diff --git a/bnet_to_aeon.py b/bnet_to_aeon.py index 1b0fea6..d27f728 100644 --- a/bnet_to_aeon.py +++ b/bnet_to_aeon.py @@ -2,4 +2,4 @@ import sys bn = BooleanNetwork.from_file(sys.argv[1]) -print(bn.to_aeon()) \ No newline at end of file +print(bn.to_aeon()) diff --git a/models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/README.md b/models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/README.md new file mode 100644 index 0000000..354d8b4 --- /dev/null +++ b/models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/README.md @@ -0,0 +1,37 @@ +# \[231\] BREAST-CANCER-SIGNALLING-PATHWAYS + + - Variables: 110 + - Inputs: 7 + - Regulations: 268 + - Publication: https://doi.org/10.1371/journal.pone.0298788 + - Source: https://github.com/Ktaoma/BoolSyn + - Keywords: source (?), curated (?), repaired (?), multi-valued (?) + + +### Modifications + +Rows deleted from the model: + +DLL_i, DLL_i +IGF1, IGF1 +NRG1, NRG1 +PG, PG +ES, ES +EGF, EGF +INS, INS + + +### Model citation + +``` +@article{bbm-231, + 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-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/metadata.json b/models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/metadata.json new file mode 100644 index 0000000..c2f0b0a --- /dev/null +++ b/models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/metadata.json @@ -0,0 +1,17 @@ +{ + "id": 231, + "name": "BREAST-CANCER-SIGNALLING-PATHWAYS", + "url-publication": "https://doi.org/10.1371/journal.pone.0298788", + "url-model": "https://github.com/Ktaoma/BoolSyn", + "keywords": [ + "source (?)", + "curated (?)", + "repaired (?)", + "multi-valued (?)" + ], + "variables": 110, + "inputs": 7, + "regulations": 268, + "notes": "### Modifications\n\nRows deleted from the model:\n\nDLL_i, DLL_i\nIGF1, IGF1\nNRG1, NRG1\nPG, PG\nES, ES\nEGF, EGF\nINS, INS\n", + "bib": "@article{bbm-231,\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-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/model.aeon b/models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/model.aeon new file mode 100644 index 0000000..f8d3389 --- /dev/null +++ b/models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/model.aeon @@ -0,0 +1,378 @@ +v_GRB2 -? 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_ESR1 -? v_CYCLIN_D_c +v_GSK3B -? v_CYCLIN_D_c +v_MYC -? 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_CASP3 -? v_HES1 +v_NCID -? v_HES1 +v_NCID -? v_HEY1 +v_IGF1 -? v_HRAS +v_NF1 -? v_HRAS +v_PI3K_c -? 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_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_GSK3B -? 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_S6K1 -? 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_PI3K_c -? 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_PGR -? v_WNT1 +v_WNT1 -? v_WNT1 +v_ABL1 -? v_YAP1 +v_LATS1 -? v_YAP1 +$v_ABL1: (v_SRC | v_GRB2) +$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_ESR1 | v_MYC))) & !(v_GSK3B | (v_CDKN2A | v_P21))) +$v_CYCS: (v_BAK1 | v_BAX) +$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_ES | (v_PGR | v_KMT2D)))) +$v_FADD: (v_TRADD | v_FAS) +$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) +$v_HES1: (v_NCID & !v_CASP3) +$v_HEY1: v_NCID +$v_HRAS: (((v_SOS1 | v_PI3K_c) & !v_NF1) | (v_PI3K_c | v_IGF1)) +$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 +$v_MTORC1_c: (v_RHEB | (v_NRG1 | v_IGF1)) +$v_MTORC2_c: (v_PIP3 & !v_S6K1) +$v_MYC: ((v_CTNNB1 | (v_PIM | (v_ERK_i | (v_STAT3 | (v_ESR1 | v_EIF4E))))) & !v_GSK3B) +$v_MYOD1: !(v_HES1 | v_ABL1) +$v_MYOG: (!v_HEY1 & v_MYOD1) +$v_NCID: v_NOTCH1 +$v_NEDD4L: !(v_S6K1 | (v_SGK1 | v_PRKACA)) +$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_PI3K_c) | (v_PI3K_c | 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)) +$v_WNT1: (v_PGR | v_WNT1) +$v_YAP1: (!v_LATS1 & v_ABL1) diff --git a/models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/model.bnet b/models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/model.bnet new file mode 100644 index 0000000..5989390 --- /dev/null +++ b/models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/model.bnet @@ -0,0 +1,111 @@ +targets,factors +v_ABL1, (v_SRC | v_GRB2) +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_ESR1 | v_MYC))) & !