From d25d41e8a439fbd0c13cb9ac6ccc347168946f4f Mon Sep 17 00:00:00 2001 From: Natalia Florekova Date: Sun, 22 Sep 2024 09:30:07 +0200 Subject: [PATCH 01/11] Added model 236 - breast cancer signalling pathways BT549 complete --- .../README.md | 37 ++ .../metadata.json | 17 + .../model.aeon | 372 ++++++++++++++++++ .../model.bnet | 110 ++++++ .../model.sbml | 1 + models/summary.csv | 1 + report/.~lock.online_only_table_1.xlsx# | 2 +- report/online_only_table_1.xlsx | Bin 58516 -> 58560 bytes .../citation.bib | 8 + .../metadata.json | 7 + .../notes.md | 11 + .../source.bnet | 110 ++++++ 12 files changed, 675 insertions(+), 1 deletion(-) create mode 100644 models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/README.md create mode 100644 models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/metadata.json create mode 100644 models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/model.aeon create mode 100644 models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/model.bnet create mode 100644 models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/model.sbml create mode 100644 sources/236_BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE/citation.bib create mode 100644 sources/236_BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE/metadata.json create mode 100644 sources/236_BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE/notes.md create mode 100644 sources/236_BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE/source.bnet diff --git a/models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/README.md b/models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/README.md new file mode 100644 index 0000000..a654dc2 --- /dev/null +++ b/models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/README.md @@ -0,0 +1,37 @@ +# \[236\] BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE + + - Variables: 109 + - Inputs: 8 + - Regulations: 263 + - Publication: https://doi.org/10.1371/journal.pone.0298788 + - Source: https://github.com/Ktaoma/BoolSyn + - Keywords: source (?), curated (?), repaired (?), multi-valued (?) + + +### Modifications + +Removed regulations: +INS +PG, PG +NRG1, NRG1 +FASLG, FASLG +ES, ES +EGF, EGF +DLL_i, DLL_i +IGF1, IGF1 + + +### Model citation + +``` +@article{bbm-236, + 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-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/metadata.json b/models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/metadata.json new file mode 100644 index 0000000..b5b5886 --- /dev/null +++ b/models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/metadata.json @@ -0,0 +1,17 @@ +{ + "id": 236, + "name": "BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-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": 263, + "notes": "### Modifications\n\nRemoved regulations:\nINS\nPG, PG\nNRG1, NRG1\nFASLG, FASLG\nES, ES\nEGF, EGF\nDLL_i, DLL_i\nIGF1, IGF1\n", + "bib": "@article{bbm-236,\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-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/model.aeon b/models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/model.aeon new file mode 100644 index 0000000..fd136ac --- /dev/null +++ b/models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/model.aeon @@ -0,0 +1,372 @@ +v_GRB2 -? v_ABL1 +v_ABL1 -? v_ABL2 +v_IGF1R -? v_AKT_i +v_IRS1 -? v_AKT_i +v_MTORC2_c -? 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_AKT_i -? v_BAX +v_BID -? v_BAX +v_BIM -? v_BAX +v_MCL1 -? v_BAX +v_P53 -? v_BAX +v_BAD -? v_BCL2 +v_BCLXL -? v_BCL2 +v_BIM -? v_BCL2 +v_CREB1 -? v_BCL2 +v_ERK_i -? v_BCL2 +v_BAD -? v_BCLXL +v_BCL2 -? v_BCLXL +v_BIM -? v_BCLXL +v_CREB1 -? v_BCLXL +v_CASP8 -? v_BID +v_P53 -? 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_CASP3 -? v_CASP9 +v_CYCS -? v_CASP9 +v_ERK_i -? v_CASP9 +v_PRKACA -? v_CASP9 +v_AKT_i -? v_CDKN2A +v_MYC -? v_CDKN2A +v_ABL2 -? v_CEBPB +v_AKT_i -? v_CREB1 +v_AKT_i -? v_CTNNB1 +v_DC -? v_CTNNB1 +v_PAK1 -? v_CTNNB1 +v_WNT1 -? v_CTNNB1 +v_CDKN2A -? v_CYCLIN_D_c +v_EIF4E -? v_CYCLIN_D_c +v_GSK3B -? v_CYCLIN_D_c +v_MYC -? v_CYCLIN_D_c +v_P21 -? v_CYCLIN_D_c +v_STAT3 -? 