diff --git a/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/README.md b/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/README.md new file mode 100644 index 0000000..f3200aa --- /dev/null +++ b/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/README.md @@ -0,0 +1,37 @@ +# \[232\] BREAST-CANCER-PATHWAYS-MCF7-COMPLETE + + - Variables: 109 + - Inputs: 8 + - Regulations: 275 + - Publication: https://doi.org/10.1371/journal.pone.0298788 + - Source: https://github.com/Ktaoma/BoolSyn + - Keywords: source (?), curated (?), repaired (?), multi-valued (?) + + +### Modifications + +Removed regulations: +WNT1, WNT1 +PG, PG +NRG1, NRG1 +DLL_i, DLL_i +EGF, EGF +ES, ES +IGF1, IGF1 +INS, INS + + +### Model citation + +``` +@article{bbm-232, + author = {Taoma, Kittisak and Ruengjitchatchawalya, Marasri and Liangruksa, Monrudee and Laomettachit, Teeraphan}, + year = {2024}, + doi = {https://doi.org/10.1371/journal.pone.0298788}, + title = {Boolean modeling of breast cancer signaling pathways uncovers mechanisms of drug synergy}, + publisher = {PLOS ONE} +} + + +``` + diff --git a/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/metadata.json b/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/metadata.json new file mode 100644 index 0000000..dfd8fb5 --- /dev/null +++ b/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/metadata.json @@ -0,0 +1,17 @@ +{ + "id": 232, + "name": "BREAST-CANCER-PATHWAYS-MCF7-COMPLETE", + "url-publication": "https://doi.org/10.1371/journal.pone.0298788", + "url-model": "https://github.com/Ktaoma/BoolSyn", + "keywords": [ + "source (?)", + "curated (?)", + "repaired (?)", + "multi-valued (?)" + ], + "variables": 109, + "inputs": 8, + "regulations": 275, + "notes": "### Modifications\n\nRemoved regulations:\nWNT1, WNT1\nPG, PG\nNRG1, NRG1\nDLL_i, DLL_i\nEGF, EGF\nES, ES\nIGF1, IGF1\nINS, INS\n", + "bib": "@article{bbm-232,\n\tauthor = {Taoma, Kittisak and Ruengjitchatchawalya, Marasri and Liangruksa, Monrudee and Laomettachit, Teeraphan},\n\tyear = {2024},\n\tdoi = {https://doi.org/10.1371/journal.pone.0298788},\n\ttitle = {Boolean modeling of breast cancer signaling pathways uncovers mechanisms of drug synergy},\n\tpublisher = {PLOS ONE}\n}\n\n" +} \ No newline at end of file diff --git a/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/model.aeon b/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/model.aeon new file mode 100644 index 0000000..ebabe30 --- /dev/null +++ b/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/model.aeon @@ -0,0 +1,384 @@ +v_GRB2 -? v_ABL1 +v_PRB -? v_ABL1 +v_SRC -? v_ABL1 +v_ABL1 -? v_ABL2 +v_IGF1 -? v_AKT_i +v_IGF1R -? v_AKT_i +v_IRS1 -? v_AKT_i +v_MTORC2_c -? v_AKT_i +v_NRG1 -? v_AKT_i +v_PDPK1 -? v_AKT_i +v_PIP3 -? v_AKT_i +v_AXIN1 -? v_APC +v_DVL1 -? v_AXIN1 +v_GSK3B -? v_AXIN1 +v_AKT_i -? v_BAD +v_ERK_i -? v_BAD +v_PAK1 -? v_BAD +v_PIM -? v_BAD +v_BID -? v_BAK1 +v_BIM -? v_BAK1 +v_MCL1 -? v_BAK1 +v_P53 -? v_BAK1 +v_BID -? v_BAX +v_BIM -? v_BAX +v_MCL1 -? v_BAX +v_P53 -? v_BAX +v_BAD -? v_BCL2 +v_BIM -? v_BCL2 +v_CREB1 -? v_BCL2 +v_ERK_i -? v_BCL2 +v_BAD -? v_BCLXL +v_BIM -? v_BCLXL +v_CREB1 -? v_BCLXL +v_CASP8 -? v_BID +v_BCL2 -? v_BIM +v_BCLXL -? v_BIM +v_FOXO1 -? v_BIM +v_FOXO3 -? v_BIM +v_CASP9 -? v_CASP3 +v_ERK_i -? v_CASP8 +v_FADD -? v_CASP8 +v_NF1 -? v_CASP8 +v_SRC -? v_CASP8 +v_AKT_i -? v_CASP9 +v_BCLXL -? v_CASP9 +v_CASP3 -? v_CASP9 +v_CASP8 -? v_CASP9 +v_CYCS -? v_CASP9 +v_ERK_i -? v_CASP9 +v_PRKACA -? v_CASP9 +v_CASP3 -? v_CDKN2A +v_MYC -? v_CDKN2A +v_SRC -? v_CDKN2A +v_ABL2 -? v_CEBPB +v_CREB1 -? v_CEBPB +v_AKT_i -? v_CREB1 +v_PTEN -? v_CREB1 +v_DC -? v_CTNNB1 +v_SRC -? v_CTNNB1 +v_WNT1 -? v_CTNNB1 +v_YAP1 -? v_CTNNB1 +v_CDKN2A -? v_CYCLIN_D_c +v_EIF4E -? v_CYCLIN_D_c +v_ESR1 -? v_CYCLIN_D_c +v_FOXO3 -? v_CYCLIN_D_c +v_GSK3B -? v_CYCLIN_D_c +v_IGF1 -? v_CYCLIN_D_c +v_KMT2D -? v_CYCLIN_D_c +v_MYC -? v_CYCLIN_D_c +v_NRG1 -? v_CYCLIN_D_c +v_P21 -? v_CYCLIN_D_c +v_TCF4 -? v_CYCLIN_D_c +v_TEAD1 -? v_CYCLIN_D_c +v_BAK1 -? v_CYCS +v_BAX -? v_CYCS +v_APC -? v_DC +v_GSK3B -? v_DC +v_FZD3 -? v_DVL1 +v_NF1 -? v_DVL1 +v_PRB -? v_E2F1 +v_EGF -? v_EGFR +v_HER2 -? v_EGFR +v_HER3 -? v_EGFR +v_MEK_i -? v_EGFR +v_IVEBP1 -? v_EIF4E +v_MEK_i -? v_ERK_i +v_AKT_i -? v_ESR1 +v_ES -? v_ESR1 +v_FOXO3 -? v_ESR1 +v_KMT2D -? v_ESR1 +v_PGR -? v_ESR1 +v_FAS -? v_FADD +v_TRADD -? v_FADD +v_AKT_i -? v_FAS +v_FASLG -? v_FAS +v_P53 -? v_FAS +v_FASLG -? v_FASLG +v_FOXO3 -? v_FASLG +v_P53 -? v_FASLG +v_AKT_i -? v_FOXO1 +v_SGK1 -? v_FOXO1 +v_AKT_i -? v_FOXO3 +v_CREB1 -? v_FZD3 +v_WNT1 -? v_FZD3 +v_STAT1 -? v_GATA3 +v_EGFR -? v_GRB2 +v_IRS1 -? v_GRB2 +v_LATS1 -? v_GRB2 +v_SRC -? v_GRB2 +v_INSR -? v_GRB7 +v_PRKACA -? v_GRB7 +v_AKT_i -? v_GSK3B +v_ERK_i -? v_GSK3B +v_EGF -? v_HER2 +v_HER3 -? v_HER2 +v_HER2 -? v_HER3 +v_NRG1 -? v_HER3 +v_NCID -? v_HES1 +v_NCID -? v_HEY1 +v_IGF1 -? v_HRAS +v_NF1 -? v_HRAS +v_PIP3 -? v_HRAS +v_SOS1 -? v_HRAS +v_PDPK1 -? v_HSP90AA1 +v_ESR1 -? v_IGF1R +v_FOXO3 -? v_IGF1R +v_IGF1 -? v_IGF1R +v_INS -? v_IGF1R +v_SRC -? v_IGF1R +v_NOS3 -? v_IL1B +v_RELA -? v_IL1B +v_IL1B -? v_IL6 +v_IL6 -? v_IL6 +v_IL6 -? v_IL6R +v_STAT5 -? v_IL8 +v_FOXO3 -? v_INSR +v_INS -? v_INSR +v_IGF1R -? v_IRS1 +v_INSR -? v_IRS1 +v_S6K1 -? v_IRS1 +v_MTORC1_c -? v_IVEBP1 +v_ABL1 -? v_JAK2 +v_IL6R -? v_JAK2 +v_IL8 -? v_JAK2 +v_IRS1 -? v_JAK2 +v_ERK_i -? v_JUN +v_MAPK8 -? v_JUN +v_PPARG -? v_JUN +v_RELA -? v_JUN +v_AKT_i -? v_KMT2D +v_PAX7 -? v_KMT2D +v_EGFR -? v_KRT14 +v_PAK2 -? v_KRT14 +v_LCK -? v_LATS1 +v_NF2 -? v_LATS1 +v_AKT_i -? v_LCK +v_ERK_i -? v_LCK +v_RAC1 -? v_MAPK8 +v_RND1 -? v_MAPK8 +v_ERK_i -? v_MCL1 +v_GSK3B -? v_MCL1 +v_AKT_i -? v_MDM2 +v_P53 -? v_MDM2 +v_RAF1 -? v_MEK_i +v_IGF1 -? v_MTORC1_c +v_NRG1 -? v_MTORC1_c +v_PIM -? v_MTORC1_c +v_RHEB -? v_MTORC1_c +v_PIP3 -? v_MTORC2_c +v_S6K1 -? v_MTORC2_c +v_CTNNB1 -? v_MYC +v_EIF4E -? v_MYC +v_ERK_i -? v_MYC +v_ESR1 -? v_MYC +v_FOXO3 -? v_MYC +v_GSK3B -? v_MYC +v_IGF1 -? v_MYC +v_KMT2D -? v_MYC +v_NRG1 -? v_MYC +v_PIM -? v_MYC +v_STAT3 -? v_MYC +v_ABL1 -? v_MYOD1 +v_HES1 -? v_MYOD1 +v_HEY1 -? v_MYOG +v_MYOD1 -? v_MYOG +v_NOTCH1 -? v_NCID +v_PRKACA -? v_NEDD4L +v_SGK1 -? v_NEDD4L +v_P53 -? v_NF1 +v_TWIST1 -? v_NF1 +v_NEDD4L -? v_NF2 +v_NOTCH1 -? v_NFKB1 +v_AKT_i -? v_NOS3 +v_HSP90AA1 -? v_NOS3 +v_CTNNB1 -? v_NOTCH1 +v_DLL_i -? v_NOTCH1 +v_LCK -? v_NOTCH1 +v_MDM2 -? v_NOTCH1 +v_AKT_i -? v_P21 +v_ERK_i -? v_P21 +v_MYC -? v_P21 +v_MDM2 -? v_P53 +v_TCF4 -? v_PAK1 +v_RAC1 -? v_PAK2 +v_SRC -? v_PAK2 +v_HES1 -? v_PAX7 +v_HEY1 -? v_PAX7 +v_MYOG -? v_PAX7 +v_NOTCH1 -? v_PAX7 +v_IGF1R -? v_PDPK1 +v_PIP3 -? v_PDPK1 +v_ERK_i -? v_PGR +v_ESR1 -? v_PGR +v_PG -? v_PGR +v_EGFR -? v_PI3K_c +v_ESR1 -? v_PI3K_c +v_IGF1R -? v_PI3K_c +v_INSR -? v_PI3K_c +v_IRS1 -? v_PI3K_c +v_RAS_i -? v_PI3K_c +v_STAT5 -? v_PIM +v_PI3K_c -? v_PIP3 +v_PTEN -? v_PIP3 +v_CEBPB -? v_PPARG +v_GATA3 -? v_PPARG +v_CYCLIN_D_c -? v_PRB +v_PRKACA -? v_PRKAA2 +v_STK11 -? v_PRKAA2 +v_AKT_i -? v_PRKACA +v_WNT1 -? v_PRKACA +v_S6K1 -? v_PTEN +v_SRC -? v_PTEN +v_AKT_i -? v_RAC1 +v_DVL1 -? v_RAC1 +v_PI3K_c -? v_RAC1 +v_HRAS -? v_RAF1 +v_RAS_i -? v_RAF1 +v_IGF1 -? v_RAS_i +v_PIP3 -? v_RAS_i +v_SOS1 -? v_RAS_i +v_NFKB1 -? v_RELA +v_PIM -? v_RELA +v_TSC2 -? v_RHEB +v_DVL1 -? v_RND1 +v_GRB7 -? v_RND1 +v_MTORC1_c -? v_S6K1 +v_MTORC1_c -? v_SGK1 +v_MTORC2_c -? v_SGK1 +v_PDPK1 -? v_SGK1 +v_GRB2 -? v_SOS1 +v_ABL1 -? v_SRC +v_PRKACA -? v_SRC +v_JAK2 -? v_STAT1 +v_SRC -? v_STAT1 +v_IL1B -? v_STAT3 +v_JAK2 -? v_STAT3 +v_MAPK8 -? v_STAT3 +v_SRC -? v_STAT3 +v_EGFR -? v_STAT5 +v_JAK2 -? v_STAT5 +v_SRC -? v_STAT5 +v_ERK_i -? v_STK11 +v_CTNNB1 -? v_TCF4 +v_JUN -? v_TCF4 +v_YAP1 -? v_TEAD1 +v_KRT14 -? v_TRADD +v_AKT_i -? v_TSC2 +v_ERK_i -? v_TSC2 +v_GSK3B -? v_TSC2 +v_PRKAA2 -? v_TSC2 +v_AKT_i -? v_TWIST1 +v_ERK_i -? v_TWIST1 +v_MAPK8 -? v_TWIST1 +v_ABL1 -? v_YAP1 +v_LATS1 -? v_YAP1 +$v_ABL1: ((v_SRC & v_GRB2) & !v_PRB) +$v_ABL2: v_ABL1 +$v_AKT_i: ((((v_MTORC2_c & v_PDPK1) & v_PIP3) & (v_IRS1 & v_IGF1R)) | (v_NRG1 | v_IGF1)) +$v_APC: v_AXIN1 +$v_AXIN1: (!v_DVL1 & v_GSK3B) +$v_BAD: !(v_PAK1 | (v_AKT_i | (v_ERK_i | v_PIM))) +$v_BAK1: (((v_BIM | v_P53) | v_BID) & !v_MCL1) +$v_BAX: (((v_BIM | v_P53) | v_BID) & !v_MCL1) +$v_BCL2: (!(v_BAD & v_BIM) | (v_CREB1 | v_ERK_i)) +$v_BCLXL: (!(v_BAD | v_BIM) & v_CREB1) +$v_BID: v_CASP8 +$v_BIM: (!(v_BCL2 & v_BCLXL) | (v_FOXO3 | v_FOXO1)) +$v_CASP3: v_CASP9 +$v_CASP8: ((v_FADD & v_NF1) & !(v_ERK_i & v_SRC)) +$v_CASP9: (((v_CYCS & v_CASP8) | v_CASP3) & !((v_ERK_i & v_PRKACA) | (v_BCLXL & v_AKT_i))) +$v_CDKN2A: (!(v_MYC | v_SRC) & v_CASP3) +$v_CEBPB: (v_ABL2 | v_CREB1) +$v_CREB1: (v_AKT_i & !v_PTEN) +$v_CTNNB1: (!v_DC & (v_WNT1 & (v_SRC & v_YAP1))) +$v_CYCLIN_D_c: (((v_TCF4 | v_TEAD1) & !