]
[]
[]
[null,"Cell division cycle 25A",null,"Cdc25A","ATM","ATM directly inhibits Cdc25A","PMID: 22263797"]
[{"$nulls":4},"miR-34c","Cdc25A is a direct target of miR-34c","PMID: 25909221"]
[{"$nulls":4},"Myc","Myc directly activates Cdc25A","PMID: 8700224"]
[{"$nulls":4},"p38MAPK","p38MAPK inhibits Cdc25A expression","PMID: 22263797"]
[{"$nulls":3},"Rule","(NOT ATM AND NOT miR_34c AND Myc) OR NOT p38MAPK",null,"Cdc25A can be activated in the presence of Myc and in the absence of ATM and in the absence of miR-34a or in the absence of p388 MAPK."]
[]
[]
[null,"Cyclin-dependent kinases 4 and 6 complex/CyclinD1 ",null,"CDK46_CycD","Cdc25A","Cdc25A activates CDK46-CycD","PMID: 28192398"]
[{"$nulls":4},"p21","p21 directly inhibits CDK46-CycD","PMID: 21616632"]
[{"$nulls":4},"miR-34c","CDK46-CycD is a direct target of miR-34c","PMID: 28839212"]
[{"$nulls":4},"GAS5","CDK46-CycD is a direct target of lncRNA GAS5","PMID: 24884417"]
[{"$nulls":3},"Rule","Cdc25A AND NOT (miR_34a AND p21 AND GAS5)",null,"CDK46-CycD can be activated in the presence of Cdc25A and in the absence of miR-34a and in the absence of p21 and in the absence of GAS5."]
[]
[]
[null,"Cyclin-dependent kinases 2 and complex/CyclinE ",null,"CDK2_CycE","E2F1","E2F1 Activates CDK2-CycE","PMID: 29754146"]
[{"$nulls":4},"p21","p21 directly inhibits CDK2-CycE","PMID: 21616632"]
[{"$nulls":4},"miR-34c","CDK2-CycE is a direct target of miR-34c","PMID: 28839212"]
[{"$nulls":3},"Rule","E2F1 AND NOT miR_34a AND NOT p21 ",null,"CDK2-CycE can be activated in the presence of Cdc25A and in the presence of E2F1 and in the absence of miR-34a and in the absence of p21."]
[]
[]
[null,"Retinoblastoma 1 protein",null,"RB1","CDK46_CycD","CDK46-CycD directly inhibits RB","PMID: 12362273"]
[{"$nulls":4},"CDK2_CycE","CDK2-CycE directly inhibits RB","PMID: 12362273"]
[{"$nulls":4},"Cdc25A","RB1 is directly inhibited by Cdc25A","PMID: 30250928"]
[{"$nulls":4},"Sirt1","RB1 is directly inhibited by Sirt1","PMID: 17620057"]
[{"$nulls":3},"Rule","NOT Sirt1 AND NOT Cdc25A AND NOT CDK46_CycD AND NOT CDK2_CycE",null,"RB can activated in the absence of CDK46-CycD and CDK2-CycE and Sirt1 and Cdc25A."]
[]
[null,"BCL2 apoptosis regulator",null,"BCL2","Cdc25A","BCL2 directly activated by Cdc25A","PMID: 18838868"]
[{"$nulls":4},"miR-34c","BCL2 is a direct target of miR-34c","PMID: 29435079"]
[{"$nulls":3},"Rule","Cdc25A AND NOT miR-34c",null,"BCL2 can be activated in the presence of Cdc25A and in the absence of miR-34c."]
[]
[null,"BCL2 associated X, apoptosis regulator",null,"BAX","BCL2","BCL2 directly inhibits BAX","PMID: 32802314"]
[{"$nulls":4},"p53_K","p53-k activates BAX","PMID: 14963330"]
[{"$nulls":3},"Rule","NOT BCL2 AND NOT p53_K",null,"BAX can be activated in the absence of BCL2 and in the presence of p53-K."]
[]
[null,"E2F transcripition factor 1",null,"E2F1","RB1","RB1 directly inhibits E2F1","PMID: 34136392"]
[{"$nulls":4},"Cdc25A","Cdc25A activates E2F1 expression","PMID: 22263797"]
[{"$nulls":4},"GAS5","E2F1 is directly target of lncRNA GAS5","PMID: 24884417"]
[{"$nulls":3},"Rule","NOT GAS5 OR (NOT RB1 AND Cdc25A)",null,"E2F1 can be activated in the presence of Cdc25A and in the absence of RB1 or in the absence of lncRNA GAS5."]
[]
[]
[null,"Caspase",null,"Caspase","BCL2","BCL2 inhibits Caspase","PMID: 10086332"]
[{"$nulls":4},"p21","p21 inhibits Caspase","PMID: 17145870"]
[{"$nulls":4},"BAX","BAX enhances Caspase activity","PMID: 9890985"]
[{"$nulls":3},"Rule","NOT (BCL2 OR p21) OR BAX",null,"Caspase can be activated in the absence of BCL2 or in the absence of p21 or in the presence of  BAX."]
[]
[null,"Proliferation",null,"Proliferation","CDK2_CycE","CDK2_CycE induces Proliferation","PMID: 25627202"]
[{"$nulls":3},"Rule","CDK2_CycE",null,"CDK2-CycE induced tumorigenesis and progression in gastric cancer cells."]
[]
[null,"Cell Cycle Arrest at G1/S checkpoint",null,"Cycle Arrest","p21","p21 induces Cell cycle arrest","PMID: 24384380"]
[{"$nulls":3},"Rule","p21 AND NOT CDK2_CycE",null,"Cell cycle arrest can be activated in the presence of p21."]
[]
[null,"Apoptosis at G1/S checkpoint",null,"Apoptosis","Caspase","Caspase induces Apoptosis","PMID: 11227675"]
[{"$nulls":3},"Rule","Caspase3 induces Apoptosis in NSCLC",null,"Caspase can activated Apoptosis in the cancer cells, in response to DNA Damage."]