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_PRB -? v_E2F1 +v_EGF -? v_EGFR +v_HER2 -? v_EGFR +v_HER3 -? 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_P53 -? v_FADD +v_TRADD -? v_FADD +v_AKT_i -? v_FAS +v_FASLG -? v_FAS +v_P53 -? v_FAS +v_SGK1 -? v_FOXO1 +v_AKT_i -? v_FOXO3 +v_ERK_i -? v_FOXO3 +v_WNT1 -? v_FZD3 +v_KMT2D -? v_GATA3 +v_STAT1 -? v_GATA3 +v_EGFR -? v_GRB2 +v_HER2 -? v_GRB2 +v_IRS1 -? v_GRB2 +v_LATS1 -? v_GRB2 +v_SRC -? v_GRB2 +v_INSR -? v_GRB7 +v_AKT_i -? v_GSK3B +v_ERK_i -? v_GSK3B +v_ESR1 -? v_HER2 +v_FOXO3 -? 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_NF1 -? v_HRAS +v_PIP3 -? v_HRAS +v_SOS1 -? v_HRAS +v_ABL1 -? v_HSP90AA1 +v_PDPK1 -? v_HSP90AA1 +v_ESR1 -? v_IGF1R +v_FOXO3 -? v_IGF1R +v_IGF1 -? v_IGF1R +v_NOS3 -? v_IL1B +v_RELA -? v_IL1B +v_IL1B -? v_IL6 +v_IL6 -? v_IL6 +v_IL6 -? v_IL6R +v_ERK_i -? v_IL8 +v_STAT5 -? v_IL8 +v_INS -? v_INSR +v_INSR -? 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_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_ESR1 -? v_MYC +v_FOXO3 -? v_MYC +v_GSK3B -? v_MYC +v_JAK2 -? v_MYC +v_PIM -? v_MYC +v_STAT3 -? v_MYC +v_HES1 -? v_MYOD1 +v_HEY1 -? v_MYOG +v_MYOD1 -? v_MYOG +v_NOTCH1 -? v_NCID +v_SGK1 -? v_NEDD4L +v_TWIST1 -? v_NF1 +v_NEDD4L -? v_NF2 +v_PAK1 -? v_NF2 +v_PAK2 -? v_NF2 +v_PRKACA -? v_NF2 +v_GSK3B -? v_NFKB1 +v_NOTCH1 -? v_NFKB1 +v_AKT_i -? v_NOS3 +v_HSP90AA1 -? v_NOS3 +v_CTNNB1 -? v_NOTCH1 +v_DLL_i -? v_NOTCH1 +v_AKT_i -? v_P21 +v_ERK_i -? v_P21 +v_MAPK8 -? v_P21 +v_MYC -? v_P21 +v_MYOG -? v_P21 +v_PIM -? v_P21 +v_MDM2 -? v_P53 +v_AKT_i -? v_PAK1 +v_TCF4 -? v_PAK1 +v_RAC1 -? v_PAK2 +v_SRC -? v_PAK2 +v_FOXO1 -? v_PAX7 +v_MYOG -? v_PAX7 +v_IGF1R -? v_PDPK1 +v_PIP3 -? v_PDPK1 +v_AKT_i -? v_PGR +v_ERK_i -? v_PGR +v_ESR1 -? v_PGR +v_P21 -? v_PGR +v_PG -? v_PGR +v_EGFR -? v_PI3K_c +v_ESR1 -? v_PI3K_c +v_IGF1R -? v_PI3K_c +v_IRS1 -? 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_STK11 -? v_PRKAA2 +v_AKT_i -? v_PRKACA +v_EGFR -? v_PRKACA +v_JUN -? 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_SRC -? v_RAC1 +v_HRAS -? v_RAF1 +v_RAS_i -? v_RAF1 +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_ERK_i -? v_S6K1 +v_MTORC1_c -? v_S6K1 +v_MTORC1_c -? v_SGK1 +v_MTORC2_c -? v_SGK1 +v_PDPK1 -? v_SGK1 +v_ABL1 -? v_SOS1 +v_GRB2 -? v_SOS1 +v_ABL1 -? v_SRC +v_PRKACA -? v_SRC +v_EGFR -? v_STAT1 +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_ERK_i -? v_STK11 +v_FOXO3 -? 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_ERK_i -? v_TWIST1 +v_PGR -? v_WNT1 +v_WNT1 -? v_WNT1 +v_ABL1 -? v_YAP1 +v_LATS1 -? v_YAP1 +$v_ABL1: v_GRB2 +$v_ABL2: v_ABL1 +$v_AKT_i: (((v_MTORC2_c | v_PDPK1) & v_PIP3) & (v_IRS1 | v_IGF1R)) +$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_AKT_i)) +$v_BCL2: (!(v_BAD | v_BIM) & (v_CREB1 & (v_ERK_i & v_BCLXL))) +$v_BCLXL: (!(v_BAD | v_BIM) & (v_CREB1 & v_BCL2)) +$v_BID: (v_CASP8 & v_P53) +$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)) +$v_CASP9: ((v_CYCS | v_CASP3) & !((v_PRKACA & v_AKT_i) | v_ERK_i)) +$v_CDKN2A: !(v_MYC & v_AKT_i) +$v_CEBPB: v_ABL2 +$v_CREB1: v_AKT_i +$v_CTNNB1: (!v_DC & (v_AKT_i & (v_WNT1 & v_PAK1))) +$v_CYCLIN_D_c: (((v_TCF4 | v_TEAD1) & !(v_GSK3B | (v_CDKN2A | v_P21))) | (v_MYC & (v_EIF4E & v_STAT3))) +$v_CYCS: (v_BAK1 | v_BAX) +$v_DC: (v_APC & v_GSK3B) +$v_DVL1: v_FZD3 +$v_E2F1: !v_PRB +$v_EGFR: (v_EGF & (v_HER2 & v_HER3)) +$v_EIF4E: !v_IVEBP1 +$v_ERK_i: v_MEK_i +$v_ESR1: ((v_ES & (v_AKT_i & v_KMT2D)) & (v_PGR & v_FOXO3)) +$v_FADD: (v_TRADD & (v_FAS & v_P53)) +$v_FAS: ((v_FASLG | v_P53) | !v_AKT_i) +$v_FOXO1: !v_SGK1 +$v_FOXO3: !(v_AKT_i | v_ERK_i) +$v_FZD3: v_WNT1 +$v_GATA3: (v_KMT2D & !v_STAT1) +$v_GRB2: (v_IRS1 | (v_HER2 & (v_LATS1 & (v_SRC & v_EGFR)))) +$v_GRB7: v_INSR +$v_GSK3B: !(v_AKT_i & v_ERK_i) +$v_HER2: (v_HER3 & (v_FOXO3 & v_ESR1)) +$v_HER3: (v_NRG1 & v_HER2) +$v_HES1: (v_NCID & !v_CASP3) +$v_HEY1: v_NCID +$v_HRAS: ((v_SOS1 | v_PIP3) & !v_NF1) +$v_HSP90AA1: (!v_PDPK1 | v_ABL1) +$v_IGF1R: (v_IGF1 & (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_ERK_i) +$v_INSR: (v_INS | v_INSR) +$v_IRS1: (!v_S6K1 | (v_INSR & v_IGF1R)) +$v_IVEBP1: !v_MTORC1_c +$v_JAK2: ((v_IL6R | (v_ABL1 | v_IL8)) | v_IRS1) +$v_JUN: ((v_RELA | (v_MAPK8 | v_PPARG)) | v_ERK_i) +$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_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_GSK3B) | ((v_STAT3 & v_JAK2) | (v_ESR1 & v_FOXO3))) | v_EIF4E) +$v_MYOD1: !v_HES1 +$v_MYOG: (!v_HEY1 | v_MYOD1) +$v_NCID: v_NOTCH1 +$v_NEDD4L: !v_SGK1 +$v_NF1: !v_TWIST1 +$v_NF2: (v_NEDD4L | !