From 883298281d3f2aa059d5c9aa07f69081fe85af22 Mon Sep 17 00:00:00 2001 From: Samuel Pastva Date: Wed, 29 Jan 2025 22:35:21 +0100 Subject: [PATCH] Add model 238. --- .../README.md | 29 + .../metadata.json | 14 + .../model.aeon | 122 ++ .../model.bnet | 34 + .../model.sbml | 1 + models/summary.csv | 1 + .../A Boolean Model For Ferroptosis.zginml | Bin 0 -> 5508 bytes .../citation.bib | 10 + .../metadata.json | 7 + .../notes.md | 3 + .../source.sbml | 1763 +++++++++++++++++ 11 files changed, 1984 insertions(+) create mode 100644 models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/README.md create mode 100644 models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/metadata.json create mode 100644 models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/model.aeon create mode 100644 models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/model.bnet create mode 100644 models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/model.sbml create mode 100644 sources/238_DNA-DAMAGE-INDUCED-FERROPTOSIS/A Boolean Model For Ferroptosis.zginml create mode 100644 sources/238_DNA-DAMAGE-INDUCED-FERROPTOSIS/citation.bib create mode 100644 sources/238_DNA-DAMAGE-INDUCED-FERROPTOSIS/metadata.json create mode 100644 sources/238_DNA-DAMAGE-INDUCED-FERROPTOSIS/notes.md create mode 100644 sources/238_DNA-DAMAGE-INDUCED-FERROPTOSIS/source.sbml diff --git a/models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/README.md b/models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/README.md new file mode 100644 index 0000000..16526e0 --- /dev/null +++ b/models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/README.md @@ -0,0 +1,29 @@ +# \[238\] DNA-DAMAGE-INDUCED-FERROPTOSIS + + - Variables: 33 + - Inputs: 1 + - Regulations: 89 + - Publication: https://doi.org/10.3390/proteomes13010006 + - Source: https://github.com/GuptaShan/A-Model-of-p53-and-ncRNAs-in-Ferroptosis + - Keywords: curated + + +### Modifications + +The model is converted from the provided GINsim file but is otherwise unmodified. + +### Model citation + +``` +@article{bbm-238, + title={DNA Damage-Induced Ferroptosis: A Boolean Model Regulating p53 and Non-Coding RNAs in Drug Resistance}, + author={Gupta, Shantanu and Silveira, Daner A and Mombach, Jos{\'e} Carlos M and Hashimoto, Ronaldo F}, + journal={Proteomes}, + volume={13}, + number={1}, + pages={6}, + year={2025}, + publisher={MDPI} +} +``` + diff --git a/models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/metadata.json b/models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/metadata.json new file mode 100644 index 0000000..f536eb5 --- /dev/null +++ b/models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/metadata.json @@ -0,0 +1,14 @@ +{ + "id": 238, + "name": "DNA-DAMAGE-INDUCED-FERROPTOSIS", + "url-publication": "https://doi.org/10.3390/proteomes13010006", + "url-model": "https://github.com/GuptaShan/A-Model-of-p53-and-ncRNAs-in-Ferroptosis", + "keywords": [ + "curated" + ], + "variables": 33, + "inputs": 1, + "regulations": 89, + "notes": "### Modifications\n\nThe model is converted from the provided GINsim file but is otherwise unmodified.", + "bib": "@article{bbm-238,\n title={DNA Damage-Induced Ferroptosis: A Boolean Model Regulating p53 and Non-Coding RNAs in Drug Resistance},\n author={Gupta, Shantanu and Silveira, Daner A and Mombach, Jos{\\'e} Carlos M and Hashimoto, Ronaldo F},\n journal={Proteomes},\n volume={13},\n number={1},\n pages={6},\n year={2025},\n publisher={MDPI}\n}" +} \ No newline at end of file diff --git a/models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/model.aeon b/models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/model.aeon new file mode 100644 index 0000000..f77a6a1 --- /dev/null +++ b/models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/model.aeon @@ -0,0 +1,122 @@ +v_DNA_damage -> v_ATM +v_Wip1 -| v_ATM +v_E2F1 -> v_ATM +v_ATM -> v_p38MAPK +v_Wip1 -| v_p38MAPK +v_ATM -| v_Mdm2 +v_Wip1 -> v_Mdm2 +v_p53 -> v_Mdm2 +v_E2F1 -> v_Wip1 +v_ATM -> v_p53 +v_p38MAPK -> v_p53 +v_Mdm2 -| v_p53 +v_Wip1 -| v_p53 +v_LncRNA_MALAT1 -| v_p53 +v_p53_A -> v_p53_INP1 +v_p53_K -> v_p53_INP1 +v_Wip1 -| v_p53_A +v_p53 -> v_p53_A +v_p53_INP1 -| v_p53_A +v_p53_K -| v_p53_A +v_Sirt_1 -| v_p53_A +v_Wip1 -| v_p53_K +v_p53 -> v_p53_K +v_p53_A -| v_p53_K +v_Sirt_1 -| v_p53_K +v_Myc -> v_Cric_NOTCH1 +v_Myc -> v_LncRNA_MALAT1 +v_p53 -> v_miR_34c +v_Cric_NOTCH1 -| v_miR_34c +v_LncRNA_MALAT1 -| v_miR_34c +v_p38MAPK -> v_Myc +v_miR_34c -| v_Myc +v_p21 -| v_Myc +v_RB -| v_Myc +v_E2F1 -> v_Myc +v_xCT -> v_Myc +v_miR_34c -| v_SOX4 +v_Myc -> v_SOX4 +v_p38MAPK -> v_p21 +v_p53_A -> v_p21 +v_Myc -| v_p21 +v_Caspase3 -| v_p21 +v_ALOX15 -| v_p21 +v_miR_34c -| v_cdk46_CycD +v_SOX4 -> v_cdk46_CycD +v_p21 -| v_cdk46_CycD +v_Cdc25 -> v_cdk46_CycD +v_ATM -| v_Cdc25 +v_p38MAPK -| v_Cdc25 +v_cdk46_CycD -| v_RB +v_ATM -> v_E2F1 +v_Myc -> v_E2F1 +v_Cdc25 -> v_E2F1 +v_RB -| v_E2F1 +v_Sirt_1 -| v_E2F1 +v_miR_34c -| v_Sirt_1 +v_E2F1 -> v_Sirt_1 +v_p53_K -| v_BCL2 +v_miR_34c -| v_BCL2 +v_E2F1 -> v_BCL2 +v_BIM -| v_BCL2 +v_SAT1 -| v_BCL2 +v_p53_K -> v_BIM +v_BCL2 -| v_BIM +v_Wip1 -| v_BAX +v_p53_K -> v_BAX +v_BCL2 -| v_BAX +v_BIM -> v_BAX +v_p21 -| v_Caspase3 +v_BIM -> v_Caspase3 +v_BAX -> v_Caspase3 +v_xCT -| v_Caspase3 +v_p53_K -> v_SAT1 +v_ATM -| v_xCT +v_p53 -| v_xCT +v_Myc -> v_xCT +v_BIM -| v_xCT +v_xCT -> v_GSH +v_GSH -> v_GPX4 +v_SAT1 -> v_ALOX15 +v_GPX4 -| v_ALOX15 +v_Mdm2 -> v_PROLIFERATION +v_LncRNA_MALAT1 -> v_DRUG_RESISTANCE +v_p21 -> v_FERROPTOSIS +v_BAX -> v_FERROPTOSIS +v_ALOX15 -> v_FERROPTOSIS +v_Caspase3 -> v_APOPTOSIS +v_p53_A -> v_SENESCENCE +v_p21 -> v_SENESCENCE +$v_ALOX15: v_SAT1 & !v_GPX4 +$v_APOPTOSIS: v_Caspase3 +$v_ATM: (v_DNA_damage & !v_Wip1) | (v_DNA_damage & v_Wip1 & v_E2F1) +$v_BAX: !v_Wip1 & v_p53_K & !v_BCL2 & v_BIM +$v_BCL2: !v_p53_K & !v_miR_34c & v_E2F1 & !v_BIM & !v_SAT1 +$v_BIM: v_p53_K & !v_BCL2 +$v_Caspase3: !v_p21 & v_BIM & v_BAX & !v_xCT +$v_Cdc25: !v_ATM & !v_p38MAPK +$v_Cric_NOTCH1: v_Myc +$v_DRUG_RESISTANCE: v_LncRNA_MALAT1 +$v_E2F1: (!v_ATM & !v_Myc & !v_RB & !v_Sirt_1) | (!v_ATM & v_Myc) | (v_ATM & !v_Myc & !v_Cdc25 & !v_RB & !v_Sirt_1) | (v_ATM & !v_Myc & v_Cdc25 & !v_RB) | (v_ATM & v_Myc) +$v_FERROPTOSIS: v_p21 & v_BAX & v_ALOX15 +$v_GPX4: v_GSH +$v_GSH: v_xCT +$v_LncRNA_MALAT1: v_Myc +$v_Mdm2: (!v_ATM & !v_Wip1 & v_p53) | (!v_ATM & v_Wip1) +$v_Myc: (!v_p38MAPK & !v_miR_34c) | (v_p38MAPK & !v_miR_34c) | (v_p38MAPK & v_miR_34c & !v_p21 & !v_RB & v_E2F1 & v_xCT) +$v_PROLIFERATION: v_Mdm2 +$v_RB: !v_cdk46_CycD +$v_SAT1: v_p53_K +$v_SENESCENCE: v_p53_A & v_p21 +$v_SOX4: !v_miR_34c & v_Myc +$v_Sirt_1: !v_miR_34c & v_E2F1 +$v_Wip1: v_E2F1 +$v_cdk46_CycD: !v_miR_34c | (v_miR_34c & v_SOX4 & !v_p21 & v_Cdc25) +$v_miR_34c: v_p53 & !v_Cric_NOTCH1 & !v_LncRNA_MALAT1 +$v_p21: (!v_p38MAPK & v_p53_A & !v_Myc & !v_ALOX15) | (v_p38MAPK & !v_p53_A & !v_Caspase3) | (v_p38MAPK & v_p53_A & !v_Myc & !v_Caspase3) | (v_p38MAPK & v_p53_A & !v_Myc & v_Caspase3 & !v_ALOX15) | (v_p38MAPK & v_p53_A & v_Myc & !v_Caspase3) +$v_p38MAPK: v_ATM & !v_Wip1 +$v_p53: (!v_ATM & v_p38MAPK & !v_Mdm2 & !v_Wip1) | (v_ATM & !v_p38MAPK & !v_LncRNA_MALAT1) | (v_ATM & v_p38MAPK & !v_Mdm2 & !v_Wip1) | (v_ATM & v_p38MAPK & !v_Mdm2 & v_Wip1 & !v_LncRNA_MALAT1) | (v_ATM & v_p38MAPK & v_Mdm2 & !v_LncRNA_MALAT1) +$v_p53_A: (!v_Wip1 & !v_p53 & !v_p53_INP1 & !v_p53_K & !v_Sirt_1) | (!v_Wip1 & v_p53 & !v_p53_K & !v_Sirt_1) +$v_p53_INP1: (!v_p53_A & v_p53_K) | v_p53_A +$v_p53_K: (!v_Wip1 & v_p53 & !v_p53_A) | (v_Wip1 & v_p53 & !v_p53_A & !v_Sirt_1) +$v_xCT: (!v_ATM & !v_p53) | (!v_ATM & v_p53 & v_Myc & !v_BIM) | (v_ATM & !v_p53) diff --git a/models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/model.bnet b/models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/model.bnet new file mode 100644 index 0000000..ef24b66 --- /dev/null +++ b/models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/model.bnet @@ -0,0 +1,34 @@ +targets,factors +v_ALOX15, (v_SAT1 & !v_GPX4) +v_APOPTOSIS, v_Caspase3 +v_ATM, ((v_DNA_damage & !v_Wip1) | ((v_DNA_damage & v_Wip1) & v_E2F1)) +v_BAX, (((!v_Wip1 & v_p53_K) & !v_BCL2) & v_BIM) +v_BCL2, ((((!v_p53_K & !v_miR_34c) & v_E2F1) & !v_BIM) & !v_SAT1) +v_BIM, (v_p53_K & !v_BCL2) +v_Caspase3, (((!v_p21 & v_BIM) & v_BAX) & !v_xCT) +v_Cdc25, (!v_ATM & !v_p38MAPK) +v_Cric_NOTCH1, v_Myc +v_DRUG_RESISTANCE, v_LncRNA_MALAT1 +v_E2F1, (((((((!v_ATM & !v_Myc) & !v_RB) & !v_Sirt_1) | (!v_ATM & v_Myc)) | ((((v_ATM & !v_Myc) & !v_Cdc25) & !v_RB) & !v_Sirt_1)) | (((v_ATM & !v_Myc) & v_Cdc25) & !v_RB)) | (v_ATM & v_Myc)) +v_FERROPTOSIS, ((v_p21 & v_BAX) & v_ALOX15) +v_GPX4, v_GSH +v_GSH, v_xCT +v_LncRNA_MALAT1, v_Myc +v_Mdm2, (((!v_ATM & !v_Wip1) & v_p53) | (!v_ATM & v_Wip1)) +v_Myc, (((!v_p38MAPK & !v_miR_34c) | (v_p38MAPK & !v_miR_34c)) | (((((v_p38MAPK & v_miR_34c) & !v_p21) & !v_RB) & v_E2F1) & v_xCT)) +v_PROLIFERATION, v_Mdm2 +v_RB, !v_cdk46_CycD +v_SAT1, v_p53_K +v_SENESCENCE, (v_p53_A & v_p21) +v_SOX4, (!v_miR_34c & v_Myc) +v_Sirt_1, (!v_miR_34c & v_E2F1) +v_Wip1, v_E2F1 +v_cdk46_CycD, (!v_miR_34c | (((v_miR_34c & v_SOX4) & !v_p21) & v_Cdc25)) +v_miR_34c, ((v_p53 & !v_Cric_NOTCH1) & !v_LncRNA_MALAT1) +v_p21, (((((((!v_p38MAPK & v_p53_A) & !v_Myc) & !v_ALOX15) | ((v_p38MAPK & !v_p53_A) & !v_Caspase3)) | (((v_p38MAPK & v_p53_A) & !v_Myc) & !v_Caspase3)) | ((((v_p38MAPK & v_p53_A) & !v_Myc) & v_Caspase3) & !v_ALOX15)) | (((v_p38MAPK & v_p53_A) & v_Myc) & !v_Caspase3)) +v_p38MAPK, (v_ATM & !v_Wip1) +v_p53, (((((((!v_ATM & v_p38MAPK) & !v_Mdm2) & !v_Wip1) | ((v_ATM & !v_p38MAPK) & !v_LncRNA_MALAT1)) | (((v_ATM & v_p38MAPK) & !v_Mdm2) & !v_Wip1)) | ((((v_ATM & v_p38MAPK) & !v_Mdm2) & v_Wip1) & !v_LncRNA_MALAT1)) | (((v_ATM & v_p38MAPK) & v_Mdm2) & !v_LncRNA_MALAT1)) +v_p53_A, (((((!v_Wip1 & !v_p53) & !v_p53_INP1) & !v_p53_K) & !v_Sirt_1) | (((!v_Wip1 & v_p53) & !v_p53_K) & !v_Sirt_1)) +v_p53_INP1, ((!v_p53_A & v_p53_K) | v_p53_A) +v_p53_K, (((!v_Wip1 & v_p53) & !v_p53_A) | (((v_Wip1 & v_p53) & !v_p53_A) & !v_Sirt_1)) +v_xCT, (((!v_ATM & !v_p53) | (((!v_ATM & v_p53) & v_Myc) & !v_BIM)) | (v_ATM & !v_p53)) diff --git a/models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/model.sbml b/models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/model.sbml new file mode 100644 index 0000000..75b6dd0 --- /dev/null +++ b/models/[id-238]__[var-33]__[in-1]__[DNA-DAMAGE-INDUCED-FERROPTOSIS]/model.sbml @@ -0,0 +1 @@ +v_SAT11v_GPX41v_Caspase31v_DNA_damage1v_Wip11v_DNA_damage1v_Wip11v_E2F11v_Wip11v_p53_K1v_BCL21v_BIM1v_p53_K1v_miR_34c1v_E2F11v_BIM1v_SAT11v_p53_K1v_BCL21v_p211v_BIM1v_BAX1v_xCT1v_ATM1v_p38MAPK1v_Myc1v_LncRNA_MALAT11v_ATM1v_Myc1v_RB1v_Sirt_11v_ATM1v_Myc1v_ATM1v_Myc1v_Cdc251v_RB1v_Sirt_11v_ATM1v_Myc1v_Cdc251v_RB1v_ATM1v_Myc1v_p211v_BAX1v_ALOX151v_GSH1v_xCT1v_Myc1v_ATM1v_Wip11v_p531v_ATM1v_Wip11v_p38MAPK1v_miR_34c1v_p38MAPK1v_miR_34c1v_p38MAPK1v_miR_34c1v_p211v_RB1v_E2F11v_xCT1v_Mdm21v_cdk46_CycD1v_p53_K1v_p53_A1v_p211v_miR_34c1v_Myc1v_miR_34c1v_E2F11v_E2F11v_miR_34c1v_miR_34c1v_SOX41v_p211v_Cdc251v_p531v_Cric_NOTCH11v_LncRNA_MALAT11v_p38MAPK1v_p53_A1v_Myc1v_ALOX151v_p38MAPK1v_p53_A1v_Caspase31v_p38MAPK1v_p53_A1v_Myc1v_Caspase31v_p38MAPK1v_p53_A1v_Myc1v_Caspase31v_ALOX151v_p38MAPK1v_p53_A1v_Myc1v_Caspase31v_ATM1v_Wip11v_ATM1v_p38MAPK1v_Mdm21v_Wip11v_ATM1v_p38MAPK1v_LncRNA_MALAT11v_ATM1v_p38MAPK1v_Mdm21v_Wip11v_ATM1v_p38MAPK1v_Mdm21v_Wip11v_LncRNA_MALAT11v_ATM1v_p38MAPK1v_Mdm21v_LncRNA_MALAT11v_Wip11v_p531v_p53_INP11v_p53_K1v_Sirt_11v_Wip11v_p531v_p53_K1v_Sirt_11v_p53_A1v_p53_K1v_p53_A1v_Wip11v_p531v_p53_A1v_Wip11v_p531v_p53_A1v_Sirt_11v_ATM1v_p531v_ATM1v_p531v_Myc1v_BIM1v_ATM1v_p531 \ No newline at end of file diff --git a/models/summary.csv b/models/summary.csv index 43c4d07..7a86eb1 100644 --- a/models/summary.csv +++ b/models/summary.csv @@ -236,3 +236,4 @@ ID, name, variables, inputs, regulations 235, BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB231-COMPLETE, 110, 7, 270 236, BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE, 109, 8, 263 237, COLORECTAL-TUMORIGENESIS-REVERSION-SWITCH, 17, 0, 44 +238, DNA-DAMAGE-INDUCED-FERROPTOSIS, 33, 1, 89 diff --git a/sources/238_DNA-DAMAGE-INDUCED-FERROPTOSIS/A Boolean Model For Ferroptosis.zginml b/sources/238_DNA-DAMAGE-INDUCED-FERROPTOSIS/A Boolean Model For Ferroptosis.zginml new file mode 100644 index 0000000000000000000000000000000000000000..673141d6d6851b56a7b61f30e36fafda012d8926 GIT binary patch literal 5508 zcma)Abx@Swzot8+ySuxUmPQr?ge8|{ft7BM1q37nX%vud=~Yssmy{9^Tw;-uMqs5R zug?AB>(@KKd++nknR(C5dp`5L=lOh|Gv@=)$Ht+?ARr*X5N$WL#P|aozuvWVANWGu zMI1qXATb|^v%ee2&(kMZ+Xv+3BI*qFaChslcK2M6r@ZOxiaf%Mr9G5c&C&Vx`d(|L 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No newline at end of file diff --git a/sources/238_DNA-DAMAGE-INDUCED-FERROPTOSIS/metadata.json b/sources/238_DNA-DAMAGE-INDUCED-FERROPTOSIS/metadata.json new file mode 100644 index 0000000..42efb57 --- /dev/null +++ b/sources/238_DNA-DAMAGE-INDUCED-FERROPTOSIS/metadata.json @@ -0,0 +1,7 @@ +{ + "id": 238, + "name": "DNA-DAMAGE-INDUCED-FERROPTOSIS", + "url-publication": "https://doi.org/10.3390/proteomes13010006", + "url-model": "https://github.com/GuptaShan/A-Model-of-p53-and-ncRNAs-in-Ferroptosis", + "keywords": ["curated"] +} \ No newline at end of file diff --git a/sources/238_DNA-DAMAGE-INDUCED-FERROPTOSIS/notes.md b/sources/238_DNA-DAMAGE-INDUCED-FERROPTOSIS/notes.md new file mode 100644 index 0000000..73b929f --- /dev/null +++ b/sources/238_DNA-DAMAGE-INDUCED-FERROPTOSIS/notes.md @@ -0,0 +1,3 @@ +### Modifications + +The model is converted from the provided GINsim file but is otherwise unmodified. \ No newline at end of file diff --git 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