(v_GSK3B | (v_CDKN2A & v_P21))) | ((v_ESR1 & (v_KMT2D & (v_FOXO3 & v_MYC))) | (v_EIF4E & (v_IGF1 | v_NRG1)))) +$v_CYCS: (v_BAK1 & v_BAX) +$v_DC: (v_APC & v_GSK3B) +$v_DVL1: (v_FZD3 & v_NF1) +$v_E2F1: !v_PRB +$v_EGFR: ((v_EGF & (v_HER2 & v_HER3)) & !v_MEK_i) +$v_EIF4E: !v_IVEBP1 +$v_ERK_i: v_MEK_i +$v_ESR1: (v_AKT_i | ((v_FOXO3 & v_KMT2D) | (v_ES & v_PGR))) +$v_FADD: (v_TRADD | v_FAS) +$v_FAS: ((v_FASLG & v_P53) & !v_AKT_i) +$v_FASLG: (v_FASLG | (v_P53 | v_FOXO3)) +$v_FOXO1: !(v_SGK1 | v_AKT_i) +$v_FOXO3: !v_AKT_i +$v_FZD3: (v_WNT1 | v_CREB1) +$v_GATA3: !v_STAT1 +$v_GRB2: (v_IRS1 | (v_LATS1 & (v_EGFR & v_SRC))) +$v_GRB7: (v_INSR & !v_PRKACA) +$v_GSK3B: !(v_AKT_i & v_ERK_i) +$v_HER2: (v_HER3 | v_EGF) +$v_HER3: (v_NRG1 | v_HER2) +$v_HES1: v_NCID +$v_HEY1: v_NCID +$v_HRAS: (((v_SOS1 | v_PIP3) & !v_NF1) | (v_PIP3 & v_IGF1)) +$v_HSP90AA1: !v_PDPK1 +$v_IGF1R: ((v_IGF1 | (v_SRC | v_INS)) | (v_FOXO3 & v_ESR1)) +$v_IL1B: (v_NOS3 & v_RELA) +$v_IL6: (v_IL1B & v_IL6) +$v_IL6R: v_IL6 +$v_IL8: v_STAT5 +$v_INSR: (v_INS | v_FOXO3) +$v_IRS1: (!v_S6K1 & (v_INSR | v_IGF1R)) +$v_IVEBP1: !v_MTORC1_c +$v_JAK2: ((v_IL6R | (v_ABL1 | v_IL8)) | v_IRS1) +$v_JUN: ((v_RELA | v_MAPK8) & (v_ERK_i & v_PPARG)) +$v_KMT2D: (v_PAX7 | !v_AKT_i) +$v_KRT14: (v_PAK2 & v_EGFR) +$v_LATS1: (v_NF2 | v_LCK) +$v_LCK: (v_ERK_i & !v_AKT_i) +$v_MAPK8: (v_RAC1 & v_RND1) +$v_MCL1: (!v_GSK3B | v_ERK_i) +$v_MDM2: (v_P53 | v_AKT_i) +$v_MEK_i: v_RAF1 +$v_MTORC1_c: ((v_PIM | v_RHEB) | (v_NRG1 | v_IGF1)) +$v_MTORC2_c: (v_PIP3 & !v_S6K1) +$v_MYC: (((v_CTNNB1 | (v_PIM | (v_ERK_i | v_STAT3))) & !v_GSK3B) | ((v_ESR1 & (v_KMT2D & v_FOXO3)) | (v_EIF4E & (v_IGF1 | v_NRG1)))) +$v_MYOD1: !(v_HES1 | v_ABL1) +$v_MYOG: (!v_HEY1 & v_MYOD1) +$v_NCID: v_NOTCH1 +$v_NEDD4L: !(v_SGK1 | v_PRKACA) +$v_NF1: (!v_TWIST1 & v_P53) +$v_NF2: v_NEDD4L +$v_NFKB1: v_NOTCH1 +$v_NOS3: (v_HSP90AA1 & v_AKT_i) +$v_NOTCH1: ((v_DLL_i & (v_CTNNB1 & v_LCK)) | v_MDM2) +$v_P21: !(v_ERK_i & (v_AKT_i & v_MYC)) +$v_P53: !v_MDM2 +$v_PAK1: v_TCF4 +$v_PAK2: (v_RAC1 & v_SRC) +$v_PAX7: (!(v_MYOG | (v_HEY1 | v_HES1)) & v_NOTCH1) +$v_PDPK1: (v_PIP3 | v_IGF1R) +$v_PGR: (v_PG & !(v_ERK_i & v_ESR1)) +$v_PI3K_c: ((v_EGFR & (v_INSR & (v_RAS_i & v_ESR1))) | (v_IRS1 & v_IGF1R)) +$v_PIM: v_STAT5 +$v_PIP3: (v_PI3K_c & !v_PTEN) +$v_PPARG: (!v_GATA3 & v_CEBPB) +$v_PRB: !v_CYCLIN_D_c +$v_PRKAA2: (v_STK11 | !v_PRKACA) +$v_PRKACA: (v_AKT_i | v_WNT1) +$v_PTEN: (v_S6K1 & !v_SRC) +$v_RAC1: ((v_PI3K_c | v_DVL1) & !v_AKT_i) +$v_RAF1: (v_HRAS | v_RAS_i) +$v_RAS_i: ((v_SOS1 & v_PIP3) | (v_PIP3 & v_IGF1)) +$v_RELA: (v_NFKB1 & v_PIM) +$v_RHEB: !v_TSC2 +$v_RND1: (v_GRB7 | v_DVL1) +$v_S6K1: v_MTORC1_c +$v_SGK1: ((v_MTORC2_c & v_MTORC1_c) & v_PDPK1) +$v_SOS1: v_GRB2 +$v_SRC: (v_PRKACA & v_ABL1) +$v_STAT1: (v_JAK2 | v_SRC) +$v_STAT3: (v_IL1B & (v_SRC & (v_MAPK8 & v_JAK2))) +$v_STAT5: (v_JAK2 & (v_SRC & v_EGFR)) +$v_STK11: !v_ERK_i +$v_TCF4: (v_CTNNB1 & v_JUN) +$v_TEAD1: v_YAP1 +$v_TRADD: !v_KRT14 +$v_TSC2: (!