(v_PAK2 & (v_PAK1 & v_PRKACA))) +$v_NFKB1: (v_NOTCH1 | v_GSK3B) +$v_NOS3: (v_HSP90AA1 & v_AKT_i) +$v_NOTCH1: (v_DLL_i & v_CTNNB1) +$v_P21: (!(v_ERK_i | (v_MYC | v_AKT_i)) & (v_MYOG & (v_MAPK8 & v_PIM))) +$v_P53: !v_MDM2 +$v_PAK1: (v_TCF4 & v_AKT_i) +$v_PAK2: (v_RAC1 | v_SRC) +$v_PAX7: (!v_MYOG & v_FOXO1) +$v_PDPK1: (v_PIP3 | v_IGF1R) +$v_PGR: ((v_P21 & v_PG) & !(v_ESR1 | (v_ERK_i | v_AKT_i))) +$v_PI3K_c: ((v_EGFR & v_ESR1) | (v_IRS1 & v_IGF1R)) +$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 +$v_PRKACA: (v_EGFR | (v_AKT_i & (v_WNT1 & v_JUN))) +$v_PTEN: (v_S6K1 | !v_SRC) +$v_RAC1: ((v_PI3K_c | (v_SRC | v_DVL1)) | !v_AKT_i) +$v_RAF1: (v_HRAS | v_RAS_i) +$v_RAS_i: (v_SOS1 | v_PIP3) +$v_RELA: (v_NFKB1 | v_PIM) +$v_RHEB: !v_TSC2 +$v_RND1: (v_GRB7 | v_DVL1) +$v_S6K1: (v_MTORC1_c & v_ERK_i) +$v_SGK1: ((v_MTORC2_c | v_MTORC1_c) | v_PDPK1) +$v_SOS1: (v_GRB2 | v_ABL1) +$v_SRC: (v_PRKACA | v_ABL1) +$v_STAT1: (v_JAK2 & (v_SRC & v_EGFR)) +$v_STAT3: ((v_IL1B | (v_SRC | v_MAPK8)) | v_JAK2) +$v_STAT5: (v_JAK2 & v_EGFR) +$v_STK11: !(v_ERK_i & v_FOXO3) +$v_TCF4: (v_CTNNB1 | v_JUN) +$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_WNT1: (v_PGR & v_WNT1) +$v_YAP1: (!v_LATS1 | v_ABL1) diff --git a/models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/model.bnet b/models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/model.bnet new file mode 100644 index 0000000..c60c1eb --- /dev/null +++ b/models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/model.bnet @@ -0,0 +1,110 @@ +targets,factors +v_ABL1, v_GRB2 +v_ABL2, v_ABL1 +v_AKT_i, (((v_MTORC2_c | v_PDPK1) & v_PIP3) & (v_IRS1 | v_IGF1R)) +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_AKT_i)) +v_BCL2, (!(v_BAD | v_BIM) & (v_CREB1 & (v_ERK_i & v_BCLXL))) +v_BCLXL, (!(v_BAD | v_BIM) & (v_CREB1 & v_BCL2)) +v_BID, (v_CASP8 & v_P53) +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_CASP3) & !((v_PRKACA & v_AKT_i) | v_ERK_i)) +v_CDKN2A, !(v_MYC & v_AKT_i) +v_CEBPB, v_ABL2 +v_CREB1, v_AKT_i +v_CTNNB1, (!v_DC & (v_AKT_i & (v_WNT1 & v_PAK1))) +v_CYCLIN_D_c, (((v_TCF4 | v_TEAD1) & !(v_GSK3B | (v_CDKN2A | v_P21))) | (v_MYC & (v_EIF4E & v_STAT3))) +v_CYCS, (v_BAK1 | v_BAX) +v_DC, (v_APC & v_GSK3B) +v_DVL1, v_FZD3 +v_E2F1, !v_PRB +v_EGFR, (v_EGF & (v_HER2 & v_HER3)) +v_EIF4E, !v_IVEBP1 +v_ERK_i, v_MEK_i +v_ESR1, ((v_ES & (v_AKT_i & v_KMT2D)) & (v_PGR & v_FOXO3)) +v_FADD, (v_TRADD & (v_FAS & v_P53)) +v_FAS, ((v_FASLG | v_P53) | !v_AKT_i) +v_FOXO1, !v_SGK1 +v_FOXO3, !(v_AKT_i | v_ERK_i) +v_FZD3, v_WNT1 +v_GATA3, (v_KMT2D & !v_STAT1) +v_GRB2, (v_IRS1 | (v_HER2 & (v_LATS1 & (v_SRC & v_EGFR)))) +v_GRB7, v_INSR +v_GSK3B, !(v_AKT_i & v_ERK_i) +v_HER2, (v_HER3 & (v_FOXO3 & v_ESR1)) +v_HER3, (v_NRG1 & v_HER2) +v_HES1, (v_NCID & !v_CASP3) +v_HEY1, v_NCID +v_HRAS, ((v_SOS1 | v_PIP3) & !v_NF1) +v_HSP90AA1, (!v_PDPK1 | v_ABL1) +v_IGF1R, (v_IGF1 & (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_ERK_i) +v_INSR, (v_INS | v_INSR) +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_PPARG)) | v_ERK_i) +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_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_GSK3B) | ((v_STAT3 & v_JAK2) | (v_ESR1 & v_FOXO3))) | v_EIF4E) +v_MYOD1, !v_HES1 +v_MYOG, (!v_HEY1 | v_MYOD1) +v_NCID, v_NOTCH1 +v_NEDD4L, !v_SGK1 +v_NF1, !v_TWIST1 +v_NF2, (v_NEDD4L | !(v_PAK2 & (v_PAK1 & v_PRKACA))) +v_NFKB1, (v_NOTCH1 | v_GSK3B) +v_NOS3, (v_HSP90AA1 & v_AKT_i) +v_NOTCH1, (v_DLL_i & v_CTNNB1) +v_P21, (!(v_ERK_i | (v_MYC | v_AKT_i)) & (v_MYOG & (v_MAPK8 & v_PIM))) +v_P53, !v_MDM2 +v_PAK1, (v_TCF4 & v_AKT_i) +v_PAK2, (v_RAC1 | v_SRC) +v_PAX7, (!v_MYOG & v_FOXO1) +v_PDPK1, (v_PIP3 | v_IGF1R) +v_PGR, ((v_P21 & v_PG) & !