(v_GSK3B | (v_CDKN2A | v_P21))) +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_ES | (v_PGR | v_KMT2D)))) +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_CASP3) +v_HEY1, v_NCID +v_HRAS, (((v_SOS1 | v_PI3K_c) & !v_NF1) | (v_PI3K_c | 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_RHEB | (v_NRG1 | v_IGF1)) +v_MTORC2_c, (v_PIP3 & !v_S6K1) +v_MYC, ((v_CTNNB1 | (v_PIM | (v_ERK_i | (v_STAT3 | (v_ESR1 | v_EIF4E))))) & !v_GSK3B) +v_MYOD1, !(v_HES1 | v_ABL1) +v_MYOG, (!v_HEY1 & v_MYOD1) +v_NCID, v_NOTCH1 +v_NEDD4L, !(v_S6K1 | (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_PI3K_c) | (v_PI3K_c | 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_WNT1, (v_PGR | v_WNT1) +v_YAP1, (!v_LATS1 & v_ABL1) diff --git a/models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/model.sbml b/models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/model.sbml new file mode 100644 index 0000000..9e1840d --- /dev/null +++ b/models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/model.sbml @@ -0,0 +1 @@ +v_SRC1v_GRB21v_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_ESR11v_MYC1v_GSK3B1v_CDKN2A1v_P211v_BAK11v_BAX1v_APC1v_GSK3B1v_FZD31v_NF11v_PRB1v_EGF1v_HER21v_HER31v_MEK_i1v_IVEBP11v_MEK_i1v_AKT_i1v_FOXO31v_ES1v_PGR1v_KMT2D1v_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_CASP31v_NCID1v_SOS11v_PI3K_c1v_NF11v_PI3K_c1v_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_RHEB1v_NRG11v_IGF11v_PIP31v_S6K11v_CTNNB11v_PIM1v_ERK_i1v_STAT31v_ESR11v_EIF4E1v_GSK3B1v_HES11v_ABL11v_HEY11v_MYOD11v_NOTCH11v_S6K11v_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_PI3K_c1v_PI3K_c1v_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_PGR1v_WNT11v_LATS11v_ABL11 \ No newline at end of file diff --git a/models/summary.csv b/models/summary.csv index 36c902f..f119f5e 100644 --- a/models/summary.csv +++ b/models/summary.csv @@ -229,3 +229,4 @@ ID, name, variables, regulations 228, INTEGRATION-OF-SIGNALING-AND-KINETIC-MODELS, 47, 9, 107 229, CALCIUM-SIGNALING-STOMATAL-CLOSURE, 52, 4, 128 230, HEPATOCYTE-GROWTH-FACTOR, 50, 5, 76 +231, BREAST-CANCER-SIGNALLING-PATHWAYS, 110, 7, 268 diff --git a/report/online_only_table_1.xlsx b/report/online_only_table_1.xlsx index 9cb2673..2986780 100644 Binary files a/report/online_only_table_1.xlsx and b/report/online_only_table_1.xlsx differ diff --git a/sources/231_BREAST-CANCER-SIGNALLING-PATHWAYS/citation.bib b/sources/231_BREAST-CANCER-SIGNALLING-PATHWAYS/citation.bib new file mode 100644 index 0000000..809c357 --- /dev/null +++ b/sources/231_BREAST-CANCER-SIGNALLING-PATHWAYS/citation.bib @@ -0,0 +1,8 @@ +@article{bbm-231, + 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/231_BREAST-CANCER-SIGNALLING-PATHWAYS/metadata.json b/sources/231_BREAST-CANCER-SIGNALLING-PATHWAYS/metadata.json new file mode 100644 index 0000000..64f4414 --- /dev/null +++ b/sources/231_BREAST-CANCER-SIGNALLING-PATHWAYS/metadata.json @@ -0,0 +1,7 @@ +{ + "id": 231, + "name": "BREAST-CANCER-SIGNALLING-PATHWAYS", + "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/231_BREAST-CANCER-SIGNALLING-PATHWAYS/notes.md b/sources/231_BREAST-CANCER-SIGNALLING-PATHWAYS/notes.md new file mode 100644 index 0000000..d911734 --- /dev/null +++ b/sources/231_BREAST-CANCER-SIGNALLING-PATHWAYS/notes.md @@ -0,0 +1,11 @@ +### Modifications + +Rows deleted from the source file: + +DLL_i, DLL_i +IGF1, IGF1 +NRG1, NRG1 +PG, PG +ES, ES +EGF, EGF +INS, INS diff --git a/sources/231_BREAST-CANCER-SIGNALLING-PATHWAYS/source.bnet b/sources/231_BREAST-CANCER-SIGNALLING-PATHWAYS/source.bnet new file mode 100644 index 0000000..3d1f0cc --- /dev/null +++ b/sources/231_BREAST-CANCER-SIGNALLING-PATHWAYS/source.bnet @@ -0,0 +1,111 @@ +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 +WNT1, PGR|WNT1 +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&!CASP3 +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|(ES|PGR|KMT2D) +EGFR, (EGF|(HER2&HER3))&!MEK_i +GRB2, IRS1|(LATS1|(EGFR|SRC)) +SOS1, GRB2 +HRAS, ((SOS1|PI3K_c)&!NF1)|(PI3K_c|IGF1) +RAS_i, (SOS1|PI3K_c)|(PI3K_c|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, RHEB|(NRG1|IGF1) +S6K1, MTORC1_c +IRS1, !S6K1&(INSR|IGF1R) +SGK1, (MTORC2_c|MTORC1_c)|PDPK1 +NEDD4L, !(S6K1|SGK1|PRKACA) +NF2, NEDD4L +LATS1, NF2|LCK +YAP1, !LATS1&ABL1 +TEAD1, YAP1 +IVEBP1, !MTORC1_c +EIF4E, !IVEBP1 +MYC, (CTNNB1|PIM|ERK_i|STAT3|ESR1|EIF4E)&!GSK3B +P21, !(ERK_i|AKT_i|MYC) +CYCLIN_D_c, ((TCF4|TEAD1|ESR1|MYC)&!(GSK3B|(CDKN2A|P21))) +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) +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 +