(v_AKT_i & v_ERK_i) | (v_PRKAA2 | v_GSK3B)) +$v_TWIST1: (v_ERK_i & (v_AKT_i & v_MAPK8)) +$v_YAP1: (!v_LATS1 & v_ABL1) diff --git a/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/model.bnet b/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/model.bnet new file mode 100644 index 0000000..27e0d01 --- /dev/null +++ b/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/model.bnet @@ -0,0 +1,110 @@ +targets,factors +v_ABL1, ((v_SRC & v_GRB2) & !v_PRB) +v_ABL2, v_ABL1 +v_AKT_i, ((((v_MTORC2_c & v_PDPK1) & v_PIP3) & (v_IRS1 & v_IGF1R)) | (v_NRG1 | v_IGF1)) +v_APC, v_AXIN1 +v_AXIN1, (!v_DVL1 & v_GSK3B) +v_BAD, !(v_PAK1 | (v_AKT_i | (v_ERK_i | v_PIM))) +v_BAK1, (((v_BIM | v_P53) | v_BID) & !v_MCL1) +v_BAX, (((v_BIM | v_P53) | v_BID) & !v_MCL1) +v_BCL2, (!(v_BAD & v_BIM) | (v_CREB1 | v_ERK_i)) +v_BCLXL, (!(v_BAD | v_BIM) & v_CREB1) +v_BID, v_CASP8 +v_BIM, (!(v_BCL2 & v_BCLXL) | (v_FOXO3 | v_FOXO1)) +v_CASP3, v_CASP9 +v_CASP8, ((v_FADD & v_NF1) & !(v_ERK_i & v_SRC)) +v_CASP9, (((v_CYCS & v_CASP8) | v_CASP3) & !((v_ERK_i & v_PRKACA) | (v_BCLXL & v_AKT_i))) +v_CDKN2A, (!(v_MYC | v_SRC) & v_CASP3) +v_CEBPB, (v_ABL2 | v_CREB1) +v_CREB1, (v_AKT_i & !v_PTEN) +v_CTNNB1, (!v_DC & (v_WNT1 & (v_SRC & v_YAP1))) +v_CYCLIN_D_c, (((v_TCF4 | v_TEAD1) & !(v_GSK3B | (v_CDKN2A & v_P21))) | ((v_ESR1 & (v_KMT2D & (v_FOXO3 & v_MYC))) | (v_EIF4E & (v_IGF1 | v_NRG1)))) +v_CYCS, (v_BAK1 & v_BAX) +v_DC, (v_APC & v_GSK3B) +v_DVL1, (v_FZD3 & v_NF1) +v_E2F1, !v_PRB +v_EGFR, ((v_EGF & (v_HER2 & v_HER3)) & !v_MEK_i) +v_EIF4E, !v_IVEBP1 +v_ERK_i, v_MEK_i +v_ESR1, (v_AKT_i | ((v_FOXO3 & v_KMT2D) | (v_ES & v_PGR))) +v_FADD, (v_TRADD | v_FAS) +v_FAS, ((v_FASLG & v_P53) & !v_AKT_i) +v_FASLG, (v_FASLG | (v_P53 | v_FOXO3)) +v_FOXO1, !(v_SGK1 | v_AKT_i) +v_FOXO3, !v_AKT_i +v_FZD3, (v_WNT1 | v_CREB1) +v_GATA3, !v_STAT1 +v_GRB2, (v_IRS1 | (v_LATS1 & (v_EGFR & v_SRC))) +v_GRB7, (v_INSR & !v_PRKACA) +v_GSK3B, !(v_AKT_i & v_ERK_i) +v_HER2, (v_HER3 | v_EGF) +v_HER3, (v_NRG1 | v_HER2) +v_HES1, v_NCID +v_HEY1, v_NCID +v_HRAS, (((v_SOS1 | v_PIP3) & !v_NF1) | (v_PIP3 & v_IGF1)) +v_HSP90AA1, !v_PDPK1 +v_IGF1R, ((v_IGF1 | (v_SRC | v_INS)) | (v_FOXO3 & v_ESR1)) +v_IL1B, (v_NOS3 & v_RELA) +v_IL6, (v_IL1B & v_IL6) +v_IL6R, v_IL6 +v_IL8, v_STAT5 +v_INSR, (v_INS | v_FOXO3) +v_IRS1, (!v_S6K1 & (v_INSR | v_IGF1R)) +v_IVEBP1, !v_MTORC1_c +v_JAK2, ((v_IL6R | (v_ABL1 | v_IL8)) | v_IRS1) +v_JUN, ((v_RELA | v_MAPK8) & (v_ERK_i & v_PPARG)) +v_KMT2D, (v_PAX7 | !v_AKT_i) +v_KRT14, (v_PAK2 & v_EGFR) +v_LATS1, (v_NF2 | v_LCK) +v_LCK, (v_ERK_i & !v_AKT_i) +v_MAPK8, (v_RAC1 & v_RND1) +v_MCL1, (!v_GSK3B | v_ERK_i) +v_MDM2, (v_P53 | v_AKT_i) +v_MEK_i, v_RAF1 +v_MTORC1_c, ((v_PIM | v_RHEB) | (v_NRG1 | v_IGF1)) +v_MTORC2_c, (v_PIP3 & !v_S6K1) +v_MYC, (((v_CTNNB1 | (v_PIM | (v_ERK_i | v_STAT3))) & !v_GSK3B) | ((v_ESR1 & (v_KMT2D & v_FOXO3)) | (v_EIF4E & (v_IGF1 | v_NRG1)))) +v_MYOD1, !(v_HES1 | v_ABL1) +v_MYOG, (!v_HEY1 & v_MYOD1) +v_NCID, v_NOTCH1 +v_NEDD4L, !