(v_ESR1 | (v_ERK_i | v_AKT_i))) +v_PI3K_c, ((v_EGFR & 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_EGFR | (v_AKT_i & (v_WNT1 & v_JUN))) +v_PTEN, (v_S6K1 | !v_SRC) +v_RAC1, ((v_PI3K_c | (v_SRC | v_DVL1)) | !v_AKT_i) +v_RAF1, (v_HRAS | v_RAS_i) +v_RAS_i, (v_SOS1 | v_PIP3) +v_RELA, (v_NFKB1 | v_PIM) +v_RHEB, !v_TSC2 +v_RND1, (v_GRB7 | v_DVL1) +v_S6K1, (v_MTORC1_c & v_ERK_i) +v_SGK1, ((v_MTORC2_c | v_MTORC1_c) | v_PDPK1) +v_SOS1, (v_GRB2 | v_ABL1) +v_SRC, (v_PRKACA | v_ABL1) +v_STAT1, (v_JAK2 & (v_SRC & v_EGFR)) +v_STAT3, ((v_IL1B | (v_SRC | v_MAPK8)) | v_JAK2) +v_STAT5, (v_JAK2 & v_EGFR) +v_STK11, !(v_ERK_i & v_FOXO3) +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_WNT1, (v_PGR & v_WNT1) +v_YAP1, (!v_LATS1 | v_ABL1) diff --git a/models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/model.sbml b/models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/model.sbml new file mode 100644 index 0000000..f364673 --- /dev/null +++ b/models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/model.sbml @@ -0,0 +1 @@ +v_GRB21v_ABL11v_MTORC2_c1v_PDPK11v_PIP31v_IRS11v_IGF1R1v_AXIN11v_DVL11v_GSK3B1v_PAK11v_AKT_i1v_ERK_i1v_PIM1v_BIM1v_P531v_BID1v_MCL11v_BIM1v_P531v_BID1v_MCL11v_AKT_i1v_BAD1v_BIM1v_CREB11v_ERK_i1v_BCLXL1v_BAD1v_BIM1v_CREB11v_BCL21v_CASP81v_P531v_BCL21v_BCLXL1v_FOXO31v_FOXO11v_CASP91v_FADD1v_NF11v_ERK_i1v_SRC1v_CYCS1v_CASP31v_PRKACA1v_AKT_i1v_ERK_i1v_MYC1v_AKT_i1v_ABL21v_AKT_i1v_DC1v_AKT_i1v_WNT11v_PAK11v_TCF41v_TEAD11v_GSK3B1v_CDKN2A1v_P211v_MYC1v_EIF4E1v_STAT31v_BAK11v_BAX1v_APC1v_GSK3B1v_FZD31v_PRB1v_EGF1v_HER21v_HER31v_IVEBP11v_MEK_i1v_ES1v_AKT_i1v_KMT2D1v_PGR1v_FOXO31v_TRADD1v_FAS1v_P531v_FASLG1v_P531v_AKT_i1v_SGK11v_AKT_i1v_ERK_i1v_WNT11v_KMT2D1v_STAT11v_IRS11v_HER21v_LATS11v_SRC1v_EGFR1v_INSR1v_AKT_i1v_ERK_i1v_HER31v_FOXO31v_ESR11v_NRG11v_HER21v_NCID1v_CASP31v_NCID1v_SOS11v_PIP31v_NF11v_PDPK11v_ABL11v_IGF11v_FOXO31v_ESR11v_NOS31v_RELA1v_IL1B1v_IL61v_IL61v_STAT51v_ERK_i1v_INS1v_INSR1v_S6K11v_INSR1v_IGF1R1v_MTORC1_c1v_IL6R1v_ABL11v_IL81v_IRS11v_RELA1v_MAPK81v_PPARG1v_ERK_i1v_PAX71v_AKT_i1v_PAK21v_EGFR1v_NF21v_LCK1v_ERK_i1v_RAC11v_RND11v_GSK3B1v_ERK_i1v_P531v_AKT_i1v_RAF11v_RHEB1v_NRG11v_IGF11v_PIP31v_S6K11v_CTNNB11v_PIM1v_GSK3B1v_STAT31v_JAK21v_ESR11v_FOXO31v_EIF4E1v_HES11v_HEY11v_MYOD11v_NOTCH11v_SGK11v_TWIST11v_NEDD4L1v_PAK21v_PAK11v_PRKACA1v_NOTCH11v_GSK3B1v_HSP90AA11v_AKT_i1v_DLL_i1v_CTNNB11v_ERK_i1v_MYC1v_AKT_i1v_MYOG1v_MAPK81v_PIM1v_MDM21v_TCF41v_AKT_i1v_RAC11v_SRC1v_MYOG1v_FOXO11v_PIP31v_IGF1R1v_P211v_PG1v_ESR11v_ERK_i1v_AKT_i1v_EGFR1v_ESR11v_IRS11v_IGF1R1v_STAT51v_PI3K_c1v_PTEN1v_GATA31v_CEBPB1v_CYCLIN_D_c1v_STK111v_EGFR1v_AKT_i1v_WNT11v_JUN1v_S6K11v_SRC1v_PI3K_c1v_SRC1v_DVL11v_AKT_i1v_HRAS1v_RAS_i1v_SOS11v_PIP31v_NFKB11v_PIM1v_TSC21v_GRB71v_DVL11v_MTORC1_c1v_ERK_i1v_MTORC2_c1v_MTORC1_c1v_PDPK11v_GRB21v_ABL11v_PRKACA1v_ABL11v_JAK21v_SRC1v_EGFR1v_IL1B1v_SRC1v_MAPK81v_JAK21v_JAK21v_EGFR1v_ERK_i1v_FOXO31v_CTNNB11v_JUN1v_YAP11v_KRT141v_AKT_i1v_ERK_i1v_PRKAA21v_GSK3B1v_ERK_i1v_PGR1v_WNT11v_LATS11v_ABL11 \ No newline at end of file diff --git a/models/summary.csv b/models/summary.csv index 9e48638..04cddc5 100644 --- a/models/summary.csv +++ b/models/summary.csv @@ -234,3 +234,4 @@ ID, name, variables, regulations 233, BREAST-CANCER-SIGNALLING-PATHWAYS-T47D-COMPLETE, 109, 8, 260 234, BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE, 111, 6, 271 235, BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB231-COMPLETE, 110, 7, 270 +236, BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE, 109, 8, 263 diff --git a/report/.~lock.online_only_table_1.xlsx# b/report/.~lock.online_only_table_1.xlsx# index e4678b5..351c5c7 100644 --- a/report/.~lock.online_only_table_1.xlsx# +++ b/report/.~lock.online_only_table_1.xlsx# @@ -1 +1 @@ -,natalie,natalie-IdeaPad-5-Pro-14ITL6,22.09.2024 09:06,file:///home/natalie/.config/libreoffice/4; \ No newline at end of file +,natalie,natalie-IdeaPad-5-Pro-14ITL6,22.09.2024 09:28,file:///home/natalie/.config/libreoffice/4; \ No newline at end of file diff --git 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zb*cqNPBE7|#bMgqSn8-bhoN2`ZaVMW1|K_NCaV(5;cDpU zyj)pTQ-;5?8X zHLq;H$7<**>^Es;>(#8j;`3xffUm-$cFt?fH@{yiU}o?=H9ZhsNG~Kf= zg6)?YYW7qxMNOcntDl)V#3+Ww(v@K9U3oJxao25oI2CJTX~YU91d zf|Yn}iR~b59)fC~Jzd|#@wFjyFF+^f-S(n1%)^uQeQ3UyAi?8_dUI>?p`(MA7591q zqb=>dNkbdSyoL!R+|bz_hiw5_CMSpQ@<&EShnY-bHR241X@*K?;z4= zfnFjSmo`Nih`nRbo%%U7f{hiQ2y`tHh{B}LZ82Jfp$vl^Mm1(2wt18pzgoE zp#gk8CG+`-`6+6&%S0fQh??W;0D`)|zY!kE@x95u{AhzJ9~fvp$NT+l+|GVE;rKUY zF#H4UZ|D5}-e!bfo%0Ut{Xp}17Hc1<(J0tJ2pcK>*Rufmrm0caK$U6w-$MO9Uy83n PrGR169GJP2pAY^oh!`+! diff --git a/sources/236_BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE/citation.bib b/sources/236_BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE/citation.bib new file mode 100644 index 0000000..f9ca099 --- /dev/null +++ b/sources/236_BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE/citation.bib @@ -0,0 +1,8 @@ +@article{bbm-236, + 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/236_BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE/metadata.json b/sources/236_BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE/metadata.json new file mode 100644 index 0000000..d18c9c3 --- /dev/null +++ b/sources/236_BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE/metadata.json @@ -0,0 +1,7 @@ +{ + "id": 236, + "name": "BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-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/236_BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE/notes.md b/sources/236_BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE/notes.md new file mode 100644 index 0000000..a18d6d7 --- /dev/null +++ b/sources/236_BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE/notes.md @@ -0,0 +1,11 @@ +### Modifications + +Removed regulations: +INS, INS +PG, PG +NRG1, NRG1 +FASLG, FASLG +ES, ES +EGF, EGF +DLL_i, DLL_i +IGF1, IGF1 diff --git a/sources/236_BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE/source.bnet b/sources/236_BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE/source.bnet new file mode 100644 index 0000000..436e036 --- /dev/null +++ b/sources/236_BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE/source.bnet @@ -0,0 +1,110 @@ +IL6, IL1B | IL6 +IL6R, IL6 +JAK2, (IL6R | ABL1 | IL8) | IRS1 +STAT5, JAK2 & EGFR +IL8, STAT5 | ERK_i +PIM, STAT5 +STAT3, (IL1B | SRC | MAPK8) | JAK2 +STAT1, JAK2 & SRC & EGFR +GATA3, KMT2D & !STAT1 +PPARG, !GATA3 & CEBPB +WNT1, PGR & WNT1 +FZD3, WNT1 +DVL1, FZD3 +AXIN1, !DVL1 & GSK3B +APC, AXIN1 +DC, APC & GSK3B +CTNNB1, !DC & (AKT_i & WNT1 & PAK1) +TCF4, CTNNB1 | JUN +PAK1, TCF4 & AKT_i +NOTCH1, DLL_i & CTNNB1 +NFKB1, NOTCH1 | GSK3B +RELA, NFKB1 | PIM +JUN, (RELA | MAPK8 | PPARG) | ERK_i +NCID, NOTCH1 +HES1, NCID & !CASP3 +HEY1, NCID +MYOD1, !HES1 +MYOG, !HEY1 | MYOD1 +PAX7, !MYOG & FOXO1 +KMT2D, PAX7 & !AKT_i +IGF1R, IGF1 & (FOXO3 & ESR1) +HER3, NRG1 & HER2 +HER2, HER3 & (FOXO3 & ESR1) +PGR, (P21 & PG) & !(ESR1 | ERK_i | AKT_i) +ESR1, (ES & AKT_i & KMT2D) & (PGR & FOXO3) +EGFR, EGF & (HER2 & HER3) +GRB2, IRS1 | (HER2 & LATS1 & SRC & EGFR) +SOS1, GRB2 | ABL1 +HRAS, (SOS1 | PIP3) & !NF1 +RAS_i, SOS1 | PIP3 +RAF1, (HRAS | RAS_i) +MEK_i, RAF1 +ERK_i, MEK_i +LCK, ERK_i +TWIST1, ERK_i +NF1, !TWIST1 +PI3K_c, (EGFR & 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) +FOXO3, !(AKT_i | ERK_i) +FOXO1, !SGK1 +CREB1, AKT_i +GSK3B, !(AKT_i & ERK_i) +TSC2, !(AKT_i | ERK_i) & (PRKAA2 & GSK3B) +RHEB, !TSC2 +MTORC1_c, RHEB & (NRG1 | IGF1) +S6K1, MTORC1_c & ERK_i +IRS1, !S6K1 | (INSR & IGF1R) +SGK1, (MTORC2_c | MTORC1_c) | PDPK1 +NEDD4L, !SGK1 +NF2, NEDD4L | !(PAK2 & PAK1 & PRKACA) +LATS1, NF2 | LCK +YAP1, !LATS1 | ABL1 +TEAD1, YAP1 +IVEBP1, !MTORC1_c +EIF4E, !IVEBP1 +MYC, (((CTNNB1 | PIM) & !GSK3B) | ((STAT3 & JAK2) | (ESR1 & FOXO3))) | EIF4E +P21, !(ERK_i | MYC | AKT_i) & (MYOG & MAPK8 & PIM) +CYCLIN_D_c, ((TCF4 | TEAD1 ) & !(GSK3B | CDKN2A | P21)) | (MYC & EIF4E & STAT3) +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) +BCLXL, !(BAD | BIM) & (CREB1 & BCL2) +BIM, !(BCL2 | BCLXL) & (FOXO3 & FOXO1) +BID, CASP8 & P53 +BAK1, ((BIM | P53) & BID) & !MCL1 +BAX, ((BIM | P53) | BID) | !(MCL1 & AKT_i) +CYCS, BAK1 | BAX +CASP9, (CYCS | CASP3) & !((PRKACA & AKT_i) | ERK_i) +CASP3, CASP9 +HSP90AA1, !PDPK1 | ABL1 +NOS3, HSP90AA1 & AKT_i +IL1B, NOS3 | RELA +STK11, !(ERK_i & FOXO3) +PRKAA2, STK11 +PAK2, RAC1 | SRC +KRT14, PAK2 & EGFR +TRADD, !KRT14 +FAS, (FASLG | P53) | !AKT_i +FADD, TRADD & FAS & P53 +CASP8, (FADD | NF1) | !