(v_SGK1 | v_PRKACA) +v_NF1, (!v_TWIST1 & v_P53) +v_NF2, v_NEDD4L +v_NFKB1, v_NOTCH1 +v_NOS3, (v_HSP90AA1 & v_AKT_i) +v_NOTCH1, ((v_DLL_i & (v_CTNNB1 & v_LCK)) | v_MDM2) +v_P21, !(v_ERK_i & (v_AKT_i & v_MYC)) +v_P53, !v_MDM2 +v_PAK1, v_TCF4 +v_PAK2, (v_RAC1 & v_SRC) +v_PAX7, (!(v_MYOG | (v_HEY1 | v_HES1)) & v_NOTCH1) +v_PDPK1, (v_PIP3 | v_IGF1R) +v_PGR, (v_PG & !(v_ERK_i & v_ESR1)) +v_PI3K_c, ((v_EGFR & (v_INSR & (v_RAS_i & v_ESR1))) | (v_IRS1 & v_IGF1R)) +v_PIM, v_STAT5 +v_PIP3, (v_PI3K_c & !v_PTEN) +v_PPARG, (!v_GATA3 & v_CEBPB) +v_PRB, !v_CYCLIN_D_c +v_PRKAA2, (v_STK11 | !v_PRKACA) +v_PRKACA, (v_AKT_i | v_WNT1) +v_PTEN, (v_S6K1 & !v_SRC) +v_RAC1, ((v_PI3K_c | v_DVL1) & !v_AKT_i) +v_RAF1, (v_HRAS | v_RAS_i) +v_RAS_i, ((v_SOS1 & v_PIP3) | (v_PIP3 & v_IGF1)) +v_RELA, (v_NFKB1 & v_PIM) +v_RHEB, !v_TSC2 +v_RND1, (v_GRB7 | v_DVL1) +v_S6K1, v_MTORC1_c +v_SGK1, ((v_MTORC2_c & v_MTORC1_c) & v_PDPK1) +v_SOS1, v_GRB2 +v_SRC, (v_PRKACA & v_ABL1) +v_STAT1, (v_JAK2 | v_SRC) +v_STAT3, (v_IL1B & (v_SRC & (v_MAPK8 & v_JAK2))) +v_STAT5, (v_JAK2 & (v_SRC & v_EGFR)) +v_STK11, !v_ERK_i +v_TCF4, (v_CTNNB1 & v_JUN) +v_TEAD1, v_YAP1 +v_TRADD, !v_KRT14 +v_TSC2, (!(v_AKT_i & v_ERK_i) | (v_PRKAA2 | v_GSK3B)) +v_TWIST1, (v_ERK_i & (v_AKT_i & v_MAPK8)) +v_YAP1, (!v_LATS1 & v_ABL1) diff --git a/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/model.sbml b/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/model.sbml new file mode 100644 index 0000000..7015c75 --- /dev/null +++ b/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/model.sbml @@ -0,0 +1 @@ +v_SRC1v_GRB21v_PRB1v_ABL11v_MTORC2_c1v_PDPK11v_PIP31v_IRS11v_IGF1R1v_NRG11v_IGF11v_AXIN11v_DVL11v_GSK3B1v_PAK11v_AKT_i1v_ERK_i1v_PIM1v_BIM1v_P531v_BID1v_MCL11v_BIM1v_P531v_BID1v_MCL11v_BAD1v_BIM1v_CREB11v_ERK_i1v_BAD1v_BIM1v_CREB11v_CASP81v_BCL21v_BCLXL1v_FOXO31v_FOXO11v_CASP91v_FADD1v_NF11v_ERK_i1v_SRC1v_CYCS1v_CASP81v_CASP31v_ERK_i1v_PRKACA1v_BCLXL1v_AKT_i1v_MYC1v_SRC1v_CASP31v_ABL21v_CREB11v_AKT_i1v_PTEN1v_DC1v_WNT11v_SRC1v_YAP11v_TCF41v_TEAD11v_GSK3B1v_CDKN2A1v_P211v_ESR11v_KMT2D1v_FOXO31v_MYC1v_EIF4E1v_IGF11v_NRG11v_BAK11v_BAX1v_APC1v_GSK3B1v_FZD31v_NF11v_PRB1v_EGF1v_HER21v_HER31v_MEK_i1v_IVEBP11v_MEK_i1v_AKT_i1v_FOXO31v_KMT2D1v_ES1v_PGR1v_TRADD1v_FAS1v_FASLG1v_P531v_AKT_i1v_FASLG1v_P531v_FOXO31v_SGK11v_AKT_i1v_AKT_i1v_WNT11v_CREB11v_STAT11v_IRS11v_LATS11v_EGFR1v_SRC1v_INSR1v_PRKACA1v_AKT_i1v_ERK_i1v_HER31v_EGF1v_NRG11v_HER21v_NCID1v_NCID1v_SOS11v_PIP31v_NF11v_PIP31v_IGF11v_PDPK11v_IGF11v_SRC1v_INS1v_FOXO31v_ESR11v_NOS31v_RELA1v_IL1B1v_IL61v_IL61v_STAT51v_INS1v_FOXO31v_S6K11v_INSR1v_IGF1R1v_MTORC1_c1v_IL6R1v_ABL11v_IL81v_IRS11v_RELA1v_MAPK81v_ERK_i1v_PPARG1v_PAX71v_AKT_i1v_PAK21v_EGFR1v_NF21v_LCK1v_ERK_i1v_AKT_i1v_RAC11v_RND11v_GSK3B1v_ERK_i1v_P531v_AKT_i1v_RAF11v_PIM1v_RHEB1v_NRG11v_IGF11v_PIP31v_S6K11v_CTNNB11v_PIM1v_ERK_i1v_STAT31v_GSK3B1v_ESR11v_KMT2D1v_FOXO31v_EIF4E1v_IGF11v_NRG11v_HES11v_ABL11v_HEY11v_MYOD11v_NOTCH11v_SGK11v_PRKACA1v_TWIST11v_P531v_NEDD4L1v_NOTCH11v_HSP90AA11v_AKT_i1v_DLL_i1v_CTNNB11v_LCK1v_MDM21v_ERK_i1v_AKT_i1v_MYC1v_MDM21v_TCF41v_RAC11v_SRC1v_MYOG1v_HEY11v_HES11v_NOTCH11v_PIP31v_IGF1R1v_PG1v_ERK_i1v_ESR11v_EGFR1v_INSR1v_RAS_i1v_ESR11v_IRS11v_IGF1R1v_STAT51v_PI3K_c1v_PTEN1v_GATA31v_CEBPB1v_CYCLIN_D_c1v_STK111v_PRKACA1v_AKT_i1v_WNT11v_S6K11v_SRC1v_PI3K_c1v_DVL11v_AKT_i1v_HRAS1v_RAS_i1v_SOS11v_PIP31v_PIP31v_IGF11v_NFKB11v_PIM1v_TSC21v_GRB71v_DVL11v_MTORC1_c1v_MTORC2_c1v_MTORC1_c1v_PDPK11v_GRB21v_PRKACA1v_ABL11v_JAK21v_SRC1v_IL1B1v_SRC1v_MAPK81v_JAK21v_JAK21v_SRC1v_EGFR1v_ERK_i1v_CTNNB11v_JUN1v_YAP11v_KRT141v_AKT_i1v_ERK_i1v_PRKAA21v_GSK3B1v_ERK_i1v_AKT_i1v_MAPK81v_LATS11v_ABL11 \ No newline at end of file diff --git a/report/.~lock.online_only_table_1.xlsx# b/report/.~lock.online_only_table_1.xlsx# deleted file mode 100644 index fc36eaf..0000000 --- a/report/.~lock.online_only_table_1.xlsx# +++ /dev/null @@ -1 +0,0 @@ -,natalie,natalie-IdeaPad-5-Pro-14ITL6,21.09.2024 20:21,file:///home/natalie/.config/libreoffice/4; \ No newline at end of file diff --git a/sources/232_BREAST-CANCER-PATHWAYS-MCF7-COMPLETE/citation.bib b/sources/232_BREAST-CANCER-PATHWAYS-MCF7-COMPLETE/citation.bib new file mode 100644 index 0000000..e728dfa --- /dev/null +++ b/sources/232_BREAST-CANCER-PATHWAYS-MCF7-COMPLETE/citation.bib @@ -0,0 +1,8 @@ +@article{bbm-232, + author = {Taoma, Kittisak and Ruengjitchatchawalya, Marasri and Liangruksa, Monrudee and Laomettachit, Teeraphan}, + year = {2024}, + doi = {https://doi.org/10.1371/journal.pone.0298788}, + title = {Boolean modeling of breast cancer signaling pathways uncovers mechanisms of drug synergy}, + publisher = {PLOS ONE} +} + diff --git a/sources/232_BREAST-CANCER-PATHWAYS-MCF7-COMPLETE/metadata.json b/sources/232_BREAST-CANCER-PATHWAYS-MCF7-COMPLETE/metadata.json new file mode 100644 index 0000000..73a1729 --- /dev/null +++ b/sources/232_BREAST-CANCER-PATHWAYS-MCF7-COMPLETE/metadata.json @@ -0,0 +1,7 @@ +{ + "id": 232, + "name": "BREAST-CANCER-PATHWAYS-MCF7-COMPLETE", + "url-publication": "https://doi.org/10.1371/journal.pone.0298788", + "url-model": "https://github.com/Ktaoma/BoolSyn", + "keywords": ["source (?)","curated (?)","repaired (?)", "multi-valued (?)"] +} diff --git a/sources/232_BREAST-CANCER-PATHWAYS-MCF7-COMPLETE/notes.md b/sources/232_BREAST-CANCER-PATHWAYS-MCF7-COMPLETE/notes.md new file mode 100644 index 0000000..370048f --- /dev/null +++ b/sources/232_BREAST-CANCER-PATHWAYS-MCF7-COMPLETE/notes.md @@ -0,0 +1,11 @@ +### Modifications + +Removed regulations: +WNT1, WNT1 +PG, PG +NRG1, NRG1 +DLL_i, DLL_i +EGF, EGF +ES, ES +IGF1, IGF1 +INS, INS diff --git a/sources/232_BREAST-CANCER-PATHWAYS-MCF7-COMPLETE/source.bnet b/sources/232_BREAST-CANCER-PATHWAYS-MCF7-COMPLETE/source.bnet new file mode 100644 index 0000000..83c1c01 --- /dev/null +++ b/sources/232_BREAST-CANCER-PATHWAYS-MCF7-COMPLETE/source.bnet @@ -0,0 +1,110 @@ +IL6, IL1B & IL6 +IL6R, IL6 +JAK2, (IL6R | ABL1 | IL8) | IRS1 +STAT5, JAK2 & SRC & EGFR +IL8, STAT5 +PIM, STAT5 +STAT3, IL1B & SRC & MAPK8 & JAK2 +STAT1, JAK2 | SRC +GATA3, !STAT1 +PPARG, !GATA3 & CEBPB +FZD3, WNT1 | CREB1 +DVL1, FZD3 & NF1 +AXIN1, !DVL1 & GSK3B +APC, AXIN1 +DC, APC & GSK3B +CTNNB1, !DC & (WNT1 & SRC & YAP1) +TCF4, CTNNB1 & JUN +PAK1, TCF4 +NOTCH1, (DLL_i & CTNNB1 & LCK) | MDM2 +NFKB1, NOTCH1 +RELA, NFKB1 & PIM +JUN, (RELA | MAPK8) & (ERK_i & PPARG) +NCID, NOTCH1 +HES1, NCID +HEY1, NCID +MYOD1, !(HES1 | ABL1) +MYOG, !HEY1 & MYOD1 +PAX7, !(MYOG | HEY1 | HES1) & NOTCH1 +KMT2D, PAX7 | !AKT_i +IGF1R, (IGF1 | SRC | INS) | (FOXO3 & ESR1) +HER3, NRG1 | HER2 +HER2, HER3 | EGF +PGR, PG & !(ERK_i & ESR1) +ESR1, AKT_i | (FOXO3 & KMT2D) | (ES & PGR) +EGFR, (EGF & (HER2 & HER3)) & !MEK_i +GRB2, IRS1 | (LATS1 & (EGFR & SRC)) +SOS1, GRB2 +HRAS, ((SOS1 | PIP3) & !NF1) | (PIP3 & IGF1) +RAS_i, (SOS1 & PIP3) | (PIP3 & IGF1) +RAF1, (HRAS | RAS_i) +MEK_i, RAF1 +ERK_i, MEK_i +LCK, ERK_i & !AKT_i +TWIST1, ERK_i & AKT_i & MAPK8 +NF1, !TWIST1 & P53 +PI3K_c, (EGFR & INSR & RAS_i & ESR1) | (IRS1 & IGF1R ) +PTEN, S6K1 & !SRC +PIP3, PI3K_c & !PTEN +PDPK1, PIP3 | IGF1R +MTORC2_c, PIP3 & !S6K1 +AKT_i, (((MTORC2_c & PDPK1) & PIP3) & (IRS1 & IGF1R)) | (NRG1 | IGF1) +FOXO3, !AKT_i +FOXO1, !(SGK1 | AKT_i) +CREB1, AKT_i & !PTEN +GSK3B, !(AKT_i & ERK_i) +TSC2, !(AKT_i & ERK_i) | (PRKAA2 | GSK3B) +RHEB, !TSC2 +MTORC1_c, (PIM | RHEB) | (NRG1 | IGF1) +S6K1, MTORC1_c +IRS1, !S6K1 & (INSR | IGF1R) +SGK1, (MTORC2_c & MTORC1_c) & PDPK1 +NEDD4L, !(SGK1 | PRKACA) +NF2, NEDD4L +LATS1, NF2 | LCK +YAP1, !LATS1 & ABL1 +TEAD1, YAP1 +IVEBP1, !MTORC1_c +EIF4E, !IVEBP1 +MYC, (((CTNNB1 | PIM | ERK_i | STAT3) & !GSK3B) | ((ESR1 & KMT2D & FOXO3 ) | (EIF4E & (IGF1 | NRG1)))) +P21, !(ERK_i & AKT_i & MYC) +CYCLIN_D_c, ((TCF4 | TEAD1) & !(GSK3B | (CDKN2A & P21))) | ((ESR1 & KMT2D & FOXO3 & MYC ) | (EIF4E & (IGF1 | NRG1))) +PRB, !CYCLIN_D_c +E2F1, !PRB +P53, !MDM2 +MDM2, P53 | AKT_i +MCL1, !GSK3B | ERK_i +BAD, !( PAK1 | AKT_i | ERK_i | PIM) +BCL2, !(BAD & BIM) | (CREB1 | ERK_i) +BCLXL, !(BAD | BIM) & CREB1 +BIM, !(BCL2 & BCLXL) | (FOXO3 | FOXO1) +BID, CASP8 +BAK1, ((BIM | P53) | BID) & !MCL1 +BAX, ((BIM | P53) | BID) & !MCL1 +CYCS, BAK1 & BAX +CASP9, ((CYCS & CASP8) | CASP3) & !((ERK_i & PRKACA) | (BCLXL & AKT_i)) +CASP3, CASP9 +HSP90AA1, !PDPK1 +NOS3, HSP90AA1 & AKT_i +IL1B, NOS3 & RELA +STK11, !ERK_i +PRKAA2, STK11 | !PRKACA +PAK2, RAC1 & SRC +KRT14, PAK2 & EGFR +TRADD, !KRT14 +FASLG, FASLG | P53 | FOXO3 +FAS, (FASLG & P53) & !AKT_i +FADD, TRADD | FAS +CASP8, (FADD & NF1) & !(ERK_i & SRC) +PRKACA, AKT_i | WNT1 +SRC, PRKACA & ABL1 +ABL1, (SRC & GRB2) & !PRB +ABL2, ABL1 +CEBPB, ABL2 | CREB1 +CDKN2A, !(MYC | SRC) & CASP3 +INSR, INS | FOXO3 +GRB7, INSR & !PRKACA +RND1, GRB7 | DVL1 +RAC1, (PI3K_c | DVL1) & !AKT_i +MAPK8, RAC1 & RND1 +