(ERK_i & SRC) +PRKACA, EGFR | (AKT_i & WNT1 & JUN) +SRC, PRKACA | ABL1 +ABL1, GRB2 +ABL2, ABL1 +CEBPB, ABL2 +CDKN2A, !(MYC & AKT_i) +INSR, INS | INSR +GRB7, INSR +RND1, GRB7 | DVL1 +RAC1, (PI3K_c | SRC | DVL1) | !AKT_i +MAPK8, RAC1 | RND1 + From acc2aecfeb448011cd108f17b29db5d89c6a5aae Mon Sep 17 00:00:00 2001 From: Natalia Florekova Date: Tue, 17 Sep 2024 10:26:22 +0200 Subject: [PATCH 02/11] Added model 231 - breast cancer signaling pathways --- bnet_to_aeon.py | 2 +- .../README.md | 37 ++ .../metadata.json | 17 + .../model.aeon | 378 ++++++++++++++++++ .../model.bnet | 111 +++++ .../model.sbml | 1 + .../citation.bib | 8 + .../metadata.json | 7 + .../notes.md | 11 + .../source.bnet | 111 +++++ 10 files changed, 682 insertions(+), 1 deletion(-) create mode 100644 models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/README.md create mode 100644 models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/metadata.json create mode 100644 models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/model.aeon create mode 100644 models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/model.bnet create mode 100644 models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/model.sbml create mode 100644 sources/231_BREAST-CANCER-SIGNALLING-PATHWAYS/citation.bib create mode 100644 sources/231_BREAST-CANCER-SIGNALLING-PATHWAYS/metadata.json create mode 100644 sources/231_BREAST-CANCER-SIGNALLING-PATHWAYS/notes.md create mode 100644 sources/231_BREAST-CANCER-SIGNALLING-PATHWAYS/source.bnet 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/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 + From f2345426bb718d38f630d390691fe096a6d1534e Mon Sep 17 00:00:00 2001 From: Samuel Pastva Date: Fri, 20 Sep 2024 14:13:45 +0200 Subject: [PATCH 03/11] New output mechanism in workflow. --- .github/workflows/integrity.yml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/.github/workflows/integrity.yml b/.github/workflows/integrity.yml index a1f1e08..595426e 100644 --- a/.github/workflows/integrity.yml +++ b/.github/workflows/integrity.yml @@ -18,9 +18,12 @@ jobs: run: rm -rf models/* - name: Run a fresh model sync. run: python3 sync.py - - name: Check if there is any change - id: get_changes - run: echo "::set-output name=changed::$(git status --porcelain | wc -l)" + - name: Check for changes + id: check_changes + run: | + if [[ -n $(git status --porcelain) ]]; then + echo "changes=true" >> "$GITHUB_OUTPUT"; + fi - name: If there are changes, fail. - if: steps.get_changes.outputs.changed != 0 + if: steps.check_changes.outputs.changed != 0 run: exit 1 \ No newline at end of file From 39114772ad7b07f1978758ce7ee855ce7eaa3eb4 Mon Sep 17 00:00:00 2001 From: Samuel Pastva Date: Fri, 20 Sep 2024 14:16:46 +0200 Subject: [PATCH 04/11] Update checkout package. --- .github/workflows/integrity.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/integrity.yml b/.github/workflows/integrity.yml index 595426e..8de1f5d 100644 --- a/.github/workflows/integrity.yml +++ b/.github/workflows/integrity.yml @@ -6,7 +6,7 @@ jobs: name: check runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Install Python. uses: actions/setup-python@v4 with: From a0182fb722861f426132d9b73f7d7bdfcdf9c917 Mon Sep 17 00:00:00 2001 From: Samuel Pastva Date: Fri, 20 Sep 2024 14:18:52 +0200 Subject: [PATCH 05/11] Update python package. --- .github/workflows/integrity.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/integrity.yml b/.github/workflows/integrity.yml index 8de1f5d..f6be364 100644 --- a/.github/workflows/integrity.yml +++ b/.github/workflows/integrity.yml @@ -8,7 +8,7 @@ jobs: steps: - uses: actions/checkout@v4 - name: Install Python. - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: '3.10' cache: 'pip' From 621b0bc7a2e67c76cb8a1723947cca93c4292f7b Mon Sep 17 00:00:00 2001 From: Natalia Florekova Date: Sat, 21 Sep 2024 19:29:58 +0200 Subject: [PATCH 06/11] Added model 232 - breast cancer signalling pathways MCF7 complete --- .../README.md | 37 ++ .../metadata.json | 17 + .../model.aeon | 384 ++++++++++++++++++ .../model.bnet | 110 +++++ .../model.sbml | 1 + report/.~lock.online_only_table_1.xlsx# | 6 +- .../citation.bib | 8 + .../metadata.json | 7 + .../notes.md | 11 + .../source.bnet | 110 +++++ 10 files changed, 690 insertions(+), 1 deletion(-) create mode 100644 models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/README.md create mode 100644 models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/metadata.json create mode 100644 models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/model.aeon create mode 100644 models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/model.bnet create mode 100644 models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/model.sbml create mode 100644 sources/232_BREAST-CANCER-PATHWAYS-MCF7-COMPLETE/citation.bib create mode 100644 sources/232_BREAST-CANCER-PATHWAYS-MCF7-COMPLETE/metadata.json create mode 100644 sources/232_BREAST-CANCER-PATHWAYS-MCF7-COMPLETE/notes.md create mode 100644 sources/232_BREAST-CANCER-PATHWAYS-MCF7-COMPLETE/source.bnet 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# index 351c5c7..8bdef99 100644 --- a/report/.~lock.online_only_table_1.xlsx# +++ b/report/.~lock.online_only_table_1.xlsx# @@ -1 +1,5 @@ -,natalie,natalie-IdeaPad-5-Pro-14ITL6,22.09.2024 09:28,file:///home/natalie/.config/libreoffice/4; \ No newline at end of file +<<<<<<< HEAD +,natalie,natalie-IdeaPad-5-Pro-14ITL6,22.09.2024 09:28,file:///home/natalie/.config/libreoffice/4; +======= +,natalie,natalie-IdeaPad-5-Pro-14ITL6,21.09.2024 17:35,file:///home/natalie/.config/libreoffice/4; +>>>>>>> 6a4ffa8 (Added model 232 - breast cancer signalling pathways MCF7 complete) 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 + From 32128ad75384228680c559d1d9c33a7af93fee50 Mon Sep 17 00:00:00 2001 From: Natalia Florekova Date: Tue, 17 Sep 2024 10:26:22 +0200 Subject: [PATCH 07/11] Added model 231 - breast cancer signaling pathways --- .gitignore | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 782cf30..ab6775e 100644 --- a/.gitignore +++ b/.gitignore @@ -6,4 +6,6 @@ __pycache__ # Default output of the bundle.py script bbm-edition -edition-* \ No newline at end of file +edition-* + +venv \ No newline at end of file From 856c71ea4a235a10907887e53f5e8e1904076e5e Mon Sep 17 00:00:00 2001 From: Natalia Florekova Date: Sun, 22 Sep 2024 09:11:57 +0200 Subject: [PATCH 08/11] Added model 234 - breast cancer signalling pathways MDAMB468 complete --- .../README.md | 2 +- .../metadata.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/models/[id-234]__[var-111]__[in-6]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE]/README.md b/models/[id-234]__[var-111]__[in-6]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE]/README.md index 29787b0..c4beb2f 100644 --- a/models/[id-234]__[var-111]__[in-6]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE]/README.md +++ b/models/[id-234]__[var-111]__[in-6]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE]/README.md @@ -26,7 +26,7 @@ was updated to: CYCLIN_D_c, (((STAT3) & !(GSK3B & (CDKN2A & P21)))) & (EIF4E & MYC & STAT3) -as the analysis +as the analysis stated that TEAD1 and TCF4 have no effect on CYCLIN_D_c. ### Model citation diff --git a/models/[id-234]__[var-111]__[in-6]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE]/metadata.json b/models/[id-234]__[var-111]__[in-6]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE]/metadata.json index bffc4c2..619ec1a 100644 --- a/models/[id-234]__[var-111]__[in-6]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE]/metadata.json +++ b/models/[id-234]__[var-111]__[in-6]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE]/metadata.json @@ -12,6 +12,6 @@ "variables": 111, "inputs": 6, "regulations": 271, - "notes": "### Modifications\n\nRemoved regulations:\nPG, PG\nNRG1, NRG1\nINS, INS\nES, ES\nEGF, EGF\nDLL_i, DLL_i\n\nRegulation:\n\nCYCLIN_D_c, (((TEAD1 | TCF4 | STAT3) & !(GSK3B & (CDKN2A & P21)))) & (EIF4E & MYC & STAT3)\n\nwas updated to:\n\nCYCLIN_D_c, (((STAT3) & !(GSK3B & (CDKN2A & P21)))) & (EIF4E & MYC & STAT3)\n\nas the analysis\n", + "notes": "### Modifications\n\nRemoved regulations:\nPG, PG\nNRG1, NRG1\nINS, INS\nES, ES\nEGF, EGF\nDLL_i, DLL_i\n\nRegulation:\n\nCYCLIN_D_c, (((TEAD1 | TCF4 | STAT3) & !(GSK3B & (CDKN2A & P21)))) & (EIF4E & MYC & STAT3)\n\nwas updated to:\n\nCYCLIN_D_c, (((STAT3) & !(GSK3B & (CDKN2A & P21)))) & (EIF4E & MYC & STAT3)\n\nas the analysis stated that TEAD1 and TCF4 have no effect on CYCLIN_D_c.\n", "bib": "@article{bbm-234,\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 From 2177149f41e0d3957937b07e0c6732dea50ebfbc Mon Sep 17 00:00:00 2001 From: Natalia Florekova Date: Sat, 21 Sep 2024 19:29:58 +0200 Subject: [PATCH 09/11] Added model 232 - breast cancer signalling pathways MCF7 complete --- report/.~lock.online_only_table_1.xlsx# | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/report/.~lock.online_only_table_1.xlsx# b/report/.~lock.online_only_table_1.xlsx# index 8bdef99..5ff0645 100644 --- a/report/.~lock.online_only_table_1.xlsx# +++ b/report/.~lock.online_only_table_1.xlsx# @@ -1,5 +1,9 @@ <<<<<<< HEAD +<<<<<<< HEAD ,natalie,natalie-IdeaPad-5-Pro-14ITL6,22.09.2024 09:28,file:///home/natalie/.config/libreoffice/4; ======= +,natalie,natalie-IdeaPad-5-Pro-14ITL6,21.09.2024 21:23,file:///home/natalie/.config/libreoffice/4; +>>>>>>> 14d1b6b (Added model 232 - breast cancer signalling pathways MCF7 complete) +======= ,natalie,natalie-IdeaPad-5-Pro-14ITL6,21.09.2024 17:35,file:///home/natalie/.config/libreoffice/4; >>>>>>> 6a4ffa8 (Added model 232 - breast cancer signalling pathways MCF7 complete) From d13fb5e4820d8e94fa8ebfcd9dab992cd40ee942 Mon Sep 17 00:00:00 2001 From: Natalia Florekova Date: Sat, 21 Sep 2024 19:29:58 +0200 Subject: [PATCH 10/11] Added model 232 - breast cancer signalling pathways MCF7 complete --- report/.~lock.online_only_table_1.xlsx# | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/report/.~lock.online_only_table_1.xlsx# b/report/.~lock.online_only_table_1.xlsx# index 5ff0645..b8e2a91 100644 --- a/report/.~lock.online_only_table_1.xlsx# +++ b/report/.~lock.online_only_table_1.xlsx# @@ -1,9 +1,13 @@ <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD ,natalie,natalie-IdeaPad-5-Pro-14ITL6,22.09.2024 09:28,file:///home/natalie/.config/libreoffice/4; ======= ,natalie,natalie-IdeaPad-5-Pro-14ITL6,21.09.2024 21:23,file:///home/natalie/.config/libreoffice/4; >>>>>>> 14d1b6b (Added model 232 - breast cancer signalling pathways MCF7 complete) ======= +,natalie,natalie-IdeaPad-5-Pro-14ITL6,22.09.2024 09:06,file:///home/natalie/.config/libreoffice/4; +>>>>>>> 2f07940 (Added model 232 - breast cancer signalling pathways MCF7 complete) +======= ,natalie,natalie-IdeaPad-5-Pro-14ITL6,21.09.2024 17:35,file:///home/natalie/.config/libreoffice/4; >>>>>>> 6a4ffa8 (Added model 232 - breast cancer signalling pathways MCF7 complete) From 4842b20c45305d461f6d892e5a05beb68c1150a7 Mon Sep 17 00:00:00 2001 From: Natalia Florekova Date: Sat, 21 Sep 2024 19:29:58 +0200 Subject: [PATCH 11/11] Added model 232 - breast cancer signalling pathways MCF7 complete --- report/.~lock.online_only_table_1.xlsx# | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/report/.~lock.online_only_table_1.xlsx# b/report/.~lock.online_only_table_1.xlsx# index b8e2a91..595fc7e 100644 --- a/report/.~lock.online_only_table_1.xlsx# +++ b/report/.~lock.online_only_table_1.xlsx# @@ -1,13 +1,19 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD ,natalie,natalie-IdeaPad-5-Pro-14ITL6,22.09.2024 09:28,file:///home/natalie/.config/libreoffice/4; ======= ,natalie,natalie-IdeaPad-5-Pro-14ITL6,21.09.2024 21:23,file:///home/natalie/.config/libreoffice/4; >>>>>>> 14d1b6b (Added model 232 - breast cancer signalling pathways MCF7 complete) ======= +======= +>>>>>>> 9ea4b1d (Added model 232 - breast cancer signalling pathways MCF7 complete) ,natalie,natalie-IdeaPad-5-Pro-14ITL6,22.09.2024 09:06,file:///home/natalie/.config/libreoffice/4; >>>>>>> 2f07940 (Added model 232 - breast cancer signalling pathways MCF7 complete) ======= +,natalie,natalie-IdeaPad-5-Pro-14ITL6,21.09.2024 21:23,file:///home/natalie/.config/libreoffice/4; +>>>>>>> 14d1b6b (Added model 232 - breast cancer signalling pathways MCF7 complete) +======= ,natalie,natalie-IdeaPad-5-Pro-14ITL6,21.09.2024 17:35,file:///home/natalie/.config/libreoffice/4; >>>>>>> 6a4ffa8 (Added model 232 - breast cancer signalling pathways MCF7 complete)