diff --git a/models/[id-239]__[var-234]__[in-69]__[M1-SYNOVIAL-MACROPHAGE]/README.md b/models/[id-239]__[var-234]__[in-69]__[M1-SYNOVIAL-MACROPHAGE]/README.md new file mode 100644 index 0000000..4afbca9 --- /dev/null +++ b/models/[id-239]__[var-234]__[in-69]__[M1-SYNOVIAL-MACROPHAGE]/README.md @@ -0,0 +1,29 @@ +# \[239\] M1-SYNOVIAL-MACROPHAGE + + - Variables: 234 + - Inputs: 69 + - Regulations: 562 + - Publication: https://doi.org/10.1038/s41540-024-00337-5 + - Source: https://www.ebi.ac.uk/biomodels/MODEL2307180001 + - Keywords: biomodels, curated, casq, repaired + + +### Modifications + +Removed unused variables: `EDA`, `HLA_DP_DQ_DR`, `ICOSLG`, `LGALS9`, `LILRB1`, `notch1`. + +### Model citation + +``` +@article{bbm-239, + title={Large-scale computational modelling of the M1 and M2 synovial macrophages in rheumatoid arthritis}, + author={Zerrouk, Naouel and Alcraft, Rachel and Hall, Benjamin A and Aug{\'e}, Franck and Niarakis, Anna}, + journal={npj Systems Biology and Applications}, + volume={10}, + number={1}, + pages={10}, + year={2024}, + publisher={Nature Publishing Group UK London} +} +``` + diff --git a/models/[id-239]__[var-234]__[in-69]__[M1-SYNOVIAL-MACROPHAGE]/metadata.json b/models/[id-239]__[var-234]__[in-69]__[M1-SYNOVIAL-MACROPHAGE]/metadata.json new file mode 100644 index 0000000..e9eedef --- /dev/null +++ b/models/[id-239]__[var-234]__[in-69]__[M1-SYNOVIAL-MACROPHAGE]/metadata.json @@ -0,0 +1,17 @@ +{ + "id": 239, + "name": "M1-SYNOVIAL-MACROPHAGE", + "url-publication": "https://doi.org/10.1038/s41540-024-00337-5", + "url-model": "https://www.ebi.ac.uk/biomodels/MODEL2307180001", + "keywords": [ + "biomodels", + "curated", + "casq", + "repaired" + ], + "variables": 234, + "inputs": 69, + "regulations": 562, + "notes": "### Modifications\n\nRemoved unused variables: `EDA`, `HLA_DP_DQ_DR`, `ICOSLG`, `LGALS9`, `LILRB1`, `notch1`.", + "bib": "@article{bbm-239,\n title={Large-scale computational modelling of the M1 and M2 synovial macrophages in rheumatoid arthritis},\n author={Zerrouk, Naouel and Alcraft, Rachel and Hall, Benjamin A and Aug{\\'e}, Franck and Niarakis, Anna},\n journal={npj Systems Biology and Applications},\n volume={10},\n number={1},\n pages={10},\n year={2024},\n publisher={Nature Publishing Group UK London}\n}" +} \ No newline at end of file diff --git a/models/[id-239]__[var-234]__[in-69]__[M1-SYNOVIAL-MACROPHAGE]/model.aeon b/models/[id-239]__[var-234]__[in-69]__[M1-SYNOVIAL-MACROPHAGE]/model.aeon new file mode 100644 index 0000000..3c925be --- /dev/null +++ b/models/[id-239]__[var-234]__[in-69]__[M1-SYNOVIAL-MACROPHAGE]/model.aeon @@ -0,0 +1,796 @@ +v_IL18_M1_macrophage___Extracellular_Space -> v_IL18_IL18R1_complex +v_TNFSF11_TNFRSF11_complex -> v_TRAF2_TRAF6_complex +v_TRAF6_ubiquitinated -> v_TRAF6_TAB1_TAB2_TAK1_complex +v_TAB2_phosphorylated -> v_TRAF6_TAB1_TAB2_TAK1_complex +v_TAB1 -> v_TRAF6_TAB1_TAB2_TAK1_complex +v_TAK1 -> v_TRAF6_TAB1_TAB2_TAK1_complex +v_TRAF2_TRAF6_complex -> v_TRAF6_TAB1_TAB2_TAK1_complex +v_RELA_NFKB1_complex_M1_macrophage___Cytoplasm -> v_RELA_NFKB1_complex_M1_macrophage___nucleus +v_CypA -> v_RELA_NFKB1_complex_M1_macrophage___nucleus +v_Prkcd -> v_RELA_NFKB1_complex_M1_macrophage___nucleus +v_TRAF6_TAB1_TAB2_TAK1_complex -> v_IKK_complex +v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex -> v_IKK_complex +v_AKT1 -> v_IKK_complex +v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex -> v_IKK_complex +v_NIK -> v_IKK_complex +v_TRADD_TRAF2_RIP1_complex -> v_IKK_complex +v_CSF2RA_CSF2RB_CSF2_complex -> v_IKK_complex +v_NFKBIA_RELA_NFKB1_complex -> v_RELA_NFKB1_complex_M1_macrophage___Cytoplasm +v_IKK_complex -> v_RELA_NFKB1_complex_M1_macrophage___Cytoplasm +v_IKKE_TBK1_TRAF3_complex -> v_RELA_NFKB1_complex_M1_macrophage___Cytoplasm +v_RELA_NFKB1_NFKBIE_complex -> v_RELA_NFKB1_complex_M1_macrophage___Cytoplasm +v_IKK1_IKK2_complex -> v_RELA_NFKB1_complex_M1_macrophage___Cytoplasm +v_TRAF6 -> v_TRAF6_IRAK1_IRAK4_complex +v_IRAK1_IRAK4_complex -> v_TRAF6_IRAK1_IRAK4_complex +v_IRAK3 -| v_TRAF6_IRAK1_IRAK4_complex +v_MEKK1 -> v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex +v_ECSIT -> v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex +v_TRAF6_ubiquitinated -> v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex +v_TAK1 -> v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex +v_TAB1 -> v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex +v_TAB2_phosphorylated -> v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex +v_TNF_M1_macrophage___Extracellular_Space -> v_TNF_TNFRSF1A_complex +v_TLR1_TLR2_biglycan_complex -> v_MYD88_TIRAP_TOLLIP_complex +v_TLR2_TLR6_biglycan_complex -> v_MYD88_TIRAP_TOLLIP_complex +v_DNA_simple_molecule -> v_TLR9_DNA_complex +v_IL1B_M1_macrophage___Extracellular_Space -> v_IL1_IL1R_complex +v_IL1R_complex -> v_IL1_IL1R_complex +v_JAK2 -> v_SHP2_GRB2_complex +v_JAK1_JAK2_complex -> v_SHP2_GRB2_complex +v_JAK1_TYK2_complex -> v_SHP2_GRB2_complex +v_JAK2_TYK2_complex -> v_SHP2_GRB2_complex +v_gal -> v_GAL_GALR2_complex +v_TRIF -> v_TRAM1_TRIF_complex +v_TRAM1 -> v_TRAM1_TRIF_complex +v_GAL_GALR2_complex -> v_GNA12_GNA13_complex +v_IRAK4_phosphorylated -> v_IRAK1_IRAK4_complex +v_IRAK1 -> v_IRAK1_IRAK4_complex +v_dsRNA_simple_molecule -> v_TLR3_dsRNA_complex +v_TRADD_TRAF2_RIP1_complex -> v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex +v_TAK1 -> v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex +v_TAB2_phosphorylated -> v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex +v_TAB1 -> v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex +v_GNB_GNG_GNAI3_complex -> v_GNB_GNG_complex +v_CCL2_CCR2_complex -> v_GNB_GNG_complex +v_CXCR1_IL8_complex -> v_GNB_GNG_complex +v_CCL21_CCR7_complex -> v_GNB_GNG_complex +v_CXCL1_CXCR1_complex -> v_GNB_GNG_complex +v_INHBB -> v_ACVR2A_ACVR2B_INHBB_complex +v_ACVR2A_ACVR2B_complex -> v_ACVR2A_ACVR2B_INHBB_complex +v_STAT3 -> v_STAT3_STAT3_complex +v_IFNb_M1_macrophage___Extracellular_Space -> v_IFNAR1_IFNAR2_IFNb_complex +v_IFNAR1_IFNAR2_complex -> v_IFNAR1_IFNAR2_IFNb_complex +v_STAT4 -> v_STAT4_STAT4_complex +v_AKT1 -| v_RXRa_NUR77_complex +v_TRAF3 -> v_IKKE_TBK1_TRAF3_complex +v_IKKE_TBK1_complex -> v_IKKE_TBK1_TRAF3_complex +v_biglycan_simple_molecule -> v_TLR1_TLR2_biglycan_complex +v_TLR1_TLR2_complex -> v_TLR1_TLR2_biglycan_complex +v_NICD -> v_NICD_CSL_SKIP_MAML1_ep300_complex +v_FASL_M1_macrophage___Extracellular_Space -> v_FASL_FAS_complex +v_FAS -> v_FASL_FAS_complex +v_Hif1a -> v_HIF1_complex +v_Hif1b -> v_HIF1_complex +v_IL12RB_IL12_complex -> v_JAK2_TYK2_complex +v_IL23R_IL12RB1_complex -> v_IL23R_IL12RB1_IL23_complex +v_IL23_M1_macrophage___Extracellular_Space -> v_IL23R_IL12RB1_IL23_complex +v_IL12_M1_macrophage___Extracellular_Space -> v_IL12RB_IL12_complex +v_IL12RB_complex -> v_IL12RB_IL12_complex +v_STAT2 -> v_STAT1_STAT2_IRF9_complex +v_STAT1 -> v_STAT1_STAT2_IRF9_complex +v_IRF9 -> v_STAT1_STAT2_IRF9_complex +v_JAK1_TYK2_complex -> v_STAT1_STAT2_IRF9_complex +v_JAK2_TYK2_complex -> v_STAT1_STAT2_IRF9_complex +v_STAT1 -> v_STAT1_STAT1_complex +v_SMAD2_phosphorylated -> v_SMAD2_SMAD4_complex +v_SMAD4 -> v_SMAD2_SMAD4_complex +v_IFNg_M1_macrophage___Extracellular_Space -> v_IFNGR1_IFNGR2_IFNg_complex +v_IFNGR1_IFNGR2_complex -> v_IFNGR1_IFNGR2_IFNg_complex +v_IL6_M1_macrophage___Extracellular_Space -> v_IL6_IL6R_IL6ST_complex +v_CXCL12_M1_macrophage___Extracellular_Space -> v_ACKR3_CXCL12_complex +v_CCL2_M1_macrophage___Extracellular_Space -> v_CCL2_CCR2_complex +v_CSF2RA_CSF2RB_complex -> v_CSF2RA_CSF2RB_CSF2_complex +v_CSF2_M1_macrophage___Extracellular_Space -> v_CSF2RA_CSF2RB_CSF2_complex +v_SMAD2_SMAD4_complex -> v_p300_SP1_complex +v_NLRP3 -> v_NLRP3_INFLAMMASOME_complex +v_Casp1 -> v_NLRP3_INFLAMMASOME_complex +v_ASC -> v_NLRP3_INFLAMMASOME_complex +v_IFNa_M1_macrophage___Extracellular_Space -> v_IFNAR1_IFNAR2_IFNa_complex +v_IFNAR1_IFNAR2_complex -> v_IFNAR1_IFNAR2_IFNa_complex +v_c5a -> v_C5a_C5aR1_complex +v_IL8_M1_macrophage___Extracellular_Space -> v_CXCR1_IL8_complex +v_CXCR1 -> v_CXCR1_IL8_complex +v_CCl21 -> v_CCL21_CCR7_complex +v_CXCL13 -> v_CXCL13_ACKR4_complex +v_IKK1_phosphorylated -> v_IKK1_IKK2_complex +v_IKK2_phosphorylated -> v_IKK1_IKK2_complex +v_TNFSF11 -> v_TNFSF11_TNFRSF11_complex +v_col4a4 -> v_ITGB1_ITGA1_col4a_complex +v_ITGB1_ITGA1_complex -> v_ITGB1_ITGA1_col4a_complex +v_col4a5 -> v_ITGB1_ITGA1_col4a_complex +v_INHBA -> v_ACVR2A_ACVR2B_INHBA_complex +v_ACVR2A_ACVR2B_complex -> v_ACVR2A_ACVR2B_INHBA_complex +v_CXCL1_M1_macrophage___Extracellular_Space -> v_CXCL1_CXCR1_complex +v_CXCR1 -> v_CXCL1_CXCR1_complex +v_IFNE -> v_IFNE_IFNAR1_IFNAR2_complex +v_IFNAR1_IFNAR2_complex -> v_IFNE_IFNAR1_IFNAR2_complex +v_biglycan_simple_molecule -> v_TLR2_TLR6_biglycan_complex +v_TLR2_TLR6_complex -> v_TLR2_TLR6_biglycan_complex +v_CRKL_phosphorylated -> v_STAT5_CRKL_complex +v_STAT5_phosphorylated -> v_STAT5_CRKL_complex +v_IL23R_IL12RB1_IL23_complex -> v_JAK1_TYK2_complex +v_IFNAR1_IFNAR2_IFNb_complex -> v_JAK1_TYK2_complex +v_IFNAR1_IFNAR2_IFNa_complex -> v_JAK1_TYK2_complex +v_IFNE_IFNAR1_IFNAR2_complex -> v_JAK1_TYK2_complex +v_IFNGR1_IFNGR2_IFNg_complex -> v_JAK1_JAK2_complex +v_cIAP1 -> v_TRADD_TRAF2_RIP1_complex +v_TRADD -> v_TRADD_TRAF2_RIP1_complex +v_IL18_M1_macrophage___Secreted_components -> v_IL18_M1_macrophage___Extracellular_Space +v_p38_MAP_KINASE_phosphorylated_M1_macrophage___Cytoplasm -> v_p38_MAP_KINASE_phosphorylated_M1_macrophage___nucleus +v_TRAF6_TAB1_TAB2_TAK1_complex -> v_NIK +v_TRADD_TRAF2_RIP1_complex -> v_NIK +v_TRAF2_TRAF6_complex -> v_NIK +v_IL1_IL1R_complex -> v_MYD88 +v_TLR5 -> v_MYD88 +v_IL18_IL18R1_complex -> v_MYD88 +v_TRAF6_TAB1_TAB2_TAK1_complex -> v_MKK3_phosphorylated +v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex -> v_MKK3_phosphorylated +v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex -> v_MKK3_phosphorylated +v_ASK1 -> v_MKK3_phosphorylated +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_IL15 +v_AP_1_phosphorylated -> v_IL15 +v_IL6_M1_macrophage___Secreted_components -> v_IL6_M1_macrophage___Extracellular_Space +v_IL1B_M1_macrophage___Secreted_components -> v_IL1B_M1_macrophage___Extracellular_Space +v_TNF_TNFRSF1A_complex -> v_TRADD +v_NFKBIA_RELA_NFKB1_complex -> v_NFKBIA_phosphorylated +v_IKK_complex -> v_NFKBIA_phosphorylated +v_IKKE_TBK1_TRAF3_complex -> v_NFKBIA_phosphorylated +v_MKK3_phosphorylated -> v_p38_MAP_KINASE_phosphorylated_M1_macrophage___Cytoplasm +v_MKK6_phosphorylated -> v_p38_MAP_KINASE_phosphorylated_M1_macrophage___Cytoplasm +v_C5a_C5aR1_complex -> v_p38_MAP_KINASE_phosphorylated_M1_macrophage___Cytoplasm +v_DUSP1 -| v_p38_MAP_KINASE_phosphorylated_M1_macrophage___Cytoplasm +v_TNF_M1_macrophage___Secreted_components -> v_TNF_M1_macrophage___Extracellular_Space +v_MYD88 -> v_IRAK4_phosphorylated +v_MYD88_TIRAP_TOLLIP_complex -> v_IRAK4_phosphorylated +v_TLR7_TLR8_ssRNA_complex -> v_IRAK4_phosphorylated +v_TLR9_DNA_complex -> v_IRAK4_phosphorylated +v_TRAF6 -> v_TRAF6_ubiquitinated +v_PP4 -| v_TRAF6_ubiquitinated +v_UEV1A_UBC13_complex -> v_TRAF6_ubiquitinated +v_IRAK1_IRAK4_complex -> v_TAB2_phosphorylated +v_NFKB1_TPL2_complex -> v_TPL2 +v_IKK_complex -> v_TPL2 +v_NFKB1_TPL2_complex -> v_NFKB1 +v_IKK_complex -> v_NFKB1 +v_TPL2 -> v_MEK1_phosphorylated +v_RAF1 -> v_MEK1_phosphorylated +v_TPL2 -> v_MEK2_phosphorylated +v_RAF1 -> v_MEK2_phosphorylated +v_MEK1_phosphorylated -> v_ERK1_phosphorylated_M1_macrophage___Cytoplasm +v_MEK2_phosphorylated -> v_ERK1_phosphorylated_M1_macrophage___Cytoplasm +v_C5a_C5aR1_complex -> v_ERK1_phosphorylated_M1_macrophage___Cytoplasm +v_GNB_GNG_GNAI3_complex -> v_ERK1_phosphorylated_M1_macrophage___Cytoplasm +v_c_FOS_M1_macrophage___nucleus -> v_AP_1 +v_c_JUN_phosphorylated_M1_macrophage___nucleus -> v_AP_1 +v_AP_1 -> v_AP_1_phosphorylated +v_p38_MAP_KINASE_phosphorylated_M1_macrophage___nucleus -> v_AP_1_phosphorylated +v_JNK1_phosphorylated_M1_macrophage___nucleus -> v_AP_1_phosphorylated +v_ERK1_phosphorylated_M1_macrophage___nucleus -> v_AP_1_phosphorylated +v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex -> v_MKK6_phosphorylated +v_TRAF6_TAB1_TAB2_TAK1_complex -> v_MKK6_phosphorylated +v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex -> v_MKK6_phosphorylated +v_ASK1 -> v_MKK6_phosphorylated +v_TRAF6_TAB1_TAB2_TAK1_complex -> v_MKK4_phosphorylated +v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex -> v_MKK4_phosphorylated +v_ASK1 -> v_MKK4_phosphorylated +v_MEKK1 -> v_MKK4_phosphorylated +v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex -> v_MKK7_phosphorylated +v_TRAF6_TAB1_TAB2_TAK1_complex -> v_MKK7_phosphorylated +v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex -> v_MKK7_phosphorylated +v_ASK1 -> v_MKK7_phosphorylated +v_MKK7_phosphorylated -> v_JNK1_phosphorylated_M1_macrophage___Cytoplasm +v_MKK4_phosphorylated -> v_JNK1_phosphorylated_M1_macrophage___Cytoplasm +v_ASK1 -> v_JNK1_phosphorylated_M1_macrophage___Cytoplasm +v_Rac1 -> v_JNK1_phosphorylated_M1_macrophage___Cytoplasm +v_JNK1_phosphorylated_M1_macrophage___Cytoplasm -> v_JNK1_phosphorylated_M1_macrophage___nucleus +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_TNFA_rna +v_AP_1_phosphorylated -> v_TNFA_rna +v_MK2_phosphorylated -> v_TNFA_rna +v_NFAT5 -> v_TNFA_rna +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_Bcl2_rna +v_STAT1_STAT2_IRF9_complex -> v_Bcl2_rna +v_STAT1_STAT1_complex -> v_Bcl2_rna +v_STAT5_CRKL_complex -> v_Bcl2_rna +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_XIAP +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_cFLIP +v_IL12_M1_macrophage___Secreted_components -> v_IL12_M1_macrophage___Extracellular_Space +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_COX2_rna +v_NFAT5 -> v_COX2_rna +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_CXCL1_M1_macrophage___Secreted_components +v_AP_1_phosphorylated -> v_CXCL1_M1_macrophage___Secreted_components +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_CCL3 +v_AP_1_phosphorylated -> v_CCL3 +v_IRF5_ubiquitinated -> v_CCL3 +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_TNFAIP3_rna +v_AP_1_phosphorylated -> v_TNFAIP3_rna +v_TRAF6_IRAK1_IRAK4_complex -> v_IRF5_ubiquitinated +v_TLR1_TLR2_biglycan_complex -> v_Rac1 +v_TLR2_TLR6_biglycan_complex -> v_Rac1 +v_RHOA -| v_Rac1 +v_Rac1 -> v_PI3K +v_TRAF6_ubiquitinated -> v_PI3K +v_C5a_C5aR1_complex -> v_PI3K +v_CSF2RA_CSF2RB_CSF2_complex -> v_PI3K +v_HRAS -> v_PI3K +v_PTK2 -> v_PI3K +v_PIK3AP1_phosphorylated -> v_PI3K +v_CD40LG_ITGB1_ITGA1_complex -> v_PI3K +v_JAK2 -> v_PI3K +v_JAK1_TYK2_complex -> v_PI3K +v_Src -> v_PI3K +v_INPP5A -| v_PI3K +v_PI3K -> v_AKT1 +v_AKT1 -| v_CASP9 +v_XIAP -| v_CASP9 +v_BAX -> v_CASP9 +v_AKT1 -| v_RAF1 +v_HRAS -> v_RAF1 +v_TLR4_Md2_CD14_fibrinogen_complex -> v_TRAM1 +v_TRAM1_TRIF_complex -> v_TRAF3 +v_IKKE_TBK1_TRAF3_complex -> v_IRF3_phosphorylated +v_IKK_complex -> v_IRF3_phosphorylated +v_IKKE_TBK1_TRAF3_complex -> v_IRF7 +v_IKK_complex -> v_IRF7 +v_OPN -> v_IRF7 +v_IRF3_phosphorylated -> v_CXCL10 +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_CXCL10 +v_AP_1_phosphorylated -> v_CXCL10 +v_IRF3_phosphorylated -> v_CXCL11 +v_IRF3_phosphorylated -> v_CXCL9 +v_IRF3_phosphorylated -> v_CD40 +v_IRF3_phosphorylated -> v_CD80 +v_IRF3_phosphorylated -> v_CD86 +v_TLR3_dsRNA_complex -> v_TRIF +v_ERK1_phosphorylated_M1_macrophage___Cytoplasm -> v_ERK1_phosphorylated_M1_macrophage___nucleus +v_cFLIP -> v_cFLIP_ubiquitinated +v_ITCH_phosphorylated -> v_cFLIP_ubiquitinated +v_JNK1_phosphorylated_M1_macrophage___Cytoplasm -> v_ITCH_phosphorylated +v_TRADD_TRAF2_RIP1_complex -> v_ASK1 +v_DAXX -> v_ASK1 +v_ERK1_phosphorylated_M1_macrophage___Cytoplasm -> v_NFAT5 +v_p38_MAP_KINASE_phosphorylated_M1_macrophage___Cytoplasm -> v_NFAT5 +v_AP_1_phosphorylated -> v_CCL5 +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_CCL5 +v_IRF5_ubiquitinated -> v_CCL5 +v_AP_1_phosphorylated -> v_JAG1 +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_JAG1 +v_AP_1_phosphorylated -> v_BCL3_rna +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_BCL3_rna +v_STAT3_STAT3_complex -> v_BCL3_rna +v_AP_1_phosphorylated -> v_MMP9 +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_MMP9 +v_AP_1_phosphorylated -> v_MMP14 +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_MMP14 +v_AP_1_phosphorylated -> v_Vegfc_rna +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_Vegfc_rna +v_NFAT5 -> v_Vegfc_rna +v_STAT3_STAT3_complex -> v_Vegfc_rna +v_HIF1_complex -> v_Vegfc_rna +v_CSF2_M1_macrophage___Secreted_components -> v_CSF2_M1_macrophage___Extracellular_Space +v_NFAT5 -> v_NOS2 +v_NOS2 -> v_NOS2_phosphorylated +v_AKT1 -> v_NOS2_phosphorylated +v_Bcl2_rna -> v_BCL2_M1_macrophage__Mitochondria_membrane +v_BCL2_M1_macrophage__Mitochondria_membrane -> v_BCL2_M1_macrophage__Mitochondria_membrane_active +v_BAD -| v_BCL2_M1_macrophage__Mitochondria_membrane_active +v_Bim -| v_BCL2_M1_macrophage__Mitochondria_membrane_active +v_MYD88_TIRAP_TOLLIP_complex -> v_FADD +v_FASL_FAS_complex -> v_FADD +v_FADD -> v_CASP8 +v_cFLIP -| v_CASP8 +v_CASP8 -> v_CASP3 +v_CASP8 -> v_CASP7 +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_TRAF1_rna +v_NFAT5 -> v_TRAF1_rna +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_CCL4 +v_AP_1_phosphorylated -> v_MMP3 +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_MMP3 +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_CCL20 +v_AP_1_phosphorylated -> v_CCL20 +v_BCL2_M1_macrophage__Mitochondria_membrane_active -| v_BAX +v_BCL2L1_M1_macrophage__Mitochondria_active -| v_BAX +v_CASP8 -> v_apoptosis_M1_macrophage_phenotype +v_CASP3 -> v_apoptosis_M1_macrophage_phenotype +v_CASP7 -> v_apoptosis_M1_macrophage_phenotype +v_p53_phosphorylated -> v_apoptosis_M1_macrophage_phenotype +v_Mcl1_rna -| v_apoptosis_M1_macrophage_phenotype +v_Bim -> v_apoptosis_M1_macrophage_phenotype +v_TNF_M1_macrophage___Secreted_components -> v_apoptosis_M1_macrophage_phenotype +v_p21_rna -| v_apoptosis_M1_macrophage_phenotype +v_FASL_M1_macrophage___Secreted_components -> v_apoptosis_M1_macrophage_phenotype +v_BCL2_M1_macrophage__Mitochondria_membrane_active -| v_apoptosis_M1_macrophage_phenotype +v_BCL2L1_M1_macrophage__Mitochondria_active -| v_apoptosis_M1_macrophage_phenotype +v_NLRP3_INFLAMMASOME_complex -> v_apoptosis_M1_macrophage_phenotype +v_p300_SP1_complex -> v_apoptosis_M1_macrophage_phenotype +v_NOS2_phosphorylated -> v_angiogenesis_signal_phenotype +v_Hif1a -> v_angiogenesis_signal_phenotype +v_CXCL12_M1_macrophage___Secreted_components -> v_angiogenesis_signal_phenotype +v_EDN1 -> v_angiogenesis_signal_phenotype +v_OPN -> v_angiogenesis_signal_phenotype +v_C5a_C5aR1_complex -> v_inflammation_signal_phenotype +v_CCL20 -> v_inflammation_signal_phenotype +v_CCL4 -> v_inflammation_signal_phenotype +v_CCL5 -> v_inflammation_signal_phenotype +v_CD40 -> v_inflammation_signal_phenotype +v_COX2_rna -> v_inflammation_signal_phenotype +v_IL15 -> v_inflammation_signal_phenotype +v_IRF7 -> v_inflammation_signal_phenotype +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_inflammation_signal_phenotype +v_IRF5_ubiquitinated -> v_inflammation_signal_phenotype +v_IL23_M1_macrophage___Secreted_components -> v_inflammation_signal_phenotype +v_IL12_M1_macrophage___Secreted_components -> v_inflammation_signal_phenotype +v_IFNb_M1_macrophage___Secreted_components -> v_inflammation_signal_phenotype +v_IFNa_M1_macrophage___Secreted_components -> v_inflammation_signal_phenotype +v_TNF_M1_macrophage___Secreted_components -> v_inflammation_signal_phenotype +v_IL18_M1_macrophage___Secreted_components -> v_inflammation_signal_phenotype +v_IL1B_M1_macrophage___Secreted_components -> v_inflammation_signal_phenotype +v_AREG -> v_inflammation_signal_phenotype +v_SEMA4A -> v_inflammation_signal_phenotype +v_ICAM1 -> v_inflammation_signal_phenotype +v_IL6_M1_macrophage___Secreted_components -> v_inflammation_signal_phenotype +v_ARRB2 -| v_inflammation_signal_phenotype +v_CCL2_M1_macrophage___Secreted_components -> v_inflammation_signal_phenotype +v_CCL3 -> v_inflammation_signal_phenotype +v_LTA -> v_inflammation_signal_phenotype +v_CXCL10 -> v_inflammation_signal_phenotype +v_CXCL9 -> v_inflammation_signal_phenotype +v_CXCL11 -> v_inflammation_signal_phenotype +v_IFNg_M1_macrophage___Secreted_components -> v_inflammation_signal_phenotype +v_MMP3 -> v_Matrix_degradation_signal_phenotype +v_MMP14 -> v_Matrix_degradation_signal_phenotype +v_MMP9 -> v_Matrix_degradation_signal_phenotype +v_vcan -| v_Matrix_degradation_signal_phenotype +v_CD40 -> v_T_cells_activation_signal_phenotype +v_CD86 -> v_T_cells_activation_signal_phenotype +v_CD80 -> v_T_cells_activation_signal_phenotype +v_CSF2_M1_macrophage___Secreted_components -> v_T_cells_activation_signal_phenotype +v_IFNa_M1_macrophage___Secreted_components -> v_T_cells_activation_signal_phenotype +v_ICAM1 -> v_T_cells_activation_signal_phenotype +v_XIAP -> v_proliferation_survival_M1_macrophage_phenotype +v_CXCL1_M1_macrophage___Secreted_components -> v_proliferation_survival_M1_macrophage_phenotype +v_ERK1_phosphorylated_M1_macrophage___nucleus -> v_proliferation_survival_M1_macrophage_phenotype +v_p38_MAP_KINASE_phosphorylated_M1_macrophage___nucleus -> v_proliferation_survival_M1_macrophage_phenotype +v_MDM2_phosphorylated -> v_proliferation_survival_M1_macrophage_phenotype +v_cFLIP -> v_proliferation_survival_M1_macrophage_phenotype +v_BCL3_rna -> v_proliferation_survival_M1_macrophage_phenotype +v_c_FOS_M1_macrophage___Cytoplasm_active -> v_proliferation_survival_M1_macrophage_phenotype +v_c_JUN_phosphorylated_M1_macrophage___Cytoplasm -> v_proliferation_survival_M1_macrophage_phenotype +v_IL12_M1_macrophage___Secreted_components -> v_proliferation_survival_M1_macrophage_phenotype +v_IL8_M1_macrophage___Secreted_components -> v_proliferation_survival_M1_macrophage_phenotype +v_CCL2_M1_macrophage___Secreted_components -> v_proliferation_survival_M1_macrophage_phenotype +v_CSF2_M1_macrophage___Secreted_components -> v_proliferation_survival_M1_macrophage_phenotype +v_HBGEF -> v_proliferation_survival_M1_macrophage_phenotype +v_p21_rna -> v_proliferation_survival_M1_macrophage_phenotype +v_p15_rna -| v_proliferation_survival_M1_macrophage_phenotype +v_IL6_M1_macrophage___Secreted_components -> v_proliferation_survival_M1_macrophage_phenotype +v_c_Myc_rna -> v_proliferation_survival_M1_macrophage_phenotype +v_p38_MAP_KINASE_phosphorylated_M1_macrophage___Cytoplasm -> v_proliferation_survival_M1_macrophage_phenotype +v_c_FOS_M1_macrophage___Cytoplasm_active -> v_osteoclastogenesis_M1_macrophage_phenotype +v_c_JUN_phosphorylated_M1_macrophage___Cytoplasm -> v_osteoclastogenesis_M1_macrophage_phenotype +v_IL1B_M1_macrophage___Secreted_components -> v_osteoclastogenesis_M1_macrophage_phenotype +v_AP_1_phosphorylated -> v_osteoclastogenesis_M1_macrophage_phenotype +v_IFNg_M1_macrophage___Secreted_components -> v_osteoclastogenesis_M1_macrophage_phenotype +v_IFNa_M1_macrophage___Secreted_components -> v_IFNa_M1_macrophage___Extracellular_Space +v_IFNb_M1_macrophage___Secreted_components -> v_IFNb_M1_macrophage___Extracellular_Space +v_AKT1 -> v_MDM2_phosphorylated +v_MDM2_phosphorylated -| v_p53_phosphorylated +v_STAT1_STAT2_IRF9_complex -> v_BCL2L1_M1_macrophage__Mitochondria +v_STAT1_STAT1_complex -> v_BCL2L1_M1_macrophage__Mitochondria +v_BCL2L1_M1_macrophage__Mitochondria -> v_BCL2L1_M1_macrophage__Mitochondria_active +v_BAD -| v_BCL2L1_M1_macrophage__Mitochondria_active +v_Bim -| v_BCL2L1_M1_macrophage__Mitochondria_active +v_STAT1_STAT2_IRF9_complex -> v_Mcl1_rna +v_STAT1_STAT1_complex -> v_Mcl1_rna +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_Mcl1_rna +v_ERK1_phosphorylated_M1_macrophage___nucleus -> v_Mcl1_rna +v_FOXO_M1_macrophage___nucleus -> v_Bim +v_IFNg_M1_macrophage___Secreted_components -> v_IFNg_M1_macrophage___Extracellular_Space +v_JAK1_JAK2_complex -> v_STAT1 +v_JAK1_TYK2_complex -> v_STAT1 +v_JAK1 -> v_STAT1 +v_JAK2 -> v_STAT1 +v_SHP2_GRB2_complex -> v_SOS1 +v_SOS1 -> v_HRAS +v_STAT1_STAT1_complex -> v_p21_rna +v_STAT1_STAT2_IRF9_complex -> v_p21_rna +v_NICD_CSL_SKIP_MAML1_ep300_complex -> v_p21_rna +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_p21_rna +v_NCID -> v_NICD +v_notch1_JAG1_complex -> v_NCID +v_gamma_secretase_complex_complex -> v_NCID +v_NICD_CSL_SKIP_MAML1_ep300_complex -> v_HES1_rna +v_NICD_CSL_SKIP_MAML1_ep300_complex -> v_HEY1_rna +v_STAT3_STAT3_complex -> v_IL10_rna +v_FOXO_M1_macrophage___nucleus -> v_IL10_rna +v_JAK1_TYK2_complex -> v_STAT3 +v_JAK2 -> v_STAT3 +v_JAK1 -> v_STAT3 +v_IL23_M1_macrophage___Secreted_components -> v_IL23_M1_macrophage___Extracellular_Space +v_c_Myc_rna -| v_p15_rna +v_FOXO_M1_macrophage___nucleus -> v_p15_rna +v_SMAD2_SARA_complex -> v_SARA +v_ACVR2A_ACVR2B_INHBA_complex -> v_SARA +v_ACVR2A_ACVR2B_INHBB_complex -> v_SARA +v_SMAD7 -| v_SARA +v_SMAD2_SARA_complex -> v_SMAD2_phosphorylated +v_ACVR2A_ACVR2B_INHBA_complex -> v_SMAD2_phosphorylated +v_ACVR2A_ACVR2B_INHBB_complex -> v_SMAD2_phosphorylated +v_SMAD7 -| v_SMAD2_phosphorylated +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_SOCS3_rna +v_AP_1_phosphorylated -> v_SOCS3_rna +v_STAT3_STAT3_complex -> v_SOCS3_rna +v_CCL2_M1_macrophage___Secreted_components -> v_CCL2_M1_macrophage___Extracellular_Space +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_CSF1_rna +v_AP_1_phosphorylated -> v_CSF1_rna +v_JAK2_TYK2_complex -> v_STAT4 +v_JAK1 -> v_STAT4 +v_STAT3_STAT3_complex -> v_IL4_rna +v_NFAT5 -> v_Vegfa_rna +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_Vegfa_rna +v_STAT3_STAT3_complex -> v_Vegfa_rna +v_NFAT5 -> v_Vegfb_rna +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_Vegfb_rna +v_STAT4_STAT4_complex -> v_Vegfb_rna +v_CXCL12_M1_macrophage___Secreted_components -> v_CXCL12_M1_macrophage___Extracellular_Space +v_ACKR3_CXCL12_complex -> v_ARRB2 +v_CCL21_CCR7_complex -> v_ARRB2 +v_CXCL13_ACKR4_complex -> v_ARRB2 +v_GNB_GNG_GNAI3_complex -> v_GNAI3 +v_CCL2_CCR2_complex -> v_GNAI3 +v_CXCR1_IL8_complex -> v_GNAI3 +v_CCL21_CCR7_complex -> v_GNAI3 +v_CXCL1_CXCR1_complex -> v_GNAI3 +v_c_FOS_M1_macrophage___Cytoplasm -> v_c_FOS_M1_macrophage___Cytoplasm_active +v_TSG6 -> v_c_FOS_M1_macrophage___Cytoplasm_active +v_c_JUN -> v_c_JUN_phosphorylated_M1_macrophage___Cytoplasm +v_JNK1_phosphorylated_M1_macrophage___Cytoplasm -> v_c_JUN_phosphorylated_M1_macrophage___Cytoplasm +v_ERK1_phosphorylated_M1_macrophage___Cytoplasm -> v_c_JUN_phosphorylated_M1_macrophage___Cytoplasm +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_c_JUN +v_JNK1_phosphorylated_M1_macrophage___nucleus -> v_c_JUN +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_c_FOS_M1_macrophage___Cytoplasm +v_c_FOS_M1_macrophage___Cytoplasm_active -> v_c_FOS_M1_macrophage___nucleus +v_c_JUN_phosphorylated_M1_macrophage___Cytoplasm -> v_c_JUN_phosphorylated_M1_macrophage___nucleus +v_NFAT5 -> v_IL18_M1_macrophage___Cytoplasm +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_IL1B_M1_macrophage___Cytoplasm +v_NFAT5 -> v_IL1B_M1_macrophage___Cytoplasm +v_AP_1_phosphorylated -> v_IL1B_M1_macrophage___Cytoplasm +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_NLRP3 +v_AP_1_phosphorylated -> v_FAS +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_FAS +v_FASL_FAS_complex -> v_DAXX +v_AKT1 -| v_FOXO_M1_macrophage___Cytoplasm +v_FOXO_M1_macrophage___Cytoplasm -> v_FOXO_M1_macrophage___nucleus +v_AKT1 -| v_FOXO_M1_macrophage___nucleus +v_FOXO_M1_macrophage___nucleus -> v_FOXO_M1_macrophage___nucleus +v_Sirt1 -> v_FOXO_M1_macrophage___nucleus +v_IL8_M1_macrophage___Secreted_components -> v_IL8_M1_macrophage___Extracellular_Space +v_GNAI3 -> v_Src +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_IL23_M1_macrophage___Secreted_components +v_AP_1_phosphorylated -> v_IL23_M1_macrophage___Secreted_components +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_IL12_M1_macrophage___Secreted_components +v_AP_1_phosphorylated -> v_IL12_M1_macrophage___Secreted_components +v_NFAT5 -> v_IL6_M1_macrophage___Secreted_components +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_IL6_M1_macrophage___Secreted_components +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_IFNg_M1_macrophage___Secreted_components +v_NFAT5 -> v_IFNg_M1_macrophage___Secreted_components +v_STAT4_STAT4_complex -> v_IFNg_M1_macrophage___Secreted_components +v_IRF7 -> v_IFNb_M1_macrophage___Secreted_components +v_IRF3_phosphorylated -> v_IFNb_M1_macrophage___Secreted_components +v_IRF7 -> v_IFNa_M1_macrophage___Secreted_components +v_IRF3_phosphorylated -> v_IFNa_M1_macrophage___Secreted_components +v_AP_1_phosphorylated -> v_FASL_M1_macrophage___Secreted_components +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_IL8_M1_macrophage___Secreted_components +v_AP_1_phosphorylated -> v_IL8_M1_macrophage___Secreted_components +v_HIF1_complex -> v_CXCL12_M1_macrophage___Secreted_components +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_CCL2_M1_macrophage___Secreted_components +v_NFAT5 -> v_CCL2_M1_macrophage___Secreted_components +v_AP_1_phosphorylated -> v_CCL2_M1_macrophage___Secreted_components +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_CSF2_M1_macrophage___Secreted_components +v_AP_1_phosphorylated -> v_CSF2_M1_macrophage___Secreted_components +v_NFAT5 -> v_CSF2_M1_macrophage___Secreted_components +v_TNFA_rna -> v_TNF_M1_macrophage___Secreted_components +v_IL18_M1_macrophage___Cytoplasm -> v_IL18_M1_macrophage___Secreted_components +v_NLRP3_INFLAMMASOME_complex -> v_IL18_M1_macrophage___Secreted_components +v_IL1B_M1_macrophage___Cytoplasm -> v_IL1B_M1_macrophage___Secreted_components +v_NLRP3_INFLAMMASOME_complex -> v_IL1B_M1_macrophage___Secreted_components +v_STAT3_STAT3_complex -> v_CD84 +v_PRKCQ -> v_IKK2_phosphorylated +v_RELA_NFKB1_NFKBIE_complex -> v_NFKBIE +v_IKK1_IKK2_complex -> v_NFKBIE +v_ITGB1_ITGA1_col4a_complex -> v_PTK2 +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_EDN1 +v_STAT4_STAT4_complex -> v_vcan +v_STAT3_STAT3_complex -> v_AREG +v_STAT1_STAT1_complex -> v_CD40LG +v_AP_1_phosphorylated -> v_SEMA4A +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_ICAM1 +v_CXCL1_M1_macrophage___Secreted_components -> v_CXCL1_M1_macrophage___Extracellular_Space +v_GNA12_GNA13_complex -> v_RHOA +v_PRKG1 -| v_RHOA +v_HLA_B_LILRB1_complex -> v_PTPN6 +v_PTPN6 -| v_SYK +v_SYK -> v_PIK3AP1_phosphorylated +v_JAK1_TYK2_complex -> v_CRKL_phosphorylated +v_JAK1_TYK2_complex -> v_STAT5_phosphorylated +v_STAT5_CRKL_complex -> v_c_Myc_rna +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_c_Myc_rna +v_ERK1_phosphorylated_M1_macrophage___nucleus -> v_c_Myc_rna +v_RELA_NFKB1_complex_M1_macrophage___nucleus -> v_CXCL16 +v_AP_1_phosphorylated -> v_LTA +v_STAT3_STAT3_complex -> v_HMGB1 +v_IL6_IL6R_IL6ST_complex -> v_JAK2 +v_CCL21_CCR7_complex -> v_JAK2 +v_CCL2_CCR2_complex -> v_JAK2 +v_CXCR1_IL8_complex -> v_JAK2 +v_IL11_IL11Ra_IL6ST_complex -> v_JAK1 +v_IL1B_M1_macrophage___Secreted_components -> v_osteoclastogenesis_signal_phenotype +v_IFNg_M1_macrophage___Secreted_components -> v_osteoclastogenesis_signal_phenotype +v_CXCL10 -> v_proliferation_survival_signal_phenotype +v_IL15 -> v_proliferation_survival_signal_phenotype +v_IL6_M1_macrophage___Secreted_components -> v_proliferation_survival_signal_phenotype +v_IL18_M1_macrophage___Secreted_components -> v_proliferation_survival_signal_phenotype +v_vcan -> v_proliferation_survival_signal_phenotype +v_AREG -> v_proliferation_survival_signal_phenotype +v_CSF2_M1_macrophage___Secreted_components -> v_proliferation_survival_signal_phenotype +v_CCL2_M1_macrophage___Secreted_components -> v_proliferation_survival_signal_phenotype +v_CXCL1_M1_macrophage___Secreted_components -> v_proliferation_survival_signal_phenotype +v_FASL_M1_macrophage___Secreted_components -> v_apoptosis_signal_phenotype +v_TNF_M1_macrophage___Secreted_components -> v_apoptosis_signal_phenotype +v_LTA -> v_apoptosis_signal_phenotype +v_FASL_M1_macrophage___Secreted_components -> v_FASL_M1_macrophage___Extracellular_Space +v_CCL20 -> v_Cell_chemotaxis_migration_signal_phenotype +v_CXCL10 -> v_Cell_chemotaxis_migration_signal_phenotype +v_CXCL11 -> v_Cell_chemotaxis_migration_signal_phenotype +v_CXCL9 -> v_Cell_chemotaxis_migration_signal_phenotype +v_CCL3 -> v_Cell_chemotaxis_migration_signal_phenotype +v_CCL5 -> v_Cell_chemotaxis_migration_signal_phenotype +v_MMP14 -> v_Cell_chemotaxis_migration_signal_phenotype +v_CXCL1_M1_macrophage___Secreted_components -> v_Cell_chemotaxis_migration_signal_phenotype +v_IL8_M1_macrophage___Secreted_components -> v_Cell_chemotaxis_migration_signal_phenotype +v_MMP3 -> v_Cell_chemotaxis_migration_signal_phenotype +v_MMP9 -> v_Cell_chemotaxis_migration_signal_phenotype +v_IL12_M1_macrophage___Secreted_components -> v_Cell_chemotaxis_migration_signal_phenotype +$v_ACKR3_CXCL12_complex: v_CXCL12_M1_macrophage___Extracellular_Space +$v_ACVR2A_ACVR2B_INHBA_complex: v_INHBA & v_ACVR2A_ACVR2B_complex +$v_ACVR2A_ACVR2B_INHBB_complex: v_INHBB & v_ACVR2A_ACVR2B_complex +$v_AKT1: v_PI3K +$v_AP_1: v_c_FOS_M1_macrophage___nucleus & v_c_JUN_phosphorylated_M1_macrophage___nucleus +$v_AP_1_phosphorylated: (v_p38_MAP_KINASE_phosphorylated_M1_macrophage___nucleus | v_JNK1_phosphorylated_M1_macrophage___nucleus | v_ERK1_phosphorylated_M1_macrophage___nucleus) & v_AP_1 +$v_AREG: v_STAT3_STAT3_complex +$v_ARRB2: v_ACKR3_CXCL12_complex | v_CCL21_CCR7_complex | v_CXCL13_ACKR4_complex +$v_ASK1: v_TRADD_TRAF2_RIP1_complex | v_DAXX +$v_BAX: !v_BCL2_M1_macrophage__Mitochondria_membrane_active & !v_BCL2L1_M1_macrophage__Mitochondria_active +$v_BCL2L1_M1_macrophage__Mitochondria: v_STAT1_STAT2_IRF9_complex & v_STAT1_STAT1_complex +$v_BCL2L1_M1_macrophage__Mitochondria_active: v_BCL2L1_M1_macrophage__Mitochondria & !v_BAD & !v_Bim +$v_BCL2_M1_macrophage__Mitochondria_membrane: v_Bcl2_rna +$v_BCL2_M1_macrophage__Mitochondria_membrane_active: v_BCL2_M1_macrophage__Mitochondria_membrane & !v_BAD & !v_Bim +$v_BCL3_rna: v_AP_1_phosphorylated & v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_STAT3_STAT3_complex +$v_Bcl2_rna: v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_STAT1_STAT2_IRF9_complex & v_STAT1_STAT1_complex & v_STAT5_CRKL_complex +$v_Bim: v_FOXO_M1_macrophage___nucleus +$v_C5a_C5aR1_complex: v_c5a +$v_CASP3: v_CASP8 +$v_CASP7: v_CASP8 +$v_CASP8: v_FADD & !v_cFLIP +$v_CASP9: v_BAX & !v_AKT1 & !v_XIAP +$v_CCL20: v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated +$v_CCL21_CCR7_complex: v_CCl21 +$v_CCL2_CCR2_complex: v_CCL2_M1_macrophage___Extracellular_Space +$v_CCL2_M1_macrophage___Extracellular_Space: v_CCL2_M1_macrophage___Secreted_components +$v_CCL2_M1_macrophage___Secreted_components: v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_NFAT5 & v_AP_1_phosphorylated +$v_CCL3: v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated & v_IRF5_ubiquitinated +$v_CCL4: v_RELA_NFKB1_complex_M1_macrophage___nucleus +$v_CCL5: v_AP_1_phosphorylated & v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_IRF5_ubiquitinated +$v_CD40: v_IRF3_phosphorylated +$v_CD40LG: v_STAT1_STAT1_complex +$v_CD80: v_IRF3_phosphorylated +$v_CD84: v_STAT3_STAT3_complex +$v_CD86: v_IRF3_phosphorylated +$v_COX2_rna: v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_NFAT5 +$v_CRKL_phosphorylated: v_JAK1_TYK2_complex +$v_CSF1_rna: v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated +$v_CSF2RA_CSF2RB_CSF2_complex: v_CSF2RA_CSF2RB_complex & v_CSF2_M1_macrophage___Extracellular_Space +$v_CSF2_M1_macrophage___Extracellular_Space: v_CSF2_M1_macrophage___Secreted_components +$v_CSF2_M1_macrophage___Secreted_components: v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated & v_NFAT5 +$v_CXCL10: v_IRF3_phosphorylated & v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated +$v_CXCL11: v_IRF3_phosphorylated +$v_CXCL12_M1_macrophage___Extracellular_Space: v_CXCL12_M1_macrophage___Secreted_components +$v_CXCL12_M1_macrophage___Secreted_components: v_HIF1_complex +$v_CXCL13_ACKR4_complex: v_CXCL13 +$v_CXCL16: v_RELA_NFKB1_complex_M1_macrophage___nucleus +$v_CXCL1_CXCR1_complex: v_CXCL1_M1_macrophage___Extracellular_Space & v_CXCR1 +$v_CXCL1_M1_macrophage___Extracellular_Space: v_CXCL1_M1_macrophage___Secreted_components +$v_CXCL1_M1_macrophage___Secreted_components: v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated +$v_CXCL9: v_IRF3_phosphorylated +$v_CXCR1_IL8_complex: v_IL8_M1_macrophage___Extracellular_Space & v_CXCR1 +$v_Cell_chemotaxis_migration_signal_phenotype: v_CCL20 | v_CXCL10 | v_CXCL11 | v_CXCL9 | v_CCL3 | v_CCL5 | v_MMP14 | v_CXCL1_M1_macrophage___Secreted_components | v_IL8_M1_macrophage___Secreted_components | v_MMP3 | v_MMP9 | v_IL12_M1_macrophage___Secreted_components +$v_DAXX: v_FASL_FAS_complex +$v_EDN1: v_RELA_NFKB1_complex_M1_macrophage___nucleus +$v_ERK1_phosphorylated_M1_macrophage___Cytoplasm: v_MEK1_phosphorylated | v_MEK2_phosphorylated | v_C5a_C5aR1_complex | v_GNB_GNG_GNAI3_complex +$v_ERK1_phosphorylated_M1_macrophage___nucleus: v_ERK1_phosphorylated_M1_macrophage___Cytoplasm +$v_FADD: v_MYD88_TIRAP_TOLLIP_complex | v_FASL_FAS_complex +$v_FAS: v_AP_1_phosphorylated & v_RELA_NFKB1_complex_M1_macrophage___nucleus +$v_FASL_FAS_complex: v_FASL_M1_macrophage___Extracellular_Space & v_FAS +$v_FASL_M1_macrophage___Extracellular_Space: v_FASL_M1_macrophage___Secreted_components +$v_FASL_M1_macrophage___Secreted_components: v_AP_1_phosphorylated +$v_FOXO_M1_macrophage___Cytoplasm: !v_AKT1 +$v_FOXO_M1_macrophage___nucleus: (v_FOXO_M1_macrophage___Cytoplasm & !v_AKT1) | (v_FOXO_M1_macrophage___nucleus & v_Sirt1) +$v_GAL_GALR2_complex: v_gal +$v_GNA12_GNA13_complex: v_GAL_GALR2_complex +$v_GNAI3: (v_CCL2_CCR2_complex | v_CXCR1_IL8_complex | v_CCL21_CCR7_complex | v_CXCL1_CXCR1_complex) & v_GNB_GNG_GNAI3_complex +$v_GNB_GNG_complex: (v_CCL2_CCR2_complex | v_CXCR1_IL8_complex | v_CCL21_CCR7_complex | v_CXCL1_CXCR1_complex) & v_GNB_GNG_GNAI3_complex +$v_HES1_rna: v_NICD_CSL_SKIP_MAML1_ep300_complex +$v_HEY1_rna: v_NICD_CSL_SKIP_MAML1_ep300_complex +$v_HIF1_complex: v_Hif1a & v_Hif1b +$v_HMGB1: v_STAT3_STAT3_complex +$v_HRAS: v_SOS1 +$v_ICAM1: v_RELA_NFKB1_complex_M1_macrophage___nucleus +$v_IFNAR1_IFNAR2_IFNa_complex: v_IFNa_M1_macrophage___Extracellular_Space & v_IFNAR1_IFNAR2_complex +$v_IFNAR1_IFNAR2_IFNb_complex: v_IFNb_M1_macrophage___Extracellular_Space & v_IFNAR1_IFNAR2_complex +$v_IFNE_IFNAR1_IFNAR2_complex: v_IFNE & v_IFNAR1_IFNAR2_complex +$v_IFNGR1_IFNGR2_IFNg_complex: v_IFNg_M1_macrophage___Extracellular_Space & v_IFNGR1_IFNGR2_complex +$v_IFNa_M1_macrophage___Extracellular_Space: v_IFNa_M1_macrophage___Secreted_components +$v_IFNa_M1_macrophage___Secreted_components: v_IRF7 & v_IRF3_phosphorylated +$v_IFNb_M1_macrophage___Extracellular_Space: v_IFNb_M1_macrophage___Secreted_components +$v_IFNb_M1_macrophage___Secreted_components: v_IRF7 & v_IRF3_phosphorylated +$v_IFNg_M1_macrophage___Extracellular_Space: v_IFNg_M1_macrophage___Secreted_components +$v_IFNg_M1_macrophage___Secreted_components: v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_NFAT5 & v_STAT4_STAT4_complex +$v_IKK1_IKK2_complex: v_IKK1_phosphorylated & v_IKK2_phosphorylated +$v_IKK2_phosphorylated: v_PRKCQ +$v_IKKE_TBK1_TRAF3_complex: v_TRAF3 & v_IKKE_TBK1_complex +$v_IKK_complex: v_TRAF6_TAB1_TAB2_TAK1_complex | v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex | v_AKT1 | v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex | v_NIK | v_TRADD_TRAF2_RIP1_complex | v_CSF2RA_CSF2RB_CSF2_complex +$v_IL10_rna: v_STAT3_STAT3_complex & v_FOXO_M1_macrophage___nucleus +$v_IL12RB_IL12_complex: v_IL12_M1_macrophage___Extracellular_Space & v_IL12RB_complex +$v_IL12_M1_macrophage___Extracellular_Space: v_IL12_M1_macrophage___Secreted_components +$v_IL12_M1_macrophage___Secreted_components: v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated +$v_IL15: v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated +$v_IL18_IL18R1_complex: v_IL18_M1_macrophage___Extracellular_Space +$v_IL18_M1_macrophage___Cytoplasm: v_NFAT5 +$v_IL18_M1_macrophage___Extracellular_Space: v_IL18_M1_macrophage___Secreted_components +$v_IL18_M1_macrophage___Secreted_components: v_IL18_M1_macrophage___Cytoplasm & v_NLRP3_INFLAMMASOME_complex +$v_IL1B_M1_macrophage___Cytoplasm: v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_NFAT5 & v_AP_1_phosphorylated +$v_IL1B_M1_macrophage___Extracellular_Space: v_IL1B_M1_macrophage___Secreted_components +$v_IL1B_M1_macrophage___Secreted_components: v_IL1B_M1_macrophage___Cytoplasm & v_NLRP3_INFLAMMASOME_complex +$v_IL1_IL1R_complex: v_IL1B_M1_macrophage___Extracellular_Space & v_IL1R_complex +$v_IL23R_IL12RB1_IL23_complex: v_IL23R_IL12RB1_complex & v_IL23_M1_macrophage___Extracellular_Space +$v_IL23_M1_macrophage___Extracellular_Space: v_IL23_M1_macrophage___Secreted_components +$v_IL23_M1_macrophage___Secreted_components: v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated +$v_IL4_rna: v_STAT3_STAT3_complex +$v_IL6_IL6R_IL6ST_complex: v_IL6_M1_macrophage___Extracellular_Space +$v_IL6_M1_macrophage___Extracellular_Space: v_IL6_M1_macrophage___Secreted_components +$v_IL6_M1_macrophage___Secreted_components: v_NFAT5 & v_RELA_NFKB1_complex_M1_macrophage___nucleus +$v_IL8_M1_macrophage___Extracellular_Space: v_IL8_M1_macrophage___Secreted_components +$v_IL8_M1_macrophage___Secreted_components: v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated +$v_IRAK1_IRAK4_complex: v_IRAK4_phosphorylated & v_IRAK1 +$v_IRAK4_phosphorylated: v_MYD88 | v_MYD88_TIRAP_TOLLIP_complex | v_TLR7_TLR8_ssRNA_complex | v_TLR9_DNA_complex +$v_IRF3_phosphorylated: v_IKKE_TBK1_TRAF3_complex | v_IKK_complex +$v_IRF5_ubiquitinated: v_TRAF6_IRAK1_IRAK4_complex +$v_IRF7: v_IKKE_TBK1_TRAF3_complex | v_IKK_complex | v_OPN +$v_ITCH_phosphorylated: v_JNK1_phosphorylated_M1_macrophage___Cytoplasm +$v_ITGB1_ITGA1_col4a_complex: (v_col4a4 & v_ITGB1_ITGA1_complex) | (v_col4a5 & v_ITGB1_ITGA1_complex) +$v_JAG1: v_AP_1_phosphorylated & v_RELA_NFKB1_complex_M1_macrophage___nucleus +$v_JAK1: v_IL11_IL11Ra_IL6ST_complex +$v_JAK1_JAK2_complex: v_IFNGR1_IFNGR2_IFNg_complex +$v_JAK1_TYK2_complex: v_IL23R_IL12RB1_IL23_complex | v_IFNAR1_IFNAR2_IFNb_complex | v_IFNAR1_IFNAR2_IFNa_complex | v_IFNE_IFNAR1_IFNAR2_complex +$v_JAK2: v_IL6_IL6R_IL6ST_complex | v_CCL21_CCR7_complex | v_CCL2_CCR2_complex | v_CXCR1_IL8_complex +$v_JAK2_TYK2_complex: v_IL12RB_IL12_complex +$v_JNK1_phosphorylated_M1_macrophage___Cytoplasm: v_MKK7_phosphorylated | v_MKK4_phosphorylated | v_ASK1 | v_Rac1 +$v_JNK1_phosphorylated_M1_macrophage___nucleus: v_JNK1_phosphorylated_M1_macrophage___Cytoplasm +$v_LTA: v_AP_1_phosphorylated +$v_MDM2_phosphorylated: v_AKT1 +$v_MEK1_phosphorylated: v_TPL2 | v_RAF1 +$v_MEK2_phosphorylated: v_TPL2 | v_RAF1 +$v_MKK3_phosphorylated: v_TRAF6_TAB1_TAB2_TAK1_complex | v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex | v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex | v_ASK1 +$v_MKK4_phosphorylated: v_TRAF6_TAB1_TAB2_TAK1_complex | v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex | v_ASK1 | v_MEKK1 +$v_MKK6_phosphorylated: v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex | v_TRAF6_TAB1_TAB2_TAK1_complex | v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex | v_ASK1 +$v_MKK7_phosphorylated: v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex | v_TRAF6_TAB1_TAB2_TAK1_complex | v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex | v_ASK1 +$v_MMP14: v_AP_1_phosphorylated & v_RELA_NFKB1_complex_M1_macrophage___nucleus +$v_MMP3: v_AP_1_phosphorylated & v_RELA_NFKB1_complex_M1_macrophage___nucleus +$v_MMP9: v_AP_1_phosphorylated & v_RELA_NFKB1_complex_M1_macrophage___nucleus +$v_MYD88: v_IL1_IL1R_complex | v_TLR5 | v_IL18_IL18R1_complex +$v_MYD88_TIRAP_TOLLIP_complex: v_TLR1_TLR2_biglycan_complex | v_TLR2_TLR6_biglycan_complex +$v_Matrix_degradation_signal_phenotype: (v_MMP3 | v_MMP14 | v_MMP9) & !v_vcan +$v_Mcl1_rna: v_STAT1_STAT2_IRF9_complex & v_STAT1_STAT1_complex & v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_ERK1_phosphorylated_M1_macrophage___nucleus +$v_NCID: v_notch1_JAG1_complex & v_gamma_secretase_complex_complex +$v_NFAT5: v_ERK1_phosphorylated_M1_macrophage___Cytoplasm | v_p38_MAP_KINASE_phosphorylated_M1_macrophage___Cytoplasm +$v_NFKB1: v_NFKB1_TPL2_complex & v_IKK_complex +$v_NFKBIA_phosphorylated: (v_IKK_complex | v_IKKE_TBK1_TRAF3_complex) & v_NFKBIA_RELA_NFKB1_complex +$v_NFKBIE: v_RELA_NFKB1_NFKBIE_complex & v_IKK1_IKK2_complex +$v_NICD: v_NCID +$v_NICD_CSL_SKIP_MAML1_ep300_complex: v_NICD +$v_NIK: v_TRAF6_TAB1_TAB2_TAK1_complex | v_TRADD_TRAF2_RIP1_complex | v_TRAF2_TRAF6_complex +$v_NLRP3: v_RELA_NFKB1_complex_M1_macrophage___nucleus +$v_NLRP3_INFLAMMASOME_complex: v_NLRP3 & v_Casp1 & v_ASC +$v_NOS2: v_NFAT5 +$v_NOS2_phosphorylated: v_NOS2 & v_AKT1 +$v_PI3K: (v_Rac1 | v_TRAF6_ubiquitinated | v_C5a_C5aR1_complex | v_CSF2RA_CSF2RB_CSF2_complex | v_HRAS | v_PTK2 | v_PIK3AP1_phosphorylated | v_CD40LG_ITGB1_ITGA1_complex | v_JAK2 | v_JAK1_TYK2_complex | v_Src) & !v_INPP5A +$v_PIK3AP1_phosphorylated: v_SYK +$v_PTK2: v_ITGB1_ITGA1_col4a_complex +$v_PTPN6: v_HLA_B_LILRB1_complex +$v_RAF1: v_HRAS & !v_AKT1 +$v_RELA_NFKB1_complex_M1_macrophage___Cytoplasm: ((v_IKK_complex | v_IKKE_TBK1_TRAF3_complex) & v_NFKBIA_RELA_NFKB1_complex) | (v_RELA_NFKB1_NFKBIE_complex & v_IKK1_IKK2_complex) +$v_RELA_NFKB1_complex_M1_macrophage___nucleus: (v_CypA | v_Prkcd) & v_RELA_NFKB1_complex_M1_macrophage___Cytoplasm +$v_RHOA: v_GNA12_GNA13_complex & !v_PRKG1 +$v_RXRa_NUR77_complex: !v_AKT1 +$v_Rac1: (v_TLR1_TLR2_biglycan_complex | v_TLR2_TLR6_biglycan_complex) & !v_RHOA +$v_SARA: (v_ACVR2A_ACVR2B_INHBA_complex | v_ACVR2A_ACVR2B_INHBB_complex) & v_SMAD2_SARA_complex & !v_SMAD7 +$v_SEMA4A: v_AP_1_phosphorylated +$v_SHP2_GRB2_complex: v_JAK2 | v_JAK1_JAK2_complex | v_JAK1_TYK2_complex | v_JAK2_TYK2_complex +$v_SMAD2_SMAD4_complex: v_SMAD2_phosphorylated & v_SMAD4 +$v_SMAD2_phosphorylated: (v_ACVR2A_ACVR2B_INHBA_complex | v_ACVR2A_ACVR2B_INHBB_complex) & v_SMAD2_SARA_complex & !v_SMAD7 +$v_SOCS3_rna: v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated & v_STAT3_STAT3_complex +$v_SOS1: v_SHP2_GRB2_complex +$v_STAT1: v_JAK1_JAK2_complex | v_JAK1_TYK2_complex | v_JAK1 | v_JAK2 +$v_STAT1_STAT1_complex: v_STAT1 +$v_STAT1_STAT2_IRF9_complex: (v_JAK1_TYK2_complex | v_JAK2_TYK2_complex) & v_STAT2 & v_STAT1 & v_IRF9 +$v_STAT3: v_JAK1_TYK2_complex | v_JAK2 | v_JAK1 +$v_STAT3_STAT3_complex: v_STAT3 +$v_STAT4: v_JAK2_TYK2_complex | v_JAK1 +$v_STAT4_STAT4_complex: v_STAT4 +$v_STAT5_CRKL_complex: v_CRKL_phosphorylated & v_STAT5_phosphorylated +$v_STAT5_phosphorylated: v_JAK1_TYK2_complex +$v_SYK: !v_PTPN6 +$v_Src: v_GNAI3 +$v_TAB2_phosphorylated: v_IRAK1_IRAK4_complex +$v_TLR1_TLR2_biglycan_complex: v_biglycan_simple_molecule & v_TLR1_TLR2_complex +$v_TLR2_TLR6_biglycan_complex: v_biglycan_simple_molecule & v_TLR2_TLR6_complex +$v_TLR3_dsRNA_complex: v_dsRNA_simple_molecule +$v_TLR9_DNA_complex: v_DNA_simple_molecule +$v_TNFAIP3_rna: v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated +$v_TNFA_rna: v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated & v_MK2_phosphorylated & v_NFAT5 +$v_TNFSF11_TNFRSF11_complex: v_TNFSF11 +$v_TNF_M1_macrophage___Extracellular_Space: v_TNF_M1_macrophage___Secreted_components +$v_TNF_M1_macrophage___Secreted_components: v_TNFA_rna +$v_TNF_TNFRSF1A_complex: v_TNF_M1_macrophage___Extracellular_Space +$v_TPL2: v_NFKB1_TPL2_complex & v_IKK_complex +$v_TRADD: v_TNF_TNFRSF1A_complex +$v_TRADD_TRAF2_RIP1_complex: v_cIAP1 | v_TRADD +$v_TRAF1_rna: v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_NFAT5 +$v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex: v_TRADD_TRAF2_RIP1_complex & v_TAK1 & v_TAB2_phosphorylated & v_TAB1 +$v_TRAF2_TRAF6_complex: v_TNFSF11_TNFRSF11_complex +$v_TRAF3: v_TRAM1_TRIF_complex +$v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex: v_MEKK1 & v_ECSIT & v_TRAF6_ubiquitinated & v_TAK1 & v_TAB1 & v_TAB2_phosphorylated +$v_TRAF6_IRAK1_IRAK4_complex: v_TRAF6 & v_IRAK1_IRAK4_complex & !v_IRAK3 +$v_TRAF6_TAB1_TAB2_TAK1_complex: v_TRAF6_ubiquitinated & v_TAB2_phosphorylated & v_TAB1 & v_TAK1 & v_TAB1 & v_TRAF2_TRAF6_complex +$v_TRAF6_ubiquitinated: v_TRAF6 & v_UEV1A_UBC13_complex & !v_PP4 +$v_TRAM1: v_TLR4_Md2_CD14_fibrinogen_complex +$v_TRAM1_TRIF_complex: v_TRIF & v_TRAM1 +$v_TRIF: v_TLR3_dsRNA_complex +$v_T_cells_activation_signal_phenotype: v_CD40 | v_CD86 | v_CD80 | v_CSF2_M1_macrophage___Secreted_components | v_IFNa_M1_macrophage___Secreted_components | v_ICAM1 +$v_Vegfa_rna: v_NFAT5 & v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_STAT3_STAT3_complex +$v_Vegfb_rna: v_NFAT5 & v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_STAT4_STAT4_complex +$v_Vegfc_rna: v_AP_1_phosphorylated & v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_NFAT5 & v_STAT3_STAT3_complex & v_HIF1_complex +$v_XIAP: v_RELA_NFKB1_complex_M1_macrophage___nucleus +$v_angiogenesis_signal_phenotype: v_NOS2_phosphorylated | v_Hif1a | v_CXCL12_M1_macrophage___Secreted_components | v_EDN1 | v_OPN +$v_apoptosis_M1_macrophage_phenotype: (v_CASP8 | v_CASP3 | v_CASP7 | v_p53_phosphorylated | v_Bim | v_TNF_M1_macrophage___Secreted_components | v_FASL_M1_macrophage___Secreted_components | v_NLRP3_INFLAMMASOME_complex | v_p300_SP1_complex) & !v_Mcl1_rna & !v_p21_rna & !v_BCL2_M1_macrophage__Mitochondria_membrane_active & !v_BCL2L1_M1_macrophage__Mitochondria_active +$v_apoptosis_signal_phenotype: v_FASL_M1_macrophage___Secreted_components | v_TNF_M1_macrophage___Secreted_components | v_LTA +$v_cFLIP: v_RELA_NFKB1_complex_M1_macrophage___nucleus +$v_cFLIP_ubiquitinated: v_cFLIP & v_ITCH_phosphorylated +$v_c_FOS_M1_macrophage___Cytoplasm: v_RELA_NFKB1_complex_M1_macrophage___nucleus +$v_c_FOS_M1_macrophage___Cytoplasm_active: v_c_FOS_M1_macrophage___Cytoplasm & v_TSG6 +$v_c_FOS_M1_macrophage___nucleus: v_c_FOS_M1_macrophage___Cytoplasm_active +$v_c_JUN: v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_JNK1_phosphorylated_M1_macrophage___nucleus +$v_c_JUN_phosphorylated_M1_macrophage___Cytoplasm: (v_JNK1_phosphorylated_M1_macrophage___Cytoplasm | v_ERK1_phosphorylated_M1_macrophage___Cytoplasm) & v_c_JUN +$v_c_JUN_phosphorylated_M1_macrophage___nucleus: v_c_JUN_phosphorylated_M1_macrophage___Cytoplasm +$v_c_Myc_rna: v_STAT5_CRKL_complex & v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_ERK1_phosphorylated_M1_macrophage___nucleus +$v_inflammation_signal_phenotype: (v_C5a_C5aR1_complex | v_CCL20 | v_CCL4 | v_CCL5 | v_CD40 | v_COX2_rna | v_IL15 | v_IRF7 | v_RELA_NFKB1_complex_M1_macrophage___nucleus | v_IRF5_ubiquitinated | v_IL23_M1_macrophage___Secreted_components | v_IL12_M1_macrophage___Secreted_components | v_IFNb_M1_macrophage___Secreted_components | v_IFNa_M1_macrophage___Secreted_components | v_TNF_M1_macrophage___Secreted_components | v_IL18_M1_macrophage___Secreted_components | v_IL1B_M1_macrophage___Secreted_components | v_AREG | v_SEMA4A | v_ICAM1 | v_IL6_M1_macrophage___Secreted_components | v_CCL2_M1_macrophage___Secreted_components | v_CCL3 | v_LTA | v_CXCL10 | v_CXCL9 | v_CXCL11 | v_IFNg_M1_macrophage___Secreted_components) & !v_ARRB2 +$v_osteoclastogenesis_M1_macrophage_phenotype: v_c_FOS_M1_macrophage___Cytoplasm_active | v_c_JUN_phosphorylated_M1_macrophage___Cytoplasm | v_IL1B_M1_macrophage___Secreted_components | v_AP_1_phosphorylated | v_IFNg_M1_macrophage___Secreted_components +$v_osteoclastogenesis_signal_phenotype: v_IL1B_M1_macrophage___Secreted_components | v_IFNg_M1_macrophage___Secreted_components +$v_p15_rna: v_FOXO_M1_macrophage___nucleus & !v_c_Myc_rna +$v_p21_rna: v_STAT1_STAT1_complex & v_STAT1_STAT2_IRF9_complex & v_NICD_CSL_SKIP_MAML1_ep300_complex & v_RELA_NFKB1_complex_M1_macrophage___nucleus +$v_p300_SP1_complex: v_SMAD2_SMAD4_complex +$v_p38_MAP_KINASE_phosphorylated_M1_macrophage___Cytoplasm: (v_MKK3_phosphorylated | v_MKK6_phosphorylated | v_C5a_C5aR1_complex) & !v_DUSP1 +$v_p38_MAP_KINASE_phosphorylated_M1_macrophage___nucleus: v_p38_MAP_KINASE_phosphorylated_M1_macrophage___Cytoplasm +$v_p53_phosphorylated: !v_MDM2_phosphorylated +$v_proliferation_survival_M1_macrophage_phenotype: (v_XIAP | v_CXCL1_M1_macrophage___Secreted_components | v_ERK1_phosphorylated_M1_macrophage___nucleus | v_p38_MAP_KINASE_phosphorylated_M1_macrophage___nucleus | v_MDM2_phosphorylated | v_cFLIP | v_BCL3_rna | v_BCL3_rna | v_c_FOS_M1_macrophage___Cytoplasm_active | v_c_JUN_phosphorylated_M1_macrophage___Cytoplasm | v_IL12_M1_macrophage___Secreted_components | v_IL8_M1_macrophage___Secreted_components | v_CCL2_M1_macrophage___Secreted_components | v_CSF2_M1_macrophage___Secreted_components | v_HBGEF | v_p21_rna | v_IL6_M1_macrophage___Secreted_components | v_c_Myc_rna | v_p38_MAP_KINASE_phosphorylated_M1_macrophage___Cytoplasm) & !v_p15_rna +$v_proliferation_survival_signal_phenotype: v_CXCL10 | v_IL15 | v_IL6_M1_macrophage___Secreted_components | v_IL18_M1_macrophage___Secreted_components | v_vcan | v_AREG | v_CSF2_M1_macrophage___Secreted_components | v_CCL2_M1_macrophage___Secreted_components | v_CXCL1_M1_macrophage___Secreted_components +$v_vcan: v_STAT4_STAT4_complex diff --git a/models/[id-239]__[var-234]__[in-69]__[M1-SYNOVIAL-MACROPHAGE]/model.bnet b/models/[id-239]__[var-234]__[in-69]__[M1-SYNOVIAL-MACROPHAGE]/model.bnet new file mode 100644 index 0000000..df0915d --- /dev/null +++ b/models/[id-239]__[var-234]__[in-69]__[M1-SYNOVIAL-MACROPHAGE]/model.bnet @@ -0,0 +1,235 @@ +targets,factors +v_ACKR3_CXCL12_complex, v_CXCL12_M1_macrophage___Extracellular_Space +v_ACVR2A_ACVR2B_INHBA_complex, (v_INHBA & v_ACVR2A_ACVR2B_complex) +v_ACVR2A_ACVR2B_INHBB_complex, (v_INHBB & v_ACVR2A_ACVR2B_complex) +v_AKT1, v_PI3K +v_AP_1, (v_c_FOS_M1_macrophage___nucleus & v_c_JUN_phosphorylated_M1_macrophage___nucleus) +v_AP_1_phosphorylated, (((v_p38_MAP_KINASE_phosphorylated_M1_macrophage___nucleus | v_JNK1_phosphorylated_M1_macrophage___nucleus) | v_ERK1_phosphorylated_M1_macrophage___nucleus) & v_AP_1) +v_AREG, v_STAT3_STAT3_complex +v_ARRB2, ((v_ACKR3_CXCL12_complex | v_CCL21_CCR7_complex) | v_CXCL13_ACKR4_complex) +v_ASK1, (v_TRADD_TRAF2_RIP1_complex | v_DAXX) +v_BAX, (!v_BCL2_M1_macrophage__Mitochondria_membrane_active & !v_BCL2L1_M1_macrophage__Mitochondria_active) +v_BCL2L1_M1_macrophage__Mitochondria, (v_STAT1_STAT2_IRF9_complex & v_STAT1_STAT1_complex) +v_BCL2L1_M1_macrophage__Mitochondria_active, ((v_BCL2L1_M1_macrophage__Mitochondria & !v_BAD) & !v_Bim) +v_BCL2_M1_macrophage__Mitochondria_membrane, v_Bcl2_rna +v_BCL2_M1_macrophage__Mitochondria_membrane_active, ((v_BCL2_M1_macrophage__Mitochondria_membrane & !v_BAD) & !v_Bim) +v_BCL3_rna, ((v_AP_1_phosphorylated & v_RELA_NFKB1_complex_M1_macrophage___nucleus) & v_STAT3_STAT3_complex) +v_Bcl2_rna, (((v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_STAT1_STAT2_IRF9_complex) & v_STAT1_STAT1_complex) & v_STAT5_CRKL_complex) +v_Bim, v_FOXO_M1_macrophage___nucleus +v_C5a_C5aR1_complex, v_c5a +v_CASP3, v_CASP8 +v_CASP7, v_CASP8 +v_CASP8, (v_FADD & !v_cFLIP) +v_CASP9, ((v_BAX & !v_AKT1) & !v_XIAP) +v_CCL20, (v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated) +v_CCL21_CCR7_complex, v_CCl21 +v_CCL2_CCR2_complex, v_CCL2_M1_macrophage___Extracellular_Space +v_CCL2_M1_macrophage___Extracellular_Space, v_CCL2_M1_macrophage___Secreted_components +v_CCL2_M1_macrophage___Secreted_components, ((v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_NFAT5) & v_AP_1_phosphorylated) +v_CCL3, ((v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated) & v_IRF5_ubiquitinated) +v_CCL4, v_RELA_NFKB1_complex_M1_macrophage___nucleus +v_CCL5, ((v_AP_1_phosphorylated & v_RELA_NFKB1_complex_M1_macrophage___nucleus) & v_IRF5_ubiquitinated) +v_CD40, v_IRF3_phosphorylated +v_CD40LG, v_STAT1_STAT1_complex +v_CD80, v_IRF3_phosphorylated +v_CD84, v_STAT3_STAT3_complex +v_CD86, v_IRF3_phosphorylated +v_COX2_rna, (v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_NFAT5) +v_CRKL_phosphorylated, v_JAK1_TYK2_complex +v_CSF1_rna, (v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated) +v_CSF2RA_CSF2RB_CSF2_complex, (v_CSF2RA_CSF2RB_complex & v_CSF2_M1_macrophage___Extracellular_Space) +v_CSF2_M1_macrophage___Extracellular_Space, v_CSF2_M1_macrophage___Secreted_components +v_CSF2_M1_macrophage___Secreted_components, ((v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated) & v_NFAT5) +v_CXCL10, ((v_IRF3_phosphorylated & v_RELA_NFKB1_complex_M1_macrophage___nucleus) & v_AP_1_phosphorylated) +v_CXCL11, v_IRF3_phosphorylated +v_CXCL12_M1_macrophage___Extracellular_Space, v_CXCL12_M1_macrophage___Secreted_components +v_CXCL12_M1_macrophage___Secreted_components, v_HIF1_complex +v_CXCL13_ACKR4_complex, v_CXCL13 +v_CXCL16, v_RELA_NFKB1_complex_M1_macrophage___nucleus +v_CXCL1_CXCR1_complex, (v_CXCL1_M1_macrophage___Extracellular_Space & v_CXCR1) +v_CXCL1_M1_macrophage___Extracellular_Space, v_CXCL1_M1_macrophage___Secreted_components +v_CXCL1_M1_macrophage___Secreted_components, (v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated) +v_CXCL9, v_IRF3_phosphorylated +v_CXCR1_IL8_complex, (v_IL8_M1_macrophage___Extracellular_Space & v_CXCR1) +v_Cell_chemotaxis_migration_signal_phenotype, (((((((((((v_CCL20 | v_CXCL10) | v_CXCL11) | v_CXCL9) | v_CCL3) | v_CCL5) | v_MMP14) | v_CXCL1_M1_macrophage___Secreted_components) | v_IL8_M1_macrophage___Secreted_components) | v_MMP3) | v_MMP9) | v_IL12_M1_macrophage___Secreted_components) +v_DAXX, v_FASL_FAS_complex +v_EDN1, v_RELA_NFKB1_complex_M1_macrophage___nucleus +v_ERK1_phosphorylated_M1_macrophage___Cytoplasm, (((v_MEK1_phosphorylated | v_MEK2_phosphorylated) | v_C5a_C5aR1_complex) | v_GNB_GNG_GNAI3_complex) +v_ERK1_phosphorylated_M1_macrophage___nucleus, v_ERK1_phosphorylated_M1_macrophage___Cytoplasm +v_FADD, (v_MYD88_TIRAP_TOLLIP_complex | v_FASL_FAS_complex) +v_FAS, (v_AP_1_phosphorylated & v_RELA_NFKB1_complex_M1_macrophage___nucleus) +v_FASL_FAS_complex, (v_FASL_M1_macrophage___Extracellular_Space & v_FAS) +v_FASL_M1_macrophage___Extracellular_Space, v_FASL_M1_macrophage___Secreted_components +v_FASL_M1_macrophage___Secreted_components, v_AP_1_phosphorylated +v_FOXO_M1_macrophage___Cytoplasm, !v_AKT1 +v_FOXO_M1_macrophage___nucleus, ((v_FOXO_M1_macrophage___Cytoplasm & !v_AKT1) | (v_FOXO_M1_macrophage___nucleus & v_Sirt1)) +v_GAL_GALR2_complex, v_gal +v_GNA12_GNA13_complex, v_GAL_GALR2_complex +v_GNAI3, ((((v_CCL2_CCR2_complex | v_CXCR1_IL8_complex) | v_CCL21_CCR7_complex) | v_CXCL1_CXCR1_complex) & v_GNB_GNG_GNAI3_complex) +v_GNB_GNG_complex, ((((v_CCL2_CCR2_complex | v_CXCR1_IL8_complex) | v_CCL21_CCR7_complex) | v_CXCL1_CXCR1_complex) & v_GNB_GNG_GNAI3_complex) +v_HES1_rna, v_NICD_CSL_SKIP_MAML1_ep300_complex +v_HEY1_rna, v_NICD_CSL_SKIP_MAML1_ep300_complex +v_HIF1_complex, (v_Hif1a & v_Hif1b) +v_HMGB1, v_STAT3_STAT3_complex +v_HRAS, v_SOS1 +v_ICAM1, v_RELA_NFKB1_complex_M1_macrophage___nucleus +v_IFNAR1_IFNAR2_IFNa_complex, (v_IFNa_M1_macrophage___Extracellular_Space & v_IFNAR1_IFNAR2_complex) +v_IFNAR1_IFNAR2_IFNb_complex, (v_IFNb_M1_macrophage___Extracellular_Space & v_IFNAR1_IFNAR2_complex) +v_IFNE_IFNAR1_IFNAR2_complex, (v_IFNE & v_IFNAR1_IFNAR2_complex) +v_IFNGR1_IFNGR2_IFNg_complex, (v_IFNg_M1_macrophage___Extracellular_Space & v_IFNGR1_IFNGR2_complex) +v_IFNa_M1_macrophage___Extracellular_Space, v_IFNa_M1_macrophage___Secreted_components +v_IFNa_M1_macrophage___Secreted_components, (v_IRF7 & v_IRF3_phosphorylated) +v_IFNb_M1_macrophage___Extracellular_Space, v_IFNb_M1_macrophage___Secreted_components +v_IFNb_M1_macrophage___Secreted_components, (v_IRF7 & v_IRF3_phosphorylated) +v_IFNg_M1_macrophage___Extracellular_Space, v_IFNg_M1_macrophage___Secreted_components +v_IFNg_M1_macrophage___Secreted_components, ((v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_NFAT5) & v_STAT4_STAT4_complex) +v_IKK1_IKK2_complex, (v_IKK1_phosphorylated & v_IKK2_phosphorylated) +v_IKK2_phosphorylated, v_PRKCQ +v_IKKE_TBK1_TRAF3_complex, (v_TRAF3 & v_IKKE_TBK1_complex) +v_IKK_complex, ((((((v_TRAF6_TAB1_TAB2_TAK1_complex | v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex) | v_AKT1) | v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex) | v_NIK) | v_TRADD_TRAF2_RIP1_complex) | v_CSF2RA_CSF2RB_CSF2_complex) +v_IL10_rna, (v_STAT3_STAT3_complex & v_FOXO_M1_macrophage___nucleus) +v_IL12RB_IL12_complex, (v_IL12_M1_macrophage___Extracellular_Space & v_IL12RB_complex) +v_IL12_M1_macrophage___Extracellular_Space, v_IL12_M1_macrophage___Secreted_components +v_IL12_M1_macrophage___Secreted_components, (v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated) +v_IL15, (v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated) +v_IL18_IL18R1_complex, v_IL18_M1_macrophage___Extracellular_Space +v_IL18_M1_macrophage___Cytoplasm, v_NFAT5 +v_IL18_M1_macrophage___Extracellular_Space, v_IL18_M1_macrophage___Secreted_components +v_IL18_M1_macrophage___Secreted_components, (v_IL18_M1_macrophage___Cytoplasm & v_NLRP3_INFLAMMASOME_complex) +v_IL1B_M1_macrophage___Cytoplasm, ((v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_NFAT5) & v_AP_1_phosphorylated) +v_IL1B_M1_macrophage___Extracellular_Space, v_IL1B_M1_macrophage___Secreted_components +v_IL1B_M1_macrophage___Secreted_components, (v_IL1B_M1_macrophage___Cytoplasm & v_NLRP3_INFLAMMASOME_complex) +v_IL1_IL1R_complex, (v_IL1B_M1_macrophage___Extracellular_Space & v_IL1R_complex) +v_IL23R_IL12RB1_IL23_complex, (v_IL23R_IL12RB1_complex & v_IL23_M1_macrophage___Extracellular_Space) +v_IL23_M1_macrophage___Extracellular_Space, v_IL23_M1_macrophage___Secreted_components +v_IL23_M1_macrophage___Secreted_components, (v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated) +v_IL4_rna, v_STAT3_STAT3_complex +v_IL6_IL6R_IL6ST_complex, v_IL6_M1_macrophage___Extracellular_Space +v_IL6_M1_macrophage___Extracellular_Space, v_IL6_M1_macrophage___Secreted_components +v_IL6_M1_macrophage___Secreted_components, (v_NFAT5 & v_RELA_NFKB1_complex_M1_macrophage___nucleus) +v_IL8_M1_macrophage___Extracellular_Space, v_IL8_M1_macrophage___Secreted_components +v_IL8_M1_macrophage___Secreted_components, (v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated) +v_IRAK1_IRAK4_complex, (v_IRAK4_phosphorylated & v_IRAK1) +v_IRAK4_phosphorylated, (((v_MYD88 | v_MYD88_TIRAP_TOLLIP_complex) | v_TLR7_TLR8_ssRNA_complex) | v_TLR9_DNA_complex) +v_IRF3_phosphorylated, (v_IKKE_TBK1_TRAF3_complex | v_IKK_complex) +v_IRF5_ubiquitinated, v_TRAF6_IRAK1_IRAK4_complex +v_IRF7, ((v_IKKE_TBK1_TRAF3_complex | v_IKK_complex) | v_OPN) +v_ITCH_phosphorylated, v_JNK1_phosphorylated_M1_macrophage___Cytoplasm +v_ITGB1_ITGA1_col4a_complex, ((v_col4a4 & v_ITGB1_ITGA1_complex) | (v_col4a5 & v_ITGB1_ITGA1_complex)) +v_JAG1, (v_AP_1_phosphorylated & v_RELA_NFKB1_complex_M1_macrophage___nucleus) +v_JAK1, v_IL11_IL11Ra_IL6ST_complex +v_JAK1_JAK2_complex, v_IFNGR1_IFNGR2_IFNg_complex +v_JAK1_TYK2_complex, (((v_IL23R_IL12RB1_IL23_complex | v_IFNAR1_IFNAR2_IFNb_complex) | v_IFNAR1_IFNAR2_IFNa_complex) | v_IFNE_IFNAR1_IFNAR2_complex) +v_JAK2, (((v_IL6_IL6R_IL6ST_complex | v_CCL21_CCR7_complex) | v_CCL2_CCR2_complex) | v_CXCR1_IL8_complex) +v_JAK2_TYK2_complex, v_IL12RB_IL12_complex +v_JNK1_phosphorylated_M1_macrophage___Cytoplasm, (((v_MKK7_phosphorylated | v_MKK4_phosphorylated) | v_ASK1) | v_Rac1) +v_JNK1_phosphorylated_M1_macrophage___nucleus, v_JNK1_phosphorylated_M1_macrophage___Cytoplasm +v_LTA, v_AP_1_phosphorylated +v_MDM2_phosphorylated, v_AKT1 +v_MEK1_phosphorylated, (v_TPL2 | v_RAF1) +v_MEK2_phosphorylated, (v_TPL2 | v_RAF1) +v_MKK3_phosphorylated, (((v_TRAF6_TAB1_TAB2_TAK1_complex | v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex) | v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex) | v_ASK1) +v_MKK4_phosphorylated, (((v_TRAF6_TAB1_TAB2_TAK1_complex | v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex) | v_ASK1) | v_MEKK1) +v_MKK6_phosphorylated, (((v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex | v_TRAF6_TAB1_TAB2_TAK1_complex) | v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex) | v_ASK1) +v_MKK7_phosphorylated, (((v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex | v_TRAF6_TAB1_TAB2_TAK1_complex) | v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex) | v_ASK1) +v_MMP14, (v_AP_1_phosphorylated & v_RELA_NFKB1_complex_M1_macrophage___nucleus) +v_MMP3, (v_AP_1_phosphorylated & v_RELA_NFKB1_complex_M1_macrophage___nucleus) +v_MMP9, (v_AP_1_phosphorylated & v_RELA_NFKB1_complex_M1_macrophage___nucleus) +v_MYD88, ((v_IL1_IL1R_complex | v_TLR5) | v_IL18_IL18R1_complex) +v_MYD88_TIRAP_TOLLIP_complex, (v_TLR1_TLR2_biglycan_complex | v_TLR2_TLR6_biglycan_complex) +v_Matrix_degradation_signal_phenotype, (((v_MMP3 | v_MMP14) | v_MMP9) & !v_vcan) +v_Mcl1_rna, (((v_STAT1_STAT2_IRF9_complex & v_STAT1_STAT1_complex) & v_RELA_NFKB1_complex_M1_macrophage___nucleus) & v_ERK1_phosphorylated_M1_macrophage___nucleus) +v_NCID, (v_notch1_JAG1_complex & v_gamma_secretase_complex_complex) +v_NFAT5, (v_ERK1_phosphorylated_M1_macrophage___Cytoplasm | v_p38_MAP_KINASE_phosphorylated_M1_macrophage___Cytoplasm) +v_NFKB1, (v_NFKB1_TPL2_complex & v_IKK_complex) +v_NFKBIA_phosphorylated, ((v_IKK_complex | v_IKKE_TBK1_TRAF3_complex) & v_NFKBIA_RELA_NFKB1_complex) +v_NFKBIE, (v_RELA_NFKB1_NFKBIE_complex & v_IKK1_IKK2_complex) +v_NICD, v_NCID +v_NICD_CSL_SKIP_MAML1_ep300_complex, v_NICD +v_NIK, ((v_TRAF6_TAB1_TAB2_TAK1_complex | v_TRADD_TRAF2_RIP1_complex) | v_TRAF2_TRAF6_complex) +v_NLRP3, v_RELA_NFKB1_complex_M1_macrophage___nucleus +v_NLRP3_INFLAMMASOME_complex, ((v_NLRP3 & v_Casp1) & v_ASC) +v_NOS2, v_NFAT5 +v_NOS2_phosphorylated, (v_NOS2 & v_AKT1) +v_PI3K, (((((((((((v_Rac1 | v_TRAF6_ubiquitinated) | v_C5a_C5aR1_complex) | v_CSF2RA_CSF2RB_CSF2_complex) | v_HRAS) | v_PTK2) | v_PIK3AP1_phosphorylated) | v_CD40LG_ITGB1_ITGA1_complex) | v_JAK2) | v_JAK1_TYK2_complex) | v_Src) & !v_INPP5A) +v_PIK3AP1_phosphorylated, v_SYK +v_PTK2, v_ITGB1_ITGA1_col4a_complex +v_PTPN6, v_HLA_B_LILRB1_complex +v_RAF1, (v_HRAS & !v_AKT1) +v_RELA_NFKB1_complex_M1_macrophage___Cytoplasm, (((v_IKK_complex | v_IKKE_TBK1_TRAF3_complex) & v_NFKBIA_RELA_NFKB1_complex) | (v_RELA_NFKB1_NFKBIE_complex & v_IKK1_IKK2_complex)) +v_RELA_NFKB1_complex_M1_macrophage___nucleus, ((v_CypA | v_Prkcd) & v_RELA_NFKB1_complex_M1_macrophage___Cytoplasm) +v_RHOA, (v_GNA12_GNA13_complex & !v_PRKG1) +v_RXRa_NUR77_complex, !v_AKT1 +v_Rac1, ((v_TLR1_TLR2_biglycan_complex | v_TLR2_TLR6_biglycan_complex) & !v_RHOA) +v_SARA, (((v_ACVR2A_ACVR2B_INHBA_complex | v_ACVR2A_ACVR2B_INHBB_complex) & v_SMAD2_SARA_complex) & !v_SMAD7) +v_SEMA4A, v_AP_1_phosphorylated +v_SHP2_GRB2_complex, (((v_JAK2 | v_JAK1_JAK2_complex) | v_JAK1_TYK2_complex) | v_JAK2_TYK2_complex) +v_SMAD2_SMAD4_complex, (v_SMAD2_phosphorylated & v_SMAD4) +v_SMAD2_phosphorylated, (((v_ACVR2A_ACVR2B_INHBA_complex | v_ACVR2A_ACVR2B_INHBB_complex) & v_SMAD2_SARA_complex) & !v_SMAD7) +v_SOCS3_rna, ((v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated) & v_STAT3_STAT3_complex) +v_SOS1, v_SHP2_GRB2_complex +v_STAT1, (((v_JAK1_JAK2_complex | v_JAK1_TYK2_complex) | v_JAK1) | v_JAK2) +v_STAT1_STAT1_complex, v_STAT1 +v_STAT1_STAT2_IRF9_complex, ((((v_JAK1_TYK2_complex | v_JAK2_TYK2_complex) & v_STAT2) & v_STAT1) & v_IRF9) +v_STAT3, ((v_JAK1_TYK2_complex | v_JAK2) | v_JAK1) +v_STAT3_STAT3_complex, v_STAT3 +v_STAT4, (v_JAK2_TYK2_complex | v_JAK1) +v_STAT4_STAT4_complex, v_STAT4 +v_STAT5_CRKL_complex, (v_CRKL_phosphorylated & v_STAT5_phosphorylated) +v_STAT5_phosphorylated, v_JAK1_TYK2_complex +v_SYK, !v_PTPN6 +v_Src, v_GNAI3 +v_TAB2_phosphorylated, v_IRAK1_IRAK4_complex +v_TLR1_TLR2_biglycan_complex, (v_biglycan_simple_molecule & v_TLR1_TLR2_complex) +v_TLR2_TLR6_biglycan_complex, (v_biglycan_simple_molecule & v_TLR2_TLR6_complex) +v_TLR3_dsRNA_complex, v_dsRNA_simple_molecule +v_TLR9_DNA_complex, v_DNA_simple_molecule +v_TNFAIP3_rna, (v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated) +v_TNFA_rna, (((v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_AP_1_phosphorylated) & v_MK2_phosphorylated) & v_NFAT5) +v_TNFSF11_TNFRSF11_complex, v_TNFSF11 +v_TNF_M1_macrophage___Extracellular_Space, v_TNF_M1_macrophage___Secreted_components +v_TNF_M1_macrophage___Secreted_components, v_TNFA_rna +v_TNF_TNFRSF1A_complex, v_TNF_M1_macrophage___Extracellular_Space +v_TPL2, (v_NFKB1_TPL2_complex & v_IKK_complex) +v_TRADD, v_TNF_TNFRSF1A_complex +v_TRADD_TRAF2_RIP1_complex, (v_cIAP1 | v_TRADD) +v_TRAF1_rna, (v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_NFAT5) +v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex, (((v_TRADD_TRAF2_RIP1_complex & v_TAK1) & v_TAB2_phosphorylated) & v_TAB1) +v_TRAF2_TRAF6_complex, v_TNFSF11_TNFRSF11_complex +v_TRAF3, v_TRAM1_TRIF_complex +v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex, (((((v_MEKK1 & v_ECSIT) & v_TRAF6_ubiquitinated) & v_TAK1) & v_TAB1) & v_TAB2_phosphorylated) +v_TRAF6_IRAK1_IRAK4_complex, ((v_TRAF6 & v_IRAK1_IRAK4_complex) & !v_IRAK3) +v_TRAF6_TAB1_TAB2_TAK1_complex, (((((v_TRAF6_ubiquitinated & v_TAB2_phosphorylated) & v_TAB1) & v_TAK1) & v_TAB1) & v_TRAF2_TRAF6_complex) +v_TRAF6_ubiquitinated, ((v_TRAF6 & v_UEV1A_UBC13_complex) & !v_PP4) +v_TRAM1, v_TLR4_Md2_CD14_fibrinogen_complex +v_TRAM1_TRIF_complex, (v_TRIF & v_TRAM1) +v_TRIF, v_TLR3_dsRNA_complex +v_T_cells_activation_signal_phenotype, (((((v_CD40 | v_CD86) | v_CD80) | v_CSF2_M1_macrophage___Secreted_components) | v_IFNa_M1_macrophage___Secreted_components) | v_ICAM1) +v_Vegfa_rna, ((v_NFAT5 & v_RELA_NFKB1_complex_M1_macrophage___nucleus) & v_STAT3_STAT3_complex) +v_Vegfb_rna, ((v_NFAT5 & v_RELA_NFKB1_complex_M1_macrophage___nucleus) & v_STAT4_STAT4_complex) +v_Vegfc_rna, ((((v_AP_1_phosphorylated & v_RELA_NFKB1_complex_M1_macrophage___nucleus) & v_NFAT5) & v_STAT3_STAT3_complex) & v_HIF1_complex) +v_XIAP, v_RELA_NFKB1_complex_M1_macrophage___nucleus +v_angiogenesis_signal_phenotype, ((((v_NOS2_phosphorylated | v_Hif1a) | v_CXCL12_M1_macrophage___Secreted_components) | v_EDN1) | v_OPN) +v_apoptosis_M1_macrophage_phenotype, ((((((((((((v_CASP8 | v_CASP3) | v_CASP7) | v_p53_phosphorylated) | v_Bim) | v_TNF_M1_macrophage___Secreted_components) | v_FASL_M1_macrophage___Secreted_components) | v_NLRP3_INFLAMMASOME_complex) | v_p300_SP1_complex) & !v_Mcl1_rna) & !v_p21_rna) & !v_BCL2_M1_macrophage__Mitochondria_membrane_active) & !v_BCL2L1_M1_macrophage__Mitochondria_active) +v_apoptosis_signal_phenotype, ((v_FASL_M1_macrophage___Secreted_components | v_TNF_M1_macrophage___Secreted_components) | v_LTA) +v_cFLIP, v_RELA_NFKB1_complex_M1_macrophage___nucleus +v_cFLIP_ubiquitinated, (v_cFLIP & v_ITCH_phosphorylated) +v_c_FOS_M1_macrophage___Cytoplasm, v_RELA_NFKB1_complex_M1_macrophage___nucleus +v_c_FOS_M1_macrophage___Cytoplasm_active, (v_c_FOS_M1_macrophage___Cytoplasm & v_TSG6) +v_c_FOS_M1_macrophage___nucleus, v_c_FOS_M1_macrophage___Cytoplasm_active +v_c_JUN, (v_RELA_NFKB1_complex_M1_macrophage___nucleus & v_JNK1_phosphorylated_M1_macrophage___nucleus) +v_c_JUN_phosphorylated_M1_macrophage___Cytoplasm, ((v_JNK1_phosphorylated_M1_macrophage___Cytoplasm | v_ERK1_phosphorylated_M1_macrophage___Cytoplasm) & v_c_JUN) +v_c_JUN_phosphorylated_M1_macrophage___nucleus, v_c_JUN_phosphorylated_M1_macrophage___Cytoplasm +v_c_Myc_rna, ((v_STAT5_CRKL_complex & v_RELA_NFKB1_complex_M1_macrophage___nucleus) & v_ERK1_phosphorylated_M1_macrophage___nucleus) +v_inflammation_signal_phenotype, ((((((((((((((((((((((((((((v_C5a_C5aR1_complex | v_CCL20) | v_CCL4) | v_CCL5) | v_CD40) | v_COX2_rna) | v_IL15) | v_IRF7) | v_RELA_NFKB1_complex_M1_macrophage___nucleus) | v_IRF5_ubiquitinated) | v_IL23_M1_macrophage___Secreted_components) | v_IL12_M1_macrophage___Secreted_components) | v_IFNb_M1_macrophage___Secreted_components) | v_IFNa_M1_macrophage___Secreted_components) | v_TNF_M1_macrophage___Secreted_components) | v_IL18_M1_macrophage___Secreted_components) | v_IL1B_M1_macrophage___Secreted_components) | v_AREG) | v_SEMA4A) | v_ICAM1) | v_IL6_M1_macrophage___Secreted_components) | v_CCL2_M1_macrophage___Secreted_components) | v_CCL3) | v_LTA) | v_CXCL10) | v_CXCL9) | v_CXCL11) | v_IFNg_M1_macrophage___Secreted_components) & !v_ARRB2) +v_osteoclastogenesis_M1_macrophage_phenotype, ((((v_c_FOS_M1_macrophage___Cytoplasm_active | v_c_JUN_phosphorylated_M1_macrophage___Cytoplasm) | v_IL1B_M1_macrophage___Secreted_components) | v_AP_1_phosphorylated) | v_IFNg_M1_macrophage___Secreted_components) +v_osteoclastogenesis_signal_phenotype, (v_IL1B_M1_macrophage___Secreted_components | v_IFNg_M1_macrophage___Secreted_components) +v_p15_rna, (v_FOXO_M1_macrophage___nucleus & !v_c_Myc_rna) +v_p21_rna, (((v_STAT1_STAT1_complex & v_STAT1_STAT2_IRF9_complex) & v_NICD_CSL_SKIP_MAML1_ep300_complex) & v_RELA_NFKB1_complex_M1_macrophage___nucleus) +v_p300_SP1_complex, v_SMAD2_SMAD4_complex +v_p38_MAP_KINASE_phosphorylated_M1_macrophage___Cytoplasm, (((v_MKK3_phosphorylated | v_MKK6_phosphorylated) | v_C5a_C5aR1_complex) & !v_DUSP1) +v_p38_MAP_KINASE_phosphorylated_M1_macrophage___nucleus, v_p38_MAP_KINASE_phosphorylated_M1_macrophage___Cytoplasm +v_p53_phosphorylated, !v_MDM2_phosphorylated +v_proliferation_survival_M1_macrophage_phenotype, (((((((((((((((((((v_XIAP | v_CXCL1_M1_macrophage___Secreted_components) | v_ERK1_phosphorylated_M1_macrophage___nucleus) | v_p38_MAP_KINASE_phosphorylated_M1_macrophage___nucleus) | v_MDM2_phosphorylated) | v_cFLIP) | v_BCL3_rna) | v_BCL3_rna) | v_c_FOS_M1_macrophage___Cytoplasm_active) | v_c_JUN_phosphorylated_M1_macrophage___Cytoplasm) | v_IL12_M1_macrophage___Secreted_components) | v_IL8_M1_macrophage___Secreted_components) | v_CCL2_M1_macrophage___Secreted_components) | v_CSF2_M1_macrophage___Secreted_components) | v_HBGEF) | v_p21_rna) | v_IL6_M1_macrophage___Secreted_components) | v_c_Myc_rna) | v_p38_MAP_KINASE_phosphorylated_M1_macrophage___Cytoplasm) & !v_p15_rna) +v_proliferation_survival_signal_phenotype, ((((((((v_CXCL10 | v_IL15) | v_IL6_M1_macrophage___Secreted_components) | v_IL18_M1_macrophage___Secreted_components) | v_vcan) | v_AREG) | v_CSF2_M1_macrophage___Secreted_components) | v_CCL2_M1_macrophage___Secreted_components) | v_CXCL1_M1_macrophage___Secreted_components) +v_vcan, v_STAT4_STAT4_complex diff --git a/models/[id-239]__[var-234]__[in-69]__[M1-SYNOVIAL-MACROPHAGE]/model.sbml b/models/[id-239]__[var-234]__[in-69]__[M1-SYNOVIAL-MACROPHAGE]/model.sbml new file mode 100644 index 0000000..2d20cc5 --- /dev/null +++ b/models/[id-239]__[var-234]__[in-69]__[M1-SYNOVIAL-MACROPHAGE]/model.sbml @@ -0,0 +1 @@ +v_CXCL12_M1_macrophage___Extracellular_Space1v_INHBA1v_ACVR2A_ACVR2B_complex1v_INHBB1v_ACVR2A_ACVR2B_complex1v_PI3K1v_c_FOS_M1_macrophage___nucleus1v_c_JUN_phosphorylated_M1_macrophage___nucleus1v_p38_MAP_KINASE_phosphorylated_M1_macrophage___nucleus1v_JNK1_phosphorylated_M1_macrophage___nucleus1v_ERK1_phosphorylated_M1_macrophage___nucleus1v_AP_11v_STAT3_STAT3_complex1v_ACKR3_CXCL12_complex1v_CCL21_CCR7_complex1v_CXCL13_ACKR4_complex1v_TRADD_TRAF2_RIP1_complex1v_DAXX1v_BCL2_M1_macrophage__Mitochondria_membrane_active1v_BCL2L1_M1_macrophage__Mitochondria_active1v_STAT1_STAT2_IRF9_complex1v_STAT1_STAT1_complex1v_BCL2L1_M1_macrophage__Mitochondria1v_BAD1v_Bim1v_Bcl2_rna1v_BCL2_M1_macrophage__Mitochondria_membrane1v_BAD1v_Bim1v_AP_1_phosphorylated1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_STAT3_STAT3_complex1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_STAT1_STAT2_IRF9_complex1v_STAT1_STAT1_complex1v_STAT5_CRKL_complex1v_FOXO_M1_macrophage___nucleus1v_c5a1v_CASP81v_CASP81v_FADD1v_cFLIP1v_BAX1v_AKT11v_XIAP1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_AP_1_phosphorylated1v_CCl211v_CCL2_M1_macrophage___Extracellular_Space1v_CCL2_M1_macrophage___Secreted_components1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_NFAT51v_AP_1_phosphorylated1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_AP_1_phosphorylated1v_IRF5_ubiquitinated1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_AP_1_phosphorylated1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_IRF5_ubiquitinated1v_IRF3_phosphorylated1v_STAT1_STAT1_complex1v_IRF3_phosphorylated1v_STAT3_STAT3_complex1v_IRF3_phosphorylated1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_NFAT51v_JAK1_TYK2_complex1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_AP_1_phosphorylated1v_CSF2RA_CSF2RB_complex1v_CSF2_M1_macrophage___Extracellular_Space1v_CSF2_M1_macrophage___Secreted_components1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_AP_1_phosphorylated1v_NFAT51v_IRF3_phosphorylated1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_AP_1_phosphorylated1v_IRF3_phosphorylated1v_CXCL12_M1_macrophage___Secreted_components1v_HIF1_complex1v_CXCL131v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_CXCL1_M1_macrophage___Extracellular_Space1v_CXCR11v_CXCL1_M1_macrophage___Secreted_components1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_AP_1_phosphorylated1v_IRF3_phosphorylated1v_IL8_M1_macrophage___Extracellular_Space1v_CXCR11v_CCL201v_CXCL101v_CXCL111v_CXCL91v_CCL31v_CCL51v_MMP141v_CXCL1_M1_macrophage___Secreted_components1v_IL8_M1_macrophage___Secreted_components1v_MMP31v_MMP91v_IL12_M1_macrophage___Secreted_components1v_FASL_FAS_complex1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_MEK1_phosphorylated1v_MEK2_phosphorylated1v_C5a_C5aR1_complex1v_GNB_GNG_GNAI3_complex1v_ERK1_phosphorylated_M1_macrophage___Cytoplasm1v_MYD88_TIRAP_TOLLIP_complex1v_FASL_FAS_complex1v_AP_1_phosphorylated1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_FASL_M1_macrophage___Extracellular_Space1v_FAS1v_FASL_M1_macrophage___Secreted_components1v_AP_1_phosphorylated1v_AKT11v_FOXO_M1_macrophage___Cytoplasm1v_AKT11v_FOXO_M1_macrophage___nucleus1v_Sirt11v_gal1v_GAL_GALR2_complex1v_CCL2_CCR2_complex1v_CXCR1_IL8_complex1v_CCL21_CCR7_complex1v_CXCL1_CXCR1_complex1v_GNB_GNG_GNAI3_complex1v_CCL2_CCR2_complex1v_CXCR1_IL8_complex1v_CCL21_CCR7_complex1v_CXCL1_CXCR1_complex1v_GNB_GNG_GNAI3_complex1v_NICD_CSL_SKIP_MAML1_ep300_complex1v_NICD_CSL_SKIP_MAML1_ep300_complex1v_Hif1a1v_Hif1b1v_STAT3_STAT3_complex1v_SOS11v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_IFNa_M1_macrophage___Extracellular_Space1v_IFNAR1_IFNAR2_complex1v_IFNb_M1_macrophage___Extracellular_Space1v_IFNAR1_IFNAR2_complex1v_IFNE1v_IFNAR1_IFNAR2_complex1v_IFNg_M1_macrophage___Extracellular_Space1v_IFNGR1_IFNGR2_complex1v_IFNa_M1_macrophage___Secreted_components1v_IRF71v_IRF3_phosphorylated1v_IFNb_M1_macrophage___Secreted_components1v_IRF71v_IRF3_phosphorylated1v_IFNg_M1_macrophage___Secreted_components1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_NFAT51v_STAT4_STAT4_complex1v_IKK1_phosphorylated1v_IKK2_phosphorylated1v_PRKCQ1v_TRAF31v_IKKE_TBK1_complex1v_TRAF6_TAB1_TAB2_TAK1_complex1v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex1v_AKT11v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex1v_NIK1v_TRADD_TRAF2_RIP1_complex1v_CSF2RA_CSF2RB_CSF2_complex1v_STAT3_STAT3_complex1v_FOXO_M1_macrophage___nucleus1v_IL12_M1_macrophage___Extracellular_Space1v_IL12RB_complex1v_IL12_M1_macrophage___Secreted_components1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_AP_1_phosphorylated1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_AP_1_phosphorylated1v_IL18_M1_macrophage___Extracellular_Space1v_NFAT51v_IL18_M1_macrophage___Secreted_components1v_IL18_M1_macrophage___Cytoplasm1v_NLRP3_INFLAMMASOME_complex1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_NFAT51v_AP_1_phosphorylated1v_IL1B_M1_macrophage___Secreted_components1v_IL1B_M1_macrophage___Cytoplasm1v_NLRP3_INFLAMMASOME_complex1v_IL1B_M1_macrophage___Extracellular_Space1v_IL1R_complex1v_IL23R_IL12RB1_complex1v_IL23_M1_macrophage___Extracellular_Space1v_IL23_M1_macrophage___Secreted_components1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_AP_1_phosphorylated1v_STAT3_STAT3_complex1v_IL6_M1_macrophage___Extracellular_Space1v_IL6_M1_macrophage___Secreted_components1v_NFAT51v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_IL8_M1_macrophage___Secreted_components1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_AP_1_phosphorylated1v_IRAK4_phosphorylated1v_IRAK11v_MYD881v_MYD88_TIRAP_TOLLIP_complex1v_TLR7_TLR8_ssRNA_complex1v_TLR9_DNA_complex1v_IKKE_TBK1_TRAF3_complex1v_IKK_complex1v_TRAF6_IRAK1_IRAK4_complex1v_IKKE_TBK1_TRAF3_complex1v_IKK_complex1v_OPN1v_JNK1_phosphorylated_M1_macrophage___Cytoplasm1v_col4a41v_ITGB1_ITGA1_complex1v_col4a51v_ITGB1_ITGA1_complex1v_AP_1_phosphorylated1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_IL11_IL11Ra_IL6ST_complex1v_IFNGR1_IFNGR2_IFNg_complex1v_IL23R_IL12RB1_IL23_complex1v_IFNAR1_IFNAR2_IFNb_complex1v_IFNAR1_IFNAR2_IFNa_complex1v_IFNE_IFNAR1_IFNAR2_complex1v_IL6_IL6R_IL6ST_complex1v_CCL21_CCR7_complex1v_CCL2_CCR2_complex1v_CXCR1_IL8_complex1v_IL12RB_IL12_complex1v_MKK7_phosphorylated1v_MKK4_phosphorylated1v_ASK11v_Rac11v_JNK1_phosphorylated_M1_macrophage___Cytoplasm1v_AP_1_phosphorylated1v_AKT11v_TPL21v_RAF11v_TPL21v_RAF11v_TRAF6_TAB1_TAB2_TAK1_complex1v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex1v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex1v_ASK11v_TRAF6_TAB1_TAB2_TAK1_complex1v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex1v_ASK11v_MEKK11v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex1v_TRAF6_TAB1_TAB2_TAK1_complex1v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex1v_ASK11v_TRAF6_ECSIT_MEKK1_TAB1_TAB2_TAK1_complex1v_TRAF6_TAB1_TAB2_TAK1_complex1v_TRAF2_RIP1_TRADD_TAK1_TAB1_TAB2_complex1v_ASK11v_AP_1_phosphorylated1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_AP_1_phosphorylated1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_AP_1_phosphorylated1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_IL1_IL1R_complex1v_TLR51v_IL18_IL18R1_complex1v_TLR1_TLR2_biglycan_complex1v_TLR2_TLR6_biglycan_complex1v_MMP31v_MMP141v_MMP91v_vcan1v_STAT1_STAT2_IRF9_complex1v_STAT1_STAT1_complex1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_ERK1_phosphorylated_M1_macrophage___nucleus1v_notch1_JAG1_complex1v_gamma_secretase_complex_complex1v_ERK1_phosphorylated_M1_macrophage___Cytoplasm1v_p38_MAP_KINASE_phosphorylated_M1_macrophage___Cytoplasm1v_NFKB1_TPL2_complex1v_IKK_complex1v_IKK_complex1v_IKKE_TBK1_TRAF3_complex1v_NFKBIA_RELA_NFKB1_complex1v_RELA_NFKB1_NFKBIE_complex1v_IKK1_IKK2_complex1v_NCID1v_NICD1v_TRAF6_TAB1_TAB2_TAK1_complex1v_TRADD_TRAF2_RIP1_complex1v_TRAF2_TRAF6_complex1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_NLRP31v_Casp11v_ASC1v_NFAT51v_NOS21v_AKT11v_Rac11v_TRAF6_ubiquitinated1v_C5a_C5aR1_complex1v_CSF2RA_CSF2RB_CSF2_complex1v_HRAS1v_PTK21v_PIK3AP1_phosphorylated1v_CD40LG_ITGB1_ITGA1_complex1v_JAK21v_JAK1_TYK2_complex1v_Src1v_INPP5A1v_SYK1v_ITGB1_ITGA1_col4a_complex1v_HLA_B_LILRB1_complex1v_HRAS1v_AKT11v_IKK_complex1v_IKKE_TBK1_TRAF3_complex1v_NFKBIA_RELA_NFKB1_complex1v_RELA_NFKB1_NFKBIE_complex1v_IKK1_IKK2_complex1v_CypA1v_Prkcd1v_RELA_NFKB1_complex_M1_macrophage___Cytoplasm1v_GNA12_GNA13_complex1v_PRKG11v_AKT11v_TLR1_TLR2_biglycan_complex1v_TLR2_TLR6_biglycan_complex1v_RHOA1v_ACVR2A_ACVR2B_INHBA_complex1v_ACVR2A_ACVR2B_INHBB_complex1v_SMAD2_SARA_complex1v_SMAD71v_AP_1_phosphorylated1v_JAK21v_JAK1_JAK2_complex1v_JAK1_TYK2_complex1v_JAK2_TYK2_complex1v_SMAD2_phosphorylated1v_SMAD41v_ACVR2A_ACVR2B_INHBA_complex1v_ACVR2A_ACVR2B_INHBB_complex1v_SMAD2_SARA_complex1v_SMAD71v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_AP_1_phosphorylated1v_STAT3_STAT3_complex1v_SHP2_GRB2_complex1v_JAK1_JAK2_complex1v_JAK1_TYK2_complex1v_JAK11v_JAK21v_STAT11v_JAK1_TYK2_complex1v_JAK2_TYK2_complex1v_STAT21v_STAT11v_IRF91v_JAK1_TYK2_complex1v_JAK21v_JAK11v_STAT31v_JAK2_TYK2_complex1v_JAK11v_STAT41v_CRKL_phosphorylated1v_STAT5_phosphorylated1v_JAK1_TYK2_complex1v_PTPN61v_GNAI31v_IRAK1_IRAK4_complex1v_biglycan_simple_molecule1v_TLR1_TLR2_complex1v_biglycan_simple_molecule1v_TLR2_TLR6_complex1v_dsRNA_simple_molecule1v_DNA_simple_molecule1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_AP_1_phosphorylated1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_AP_1_phosphorylated1v_MK2_phosphorylated1v_NFAT51v_TNFSF111v_TNF_M1_macrophage___Secreted_components1v_TNFA_rna1v_TNF_M1_macrophage___Extracellular_Space1v_NFKB1_TPL2_complex1v_IKK_complex1v_TNF_TNFRSF1A_complex1v_cIAP11v_TRADD1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_NFAT51v_TRADD_TRAF2_RIP1_complex1v_TAK11v_TAB2_phosphorylated1v_TAB11v_TNFSF11_TNFRSF11_complex1v_TRAM1_TRIF_complex1v_MEKK11v_ECSIT1v_TRAF6_ubiquitinated1v_TAK11v_TAB11v_TAB2_phosphorylated1v_TRAF61v_IRAK1_IRAK4_complex1v_IRAK31v_TRAF6_ubiquitinated1v_TAB2_phosphorylated1v_TAB11v_TAK11v_TAB11v_TRAF2_TRAF6_complex1v_TRAF61v_UEV1A_UBC13_complex1v_PP41v_TLR4_Md2_CD14_fibrinogen_complex1v_TRIF1v_TRAM11v_TLR3_dsRNA_complex1v_CD401v_CD861v_CD801v_CSF2_M1_macrophage___Secreted_components1v_IFNa_M1_macrophage___Secreted_components1v_ICAM11v_NFAT51v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_STAT3_STAT3_complex1v_NFAT51v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_STAT4_STAT4_complex1v_AP_1_phosphorylated1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_NFAT51v_STAT3_STAT3_complex1v_HIF1_complex1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_NOS2_phosphorylated1v_Hif1a1v_CXCL12_M1_macrophage___Secreted_components1v_EDN11v_OPN1v_CASP81v_CASP31v_CASP71v_p53_phosphorylated1v_Bim1v_TNF_M1_macrophage___Secreted_components1v_FASL_M1_macrophage___Secreted_components1v_NLRP3_INFLAMMASOME_complex1v_p300_SP1_complex1v_Mcl1_rna1v_p21_rna1v_BCL2_M1_macrophage__Mitochondria_membrane_active1v_BCL2L1_M1_macrophage__Mitochondria_active1v_FASL_M1_macrophage___Secreted_components1v_TNF_M1_macrophage___Secreted_components1v_LTA1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_cFLIP1v_ITCH_phosphorylated1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_c_FOS_M1_macrophage___Cytoplasm1v_TSG61v_c_FOS_M1_macrophage___Cytoplasm_active1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_JNK1_phosphorylated_M1_macrophage___nucleus1v_JNK1_phosphorylated_M1_macrophage___Cytoplasm1v_ERK1_phosphorylated_M1_macrophage___Cytoplasm1v_c_JUN1v_c_JUN_phosphorylated_M1_macrophage___Cytoplasm1v_STAT5_CRKL_complex1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_ERK1_phosphorylated_M1_macrophage___nucleus1v_C5a_C5aR1_complex1v_CCL201v_CCL41v_CCL51v_CD401v_COX2_rna1v_IL151v_IRF71v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_IRF5_ubiquitinated1v_IL23_M1_macrophage___Secreted_components1v_IL12_M1_macrophage___Secreted_components1v_IFNb_M1_macrophage___Secreted_components1v_IFNa_M1_macrophage___Secreted_components1v_TNF_M1_macrophage___Secreted_components1v_IL18_M1_macrophage___Secreted_components1v_IL1B_M1_macrophage___Secreted_components1v_AREG1v_SEMA4A1v_ICAM11v_IL6_M1_macrophage___Secreted_components1v_CCL2_M1_macrophage___Secreted_components1v_CCL31v_LTA1v_CXCL101v_CXCL91v_CXCL111v_IFNg_M1_macrophage___Secreted_components1v_ARRB21v_c_FOS_M1_macrophage___Cytoplasm_active1v_c_JUN_phosphorylated_M1_macrophage___Cytoplasm1v_IL1B_M1_macrophage___Secreted_components1v_AP_1_phosphorylated1v_IFNg_M1_macrophage___Secreted_components1v_IL1B_M1_macrophage___Secreted_components1v_IFNg_M1_macrophage___Secreted_components1v_FOXO_M1_macrophage___nucleus1v_c_Myc_rna1v_STAT1_STAT1_complex1v_STAT1_STAT2_IRF9_complex1v_NICD_CSL_SKIP_MAML1_ep300_complex1v_RELA_NFKB1_complex_M1_macrophage___nucleus1v_SMAD2_SMAD4_complex1v_MKK3_phosphorylated1v_MKK6_phosphorylated1v_C5a_C5aR1_complex1v_DUSP11v_p38_MAP_KINASE_phosphorylated_M1_macrophage___Cytoplasm1v_MDM2_phosphorylated1v_XIAP1v_CXCL1_M1_macrophage___Secreted_components1v_ERK1_phosphorylated_M1_macrophage___nucleus1v_p38_MAP_KINASE_phosphorylated_M1_macrophage___nucleus1v_MDM2_phosphorylated1v_cFLIP1v_BCL3_rna1v_BCL3_rna1v_c_FOS_M1_macrophage___Cytoplasm_active1v_c_JUN_phosphorylated_M1_macrophage___Cytoplasm1v_IL12_M1_macrophage___Secreted_components1v_IL8_M1_macrophage___Secreted_components1v_CCL2_M1_macrophage___Secreted_components1v_CSF2_M1_macrophage___Secreted_components1v_HBGEF1v_p21_rna1v_IL6_M1_macrophage___Secreted_components1v_c_Myc_rna1v_p38_MAP_KINASE_phosphorylated_M1_macrophage___Cytoplasm1v_p15_rna1v_CXCL101v_IL151v_IL6_M1_macrophage___Secreted_components1v_IL18_M1_macrophage___Secreted_components1v_vcan1v_AREG1v_CSF2_M1_macrophage___Secreted_components1v_CCL2_M1_macrophage___Secreted_components1v_CXCL1_M1_macrophage___Secreted_components1v_STAT4_STAT4_complex1 \ No newline at end of file diff --git a/models/[id-240]__[var-197]__[in-52]__[M2-SYNOVIAL-MACROPHAGE]/README.md b/models/[id-240]__[var-197]__[in-52]__[M2-SYNOVIAL-MACROPHAGE]/README.md new file mode 100644 index 0000000..1c702f6 --- /dev/null +++ b/models/[id-240]__[var-197]__[in-52]__[M2-SYNOVIAL-MACROPHAGE]/README.md @@ -0,0 +1,29 @@ +# \[240\] M2-SYNOVIAL-MACROPHAGE + + - Variables: 197 + - Inputs: 52 + - Regulations: 430 + - Publication: https://doi.org/10.1038/s41540-024-00337-5 + - Source: https://www.ebi.ac.uk/biomodels/MODEL2307180002 + - Keywords: biomodels, curated, casq, repaired + + +### Modifications + +Removed unused variables: `CD40LG`, `EPHB1`, `HLA_DP_DQ_DR`, `LILRB1`, `MK2_phosphorylated` + +### Model citation + +``` +@article{bbm-240, + title={Large-scale computational modelling of the M1 and M2 synovial macrophages in rheumatoid arthritis}, + author={Zerrouk, Naouel and Alcraft, Rachel and Hall, Benjamin A and Aug{\'e}, Franck and Niarakis, Anna}, + journal={npj Systems Biology and Applications}, + volume={10}, + number={1}, + pages={10}, + year={2024}, + publisher={Nature Publishing Group UK London} +} +``` + diff --git a/models/[id-240]__[var-197]__[in-52]__[M2-SYNOVIAL-MACROPHAGE]/metadata.json b/models/[id-240]__[var-197]__[in-52]__[M2-SYNOVIAL-MACROPHAGE]/metadata.json new file mode 100644 index 0000000..8c7ce5f --- /dev/null +++ b/models/[id-240]__[var-197]__[in-52]__[M2-SYNOVIAL-MACROPHAGE]/metadata.json @@ -0,0 +1,17 @@ +{ + "id": 240, + "name": "M2-SYNOVIAL-MACROPHAGE", + "url-publication": "https://doi.org/10.1038/s41540-024-00337-5", + "url-model": "https://www.ebi.ac.uk/biomodels/MODEL2307180002", + "keywords": [ + "biomodels", + "curated", + "casq", + "repaired" + ], + "variables": 197, + "inputs": 52, + "regulations": 430, + "notes": "### Modifications\n\nRemoved unused variables: `CD40LG`, `EPHB1`, `HLA_DP_DQ_DR`, `LILRB1`, `MK2_phosphorylated`", + "bib": "@article{bbm-240,\n title={Large-scale computational modelling of the M1 and M2 synovial macrophages in rheumatoid arthritis},\n author={Zerrouk, Naouel and Alcraft, Rachel and Hall, Benjamin A and Aug{\\'e}, Franck and Niarakis, Anna},\n journal={npj Systems Biology and Applications},\n volume={10},\n number={1},\n pages={10},\n year={2024},\n publisher={Nature Publishing Group UK London}\n}" +} \ No newline at end of file diff --git a/models/[id-240]__[var-197]__[in-52]__[M2-SYNOVIAL-MACROPHAGE]/model.aeon b/models/[id-240]__[var-197]__[in-52]__[M2-SYNOVIAL-MACROPHAGE]/model.aeon new file mode 100644 index 0000000..1e6f0d4 --- /dev/null +++ b/models/[id-240]__[var-197]__[in-52]__[M2-SYNOVIAL-MACROPHAGE]/model.aeon @@ -0,0 +1,627 @@ +v_VEGFa_M2_macrophage__extracellular_space -> v_VegfR1_Vegfa_complex +v_VegfR1 -> v_VegfR1_Vegfa_complex +v_NFKBIA_RELA_NFKB1_complex -> v_RELA_NFKB1_complex_M2_macrophage__cytoplasm +v_IKK_complex -> v_RELA_NFKB1_complex_M2_macrophage__cytoplasm +v_Syk_phosphorylated -> v_RELA_NFKB1_complex_M2_macrophage__cytoplasm +v_RELA_NFKB1_NFKBIE_complex -> v_RELA_NFKB1_complex_M2_macrophage__cytoplasm +v_IKK1_IKK2_complex -> v_RELA_NFKB1_complex_M2_macrophage__cytoplasm +v_AKT1_phosphorylated -> v_IKK_complex +v_TAK1_phosphorylated -> v_IKK_complex +v_TRAF6_ubiquitinated -> v_IKK_complex +v_TCF_LEF -> v_CTNNB1_TCF_LEF_complex +v_CTNNB1 -> v_CTNNB1_TCF_LEF_complex +v_CSF1R -> v_CSF1R_CSF1_complex +v_CSF1_M2_macrophage__extracellular_space -> v_CSF1R_CSF1_complex +v_IL4 -> v_IL4_IL4Ra_complex +v_IL4R -> v_IL4_IL4Ra_complex +v_IL8_M2_macrophage__extracellular_space -> v_CXCR1_IL8_complex +v_PRL -> v_PRL_PRLR_complex +v_c5a -> v_C5a_C5aR1_complex +v_AKT1_phosphorylated -| v_RXRa_NUR77_complex +v_SMAD2_SMAD4_complex -> v_p300_SP1_complex +v_smad1_phosphorylated -> v_smad4_smad1_complex +v_SMAD4 -> v_smad4_smad1_complex +v_SMAD2_phosphorylated -> v_SMAD2_SMAD4_complex +v_SMAD4 -> v_SMAD2_SMAD4_complex +v_STAT3 -> v_STAT3_STAT3_complex +v_SMAD2_SMAD4_complex -> v_RBL1_E2F4_DP1_complex +v_IL34 -> v_CSFR1R_IL34_complex +v_CSF1R -> v_CSFR1R_IL34_complex +v_Vegfb_M2_macrophage__extracellular_space -> v_VegfR1_vegfb_complex +v_VegfR1 -> v_VegfR1_vegfb_complex +v_IKK1_phosphorylated -> v_IKK1_IKK2_complex +v_IKK2_phosphorylated -> v_IKK1_IKK2_complex +v_Vegfc_M2_macrophage__extracellular_space -> v_VegfR2_vegfc_nrp2_complex +v_Vegfc_M2_macrophage__extracellular_space -> v_vegfc_vegfr3_complex +v_RELA_NFKB1_complex_M2_macrophage__cytoplasm -> v_RELA_NFKB1_complex_M2_macrophage_nucleus +v_Prkcd -> v_RELA_NFKB1_complex_M2_macrophage_nucleus +v_Sirt1 -| v_RELA_NFKB1_complex_M2_macrophage_nucleus +v_NLRP3 -> v_NLRP3_INFLAMMASOME_complex +v_Casp1 -> v_NLRP3_INFLAMMASOME_complex +v_ASC -> v_NLRP3_INFLAMMASOME_complex +v_CCl21 -> v_CCL21_CCR7_complex +v_immune_complex_complex -> v_immune_complex_CD16a_complex +v_C5a_C5aR1_complex -> v_immune_complex_CD16a_complex +v_GNB_GNG_GNAI3_complex -> v_GNB_GNG_complex +v_CXCR1_IL8_complex -> v_GNB_GNG_complex +v_CCL21_CCR7_complex -> v_GNB_GNG_complex +v_CXCL13 -> v_CXCL13_ACKR4_complex +v_GSK3b_APC_AXIN1_CTNNB1_CK1A_complex -> v_GSK3b_APC_AXIN1_CK1A_complex +v_Dvl1 -> v_GSK3b_APC_AXIN1_CK1A_complex +v_GAS6 -> v_GAS6_MERTK_complex +v_immune_complex_complex -> v_immune_complex_CD32b_complex +v_FASL_M2_macrophage__extracellular_space -> v_FASL_FAS_complex +v_FAS -> v_FASL_FAS_complex +v_IL23R_IL12RB1_complex -> v_IL23R_IL12RB1_IL23_complex +v_IL23_M2_macrophage__extracellular_space -> v_IL23R_IL12RB1_IL23_complex +v_immune_complex_complex -> v_immune_complex_CD64_complex +v_C5a_C5aR1_complex -> v_immune_complex_CD64_complex +v_IL10R1_IL10R2_complex -> v_IL10R1_IL10R2_IL10_complex +v_IL10_M2_macrophage__extracellular_space -> v_IL10R1_IL10R2_IL10_complex +v_STAT6 -> v_STAT6_STAT6_complex +v_TGFB1_M2_macrophage__extracellular_space -> v_TGFBR1_TGFBR2_TGFB1_complex +v_TGFBR1_TGFBR2_complex -> v_TGFBR1_TGFBR2_TGFB1_complex +v_gal -> v_GAL_GALR2_complex +v_GAL_GALR2_complex -> v_GNA12_GNA13_complex +v_immune_complex_complex -> v_immune_complex_CD32a_complex +v_CD32a -> v_immune_complex_CD32a_complex +v_C5a_C5aR1_complex -> v_immune_complex_CD32a_complex +v_SEMA4D -> v_SEMA4_PLXNB2_MET_complex +v_PLXNB2_MET_complex -> v_SEMA4_PLXNB2_MET_complex +v_SEMA4A_M2_macrophage__extracellular_space -> v_SEMA4_PLXNB2_MET_complex +v_col4a4 -> v_ITGB1_ITGA1_col4a_complex +v_ITGB1_ITGA1_complex -> v_ITGB1_ITGA1_col4a_complex +v_col4a5 -> v_ITGB1_ITGA1_col4a_complex +v_IL23R_IL12RB1_IL23_complex -> v_JAK1_TYK2_complex +v_IL10R1_IL10R2_IL10_complex -> v_JAK1_TYK2_complex +v_IL4_IL4Ra_complex -> v_JAK1_TYK2_complex +v_p38_MAP_KINASE_phosphorylated_M2_macrophage__cytoplasm -> v_p38_MAP_KINASE_phosphorylated_M2_macrophage_nucleus +v_ASK1 -> v_MKK3_phosphorylated +v_GSK3B -| v_CREB1_phosphorylated +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_IL15 +v_CREB1_phosphorylated -> v_IL15 +v_C_EBPb_phosphorylated -> v_IL15 +v_NFKBIA_RELA_NFKB1_complex -> v_NFKBIA_phosphorylated +v_IKK_complex -> v_NFKBIA_phosphorylated +v_Syk_phosphorylated -> v_NFKBIA_phosphorylated +v_MKK3_phosphorylated -> v_p38_MAP_KINASE_phosphorylated_M2_macrophage__cytoplasm +v_MKK6_phosphorylated -> v_p38_MAP_KINASE_phosphorylated_M2_macrophage__cytoplasm +v_C5a_C5aR1_complex -> v_p38_MAP_KINASE_phosphorylated_M2_macrophage__cytoplasm +v_DUSP1 -| v_p38_MAP_KINASE_phosphorylated_M2_macrophage__cytoplasm +v_NFKB1_TPL2_complex -> v_TPL2 +v_IKK_complex -> v_TPL2 +v_NFKB1_TPL2_complex -> v_NFKB1 +v_IKK_complex -> v_NFKB1 +v_TPL2 -> v_MEK1_phosphorylated +v_RAF1 -> v_MEK1_phosphorylated +v_TPL2 -> v_MEK2_phosphorylated +v_RAF1 -> v_MEK2_phosphorylated +v_MEK1_phosphorylated -> v_ERK1_phosphorylated_M2_macrophage__cytoplasm +v_MEK2_phosphorylated -> v_ERK1_phosphorylated_M2_macrophage__cytoplasm +v_C5a_C5aR1_complex -> v_ERK1_phosphorylated_M2_macrophage__cytoplasm +v_ASK1 -> v_MKK6_phosphorylated +v_ASK1 -> v_MKK4_phosphorylated +v_MEKK1 -> v_MKK4_phosphorylated +v_ASK1 -> v_MKK7_phosphorylated +v_MKK7_phosphorylated -> v_JNK1_phosphorylated_M2_macrophage__cytoplasm +v_MKK4_phosphorylated -> v_JNK1_phosphorylated_M2_macrophage__cytoplasm +v_ASK1 -> v_JNK1_phosphorylated_M2_macrophage__cytoplasm +v_Rac1 -> v_JNK1_phosphorylated_M2_macrophage__cytoplasm +v_JNK1_phosphorylated_M2_macrophage__cytoplasm -> v_JNK1_phosphorylated_M2_macrophage_nucleus +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_CSF2_rna +v_CREB1_phosphorylated -> v_CSF2_rna +v_C_EBPb_phosphorylated -> v_CSF2_rna +v_NFAT5_phosphorylated -> v_CSF2_rna +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_Bcl2_rna +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_XIAP +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_COX2_rna +v_NFAT5_phosphorylated -> v_COX2_rna +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_TNFAIP3_rna +v_CREB1_phosphorylated -> v_TNFAIP3_rna +v_C_EBPb_phosphorylated -> v_TNFAIP3_rna +v_Syk_phosphorylated -> v_PI3K +v_C5a_C5aR1_complex -> v_PI3K +v_SHIP1 -| v_PI3K +v_GAB2_phosphorylated -> v_PI3K +v_HRAS -> v_PI3K +v_CSF1R_CSF1_complex -> v_PI3K +v_VegfR1_vegfb_complex -> v_PI3K +v_VegfR1_Vegfa_complex -> v_PI3K +v_VegfR2_vegfc_nrp2_complex -> v_PI3K +v_TGFBR1_TGFBR2_TGFB1_complex -> v_PI3K +v_Src -> v_PI3K +v_GNB_GNG_complex -> v_PI3K +v_GAS6_MERTK_complex -> v_PI3K +v_PIK3AP1_phosphorylated -> v_PI3K +v_CD40LG_ITGB1_ITGA1_complex -> v_PI3K +v_PTK2 -> v_PI3K +v_JAK1_TYK2_complex -> v_PI3K +v_TRAF6_ubiquitinated -> v_PI3K +v_PTPN6 -| v_PI3K +v_PI3K -> v_AKT1_phosphorylated +v_AKT1_phosphorylated -| v_CASP9 +v_XIAP -| v_CASP9 +v_BAX -> v_CASP9 +v_AKT1_phosphorylated -> v_AKT1 +v_AKT1_phosphorylated -> v_RAF1 +v_PRKCD -> v_RAF1 +v_HRAS -> v_RAF1 +v_IKK_complex -> v_IRF7 +v_OPN -> v_IRF7 +v_ERK1_phosphorylated_M2_macrophage__cytoplasm -> v_ERK1_phosphorylated_M2_macrophage_nucleus +v_p38_MAP_KINASE_phosphorylated_M2_macrophage_nucleus -> v_MSK1_phosphorylated +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_cFLIP +v_JNK1_phosphorylated_M2_macrophage__cytoplasm -> v_ITCH_phosphorylated +v_p38_MAP_KINASE_phosphorylated_M2_macrophage_nucleus -> v_C_EBPb_phosphorylated +v_CREB1_phosphorylated -> v_C_EBPb_phosphorylated +v_ERK1_phosphorylated_M2_macrophage__cytoplasm -> v_C_EBPb_phosphorylated +v_DAXX -> v_ASK1 +v_CSF1R_CSF1_complex -> v_Prkcd +v_CSFR1R_IL34_complex -> v_Prkcd +v_ERK1_phosphorylated_M2_macrophage__cytoplasm -> v_NFAT5_phosphorylated +v_p38_MAP_KINASE_phosphorylated_M2_macrophage__cytoplasm -> v_NFAT5_phosphorylated +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_JAG1 +v_CREB1_phosphorylated -> v_JAG1 +v_C_EBPb_phosphorylated -> v_JAG1 +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_BCL3_rna +v_C_EBPb_phosphorylated -> v_BCL3_rna +v_STAT3_STAT3_complex -> v_BCL3_rna +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_MMP9 +v_CREB1_phosphorylated -> v_MMP9 +v_C_EBPb_phosphorylated -> v_MMP9 +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_MMP14 +v_CREB1_phosphorylated -> v_MMP14 +v_C_EBPb_phosphorylated -> v_MMP14 +v_Vegfc_M2_macrophage__secreted_components -> v_Vegfc_M2_macrophage__extracellular_space +v_STAT3_STAT3_complex -> v_CD32a +v_HCK -> v_Syk_phosphorylated +v_immune_complex_CD16a_complex -> v_Syk_phosphorylated +v_immune_complex_CD32a_complex -> v_Syk_phosphorylated +v_immune_complex_CD64_complex -> v_Syk_phosphorylated +v_HCK -> v_GAB2_phosphorylated +v_Syk_phosphorylated -> v_PLCG2 +v_PI3K -> v_PLCG2 +v_VegfR1_Vegfa_complex -> v_PLCG2 +v_VegfR1_vegfb_complex -> v_PLCG2 +v_GNB_GNG_complex -> v_PLCG2 +v_PIP2_simple_molecule -> v_DAG_simple_molecule +v_PLCG2 -> v_DAG_simple_molecule +v_PIP2_simple_molecule -> v_IP3_simple_molecule +v_PLCG2 -> v_IP3_simple_molecule +v_DAG_simple_molecule -> v_PRKCD +v_immune_complex_CD32b_complex -> v_SHIP1 +v_Bcl2_rna -> v_BCL2_M2_macrophage_mitochondrion_membrane +v_BCL2_M2_macrophage_mitochondrion_membrane -> v_BCL2_M2_macrophage_mitochondrion_membrane_active +v_BAD -| v_BCL2_M2_macrophage_mitochondrion_membrane_active +v_Bim -| v_BCL2_M2_macrophage_mitochondrion_membrane_active +v_RXRa_NUR77_complex -| v_BCL2_M2_macrophage_mitochondrion_membrane_active +v_CASP8 -> v_CASP3 +v_CASP9 -> v_CASP3 +v_CASP8 -> v_CASP7 +v_CASP9 -> v_CASP7 +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_TRAF1_rna +v_NFAT5_phosphorylated -> v_TRAF1_rna +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_MMP3 +v_CREB1_phosphorylated -> v_MMP3 +v_C_EBPb_phosphorylated -> v_MMP3 +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_CCL20 +v_C_EBPb_phosphorylated -> v_CCL20 +v_CREB1_phosphorylated -> v_CCL20 +v_CSF1_M2_macrophage__secreted_components -> v_CSF1_M2_macrophage__extracellular_space +v_BCL2_M2_macrophage_mitochondrion_membrane_active -| v_BAX +v_BCL2L1 -| v_BAX +v_mcl1 -| v_BAX +v_CASP8 -> v_apoptosis_M2_macrophage_phenotype +v_CASP3 -> v_apoptosis_M2_macrophage_phenotype +v_CASP7 -> v_apoptosis_M2_macrophage_phenotype +v_p53_phosphorylated_M2_macrophage__cytoplasm -> v_apoptosis_M2_macrophage_phenotype +v_Bim -> v_apoptosis_M2_macrophage_phenotype +v_FASL_M2_macrophage__secreted_components -> v_apoptosis_M2_macrophage_phenotype +v_NLRP3_INFLAMMASOME_complex -> v_apoptosis_M2_macrophage_phenotype +v_RXRa_NUR77_complex -> v_apoptosis_M2_macrophage_phenotype +v_BCL2_M2_macrophage_mitochondrion_membrane_active -| v_apoptosis_M2_macrophage_phenotype +v_mcl1 -| v_apoptosis_M2_macrophage_phenotype +v_BCL2L1 -| v_apoptosis_M2_macrophage_phenotype +v_OPN -> v_angiogenesis_signal_phenotype +v_Vegfc_M2_macrophage__secreted_components -> v_angiogenesis_signal_phenotype +v_VEGFa_M2_macrophage__secreted_components -> v_angiogenesis_signal_phenotype +v_Vegfb_M2_macrophage__secreted_components -> v_angiogenesis_signal_phenotype +v_C5a_C5aR1_complex -> v_inflammation_signal_phenotype +v_CCL20 -> v_inflammation_signal_phenotype +v_COX2_rna -> v_inflammation_signal_phenotype +v_IL15 -> v_inflammation_signal_phenotype +v_IRF7 -> v_inflammation_signal_phenotype +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_inflammation_signal_phenotype +v_PPARg_rna -| v_inflammation_signal_phenotype +v_TGFB1_M2_macrophage__secreted_components -| v_inflammation_signal_phenotype +v_IL23_M2_macrophage__secreted_components -> v_inflammation_signal_phenotype +v_IL10_M2_macrophage__secreted_components -| v_inflammation_signal_phenotype +v_CCL18 -> v_inflammation_signal_phenotype +v_ARRB2 -| v_inflammation_signal_phenotype +v_SEMA4A_M2_macrophage__secreted_components -> v_inflammation_signal_phenotype +v_sema7a -> v_inflammation_signal_phenotype +v_MMP3 -> v_Matrix_degradation_signal_phenotype +v_MMP14 -> v_Matrix_degradation_signal_phenotype +v_MMP9 -> v_Matrix_degradation_signal_phenotype +v_col4a3 -| v_Matrix_degradation_signal_phenotype +v_PDGFC -> v_Matrix_degradation_signal_phenotype +v_CSF1_M2_macrophage__secreted_components -> v_T_cells_activation_signal_phenotype +v_CCL18 -> v_T_cells_activation_signal_phenotype +v_CD86 -> v_T_cells_activation_signal_phenotype +v_XIAP -> v_proliferation_survival_M2_macrophage_phenotype +v_ERK1_phosphorylated_M2_macrophage_nucleus -> v_proliferation_survival_M2_macrophage_phenotype +v_p38_MAP_KINASE_phosphorylated_M2_macrophage_nucleus -> v_proliferation_survival_M2_macrophage_phenotype +v_BCL2L1 -> v_proliferation_survival_M2_macrophage_phenotype +v_MDM2_phosphorylated -> v_proliferation_survival_M2_macrophage_phenotype +v_CREB1_phosphorylated -> v_proliferation_survival_M2_macrophage_phenotype +v_TGFB1_M2_macrophage__secreted_components -> v_proliferation_survival_M2_macrophage_phenotype +v_p15_rna -| v_proliferation_survival_M2_macrophage_phenotype +v_cFLIP -> v_proliferation_survival_M2_macrophage_phenotype +v_BCL3_rna -> v_proliferation_survival_M2_macrophage_phenotype +v_Vegfc_M2_macrophage__secreted_components -> v_proliferation_survival_M2_macrophage_phenotype +v_CSF1_M2_macrophage__secreted_components -> v_proliferation_survival_M2_macrophage_phenotype +v_IL8_M2_macrophage__secreted_components -> v_proliferation_survival_M2_macrophage_phenotype +v_VEGFa_M2_macrophage__secreted_components -> v_proliferation_survival_M2_macrophage_phenotype +v_Vegfb_M2_macrophage__secreted_components -> v_proliferation_survival_M2_macrophage_phenotype +v_HBGEF -> v_proliferation_survival_M2_macrophage_phenotype +v_cMyc_phosphorylated -> v_proliferation_survival_M2_macrophage_phenotype +v_AKT1_phosphorylated -> v_MDM2_phosphorylated +v_p53 -> v_p53_phosphorylated_M2_macrophage__cytoplasm +v_MDM2_phosphorylated -| v_p53_phosphorylated_M2_macrophage__cytoplasm +v_BAD -| v_BCL2L1 +v_Bim -| v_BCL2L1 +v_CREB1_phosphorylated -> v_Mcl1_rna +v_AKT1_phosphorylated -| v_FOXO1 +v_mcl1 -| v_FOXO1 +v_FOXO1 -> v_Bim +v_STAT3_STAT3_complex -> v_c_Myc_rna +v_RBL1_E2F4_DP1_complex -| v_c_Myc_rna +v_TGFB1_M2_macrophage__secreted_components -> v_TGFB1_M2_macrophage__extracellular_space +v_TGFBR1_TGFBR2_TGFB1_complex -> v_DAXX +v_FASL_FAS_complex -> v_DAXX +v_SMAD2_SARA_complex -> v_SMAD2_phosphorylated +v_TGFBR1_TGFBR2_TGFB1_complex -> v_SMAD2_phosphorylated +v_SMAD7 -| v_SMAD2_phosphorylated +v_SMAD2_SARA_complex -> v_SARA +v_TGFBR1_TGFBR2_TGFB1_complex -> v_SARA +v_SMAD7 -| v_SARA +v_FOXO1 -> v_p15_rna +v_IL10_M2_macrophage__secreted_components -> v_IL10_M2_macrophage__extracellular_space +v_JAK1 -> v_STAT3 +v_JAK1_TYK2_complex -> v_STAT3 +v_JAK2 -> v_STAT3 +v_IL23_M2_macrophage__secreted_components -> v_IL23_M2_macrophage__extracellular_space +v_STAT3_STAT3_complex -> v_klf4 +v_C_EBPb_phosphorylated -> v_PPARg_rna +v_FADD -> v_CASP8 +v_cMyc_phosphorylated -> v_p53 +v_cFLIP -> v_cFLIP_ubiquitinated +v_ITCH_phosphorylated -> v_cFLIP_ubiquitinated +v_klf4 -> v_IL6_rna +v_CREB1_phosphorylated -> v_IL6_rna +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_IL6_rna +v_NFAT5_phosphorylated -> v_IL6_rna +v_IRF7 -> v_IFNa_rna +v_IRF7 -> v_IFNb_rna +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_IL12_rna +v_TGFBR1_TGFBR2_TGFB1_complex -> v_Shc_phosphorylated +v_VegfR2_vegfc_nrp2_complex -> v_Shc_phosphorylated +v_Src -> v_Shc_phosphorylated +v_JAK2 -> v_Shc_phosphorylated +v_JAK1_TYK2_complex -> v_Shc_phosphorylated +v_Shc_phosphorylated -> v_Grb2 +v_CSF1R_CSF1_complex -> v_Grb2 +v_CSFR1R_IL34_complex -> v_Grb2 +v_vegfc_vegfr3_complex -> v_Grb2 +v_Grb2 -> v_SOS1 +v_SOS1 -> v_HRAS +v_EFNB1_EPHB1_complex -> v_HRAS +v_GAS6_MERTK_complex -> v_HRAS +v_STAT3_STAT3_complex -> v_IL4 +v_STAT6_STAT6_complex -> v_IL4 +v_STAT3_STAT3_complex -> v_CD32b_rna +v_c_Myc_rna -> v_cMyc +v_cMyc -> v_cMyc_phosphorylated +v_ERK1_phosphorylated_M2_macrophage__cytoplasm -> v_cMyc_phosphorylated +v_VEGFa_M2_macrophage__secreted_components -> v_VEGFa_M2_macrophage__extracellular_space +v_Vegfb_M2_macrophage__secreted_components -> v_Vegfb_M2_macrophage__extracellular_space +v_NFAT5_phosphorylated -> v_Vegfa_rna +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_Vegfa_rna +v_C_EBPb_phosphorylated -> v_Vegfa_rna +v_STAT3_STAT3_complex -> v_Vegfa_rna +v_STAT6_STAT6_complex -> v_IL4R +v_JAK1 -> v_STAT6 +v_JAK1_TYK2_complex -> v_STAT6 +v_TGFBR1_TGFBR2_TGFB1_complex -> v_TAK1_phosphorylated +v_FZD5_LRP5_wnt5a_complex -> v_Dvl1 +v_WNT5B_FZD1_LRP5_complex -> v_Dvl1 +v_Dvl1 -> v_Rac1 +v_NRP1_PLXNA1_sema3A_complex -| v_Rac1 +v_RHOA -| v_Rac1 +v_SEMA4_PLXNB2_MET_complex -| v_Rac1 +v_GSK3b_APC_AXIN1_CTNNB1_CK1A_complex -> v_CTNNB1 +v_Dvl1 -> v_CTNNB1 +v_NLK_phosphorylated -| v_TCF_LEF +v_TAK1_phosphorylated -> v_NLK_phosphorylated +v_CTNNB1_TCF_LEF_complex -> v_FN1 +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_NLRP3 +v_NFAT5_phosphorylated -> v_IL18_M2_macrophage__cytoplasm +v_IL18_M2_macrophage__cytoplasm -> v_IL18_M2_macrophage__cytoplasm_active +v_NLRP3_INFLAMMASOME_complex -> v_IL18_M2_macrophage__cytoplasm_active +v_NLRP3_INFLAMMASOME_complex -> v_IL1B +v_p53_phosphorylated_M2_macrophage_nucleus -> v_FAS +v_FASL_FAS_complex -> v_FADD +v_IL8_M2_macrophage__secreted_components -> v_IL8_M2_macrophage__extracellular_space +v_GNB_GNG_GNAI3_complex -> v_GNAI3 +v_CXCR1_IL8_complex -> v_GNAI3 +v_CCL21_CCR7_complex -> v_GNAI3 +v_GNAI3 -> v_Src +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_Vegfc_M2_macrophage__secreted_components +v_C_EBPb_phosphorylated -> v_Vegfc_M2_macrophage__secreted_components +v_NFAT5_phosphorylated -> v_Vegfc_M2_macrophage__secreted_components +v_STAT3_STAT3_complex -> v_Vegfc_M2_macrophage__secreted_components +v_CREB1_phosphorylated -> v_Vegfc_M2_macrophage__secreted_components +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_IL23_M2_macrophage__secreted_components +v_STAT3_STAT3_complex -> v_IL10_M2_macrophage__secreted_components +v_klf4 -> v_IL10_M2_macrophage__secreted_components +v_C_EBPb_phosphorylated -> v_IL10_M2_macrophage__secreted_components +v_FOXO1 -> v_IL10_M2_macrophage__secreted_components +v_FOXO1 -> v_FASL_M2_macrophage__secreted_components +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_CSF1_M2_macrophage__secreted_components +v_C_EBPb_phosphorylated -> v_CSF1_M2_macrophage__secreted_components +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_IL8_M2_macrophage__secreted_components +v_Vegfa_rna -> v_VEGFa_M2_macrophage__secreted_components +v_NFAT5_phosphorylated -> v_Vegfb_M2_macrophage__secreted_components +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_Vegfb_M2_macrophage__secreted_components +v_CREB1_phosphorylated -> v_Vegfb_M2_macrophage__secreted_components +v_C_EBPb_phosphorylated -> v_Vegfb_M2_macrophage__secreted_components +v_STAT3_STAT3_complex -> v_Vegfb_M2_macrophage__secreted_components +v_CXCL13_ACKR4_complex -> v_ARRB2 +v_C_EBPb_phosphorylated -> v_CD84 +v_RELA_NFKB1_NFKBIE_complex -> v_NFKBIE +v_IKK1_IKK2_complex -> v_NFKBIE +v_PRKCQ -> v_IKK2_phosphorylated +v_SH2D1A -> v_PRKCQ +v_ARI_ARII_bmp6_complex -> v_smad1_phosphorylated +v_C_EBPb_phosphorylated -> v_sema7a +v_CREB1_phosphorylated -> v_EDA +v_C_EBPb_phosphorylated -> v_PDGFC +v_C_EBPb_phosphorylated -> v_SEMA4A_M2_macrophage__secreted_components +v_GNA12_GNA13_complex -> v_RHOA +v_ARHGEF12 -> v_RHOA +v_HLA_B_LILRB1_complex -> v_PTPN6 +v_C5a_C5aR1_complex -> v_PTPN6 +v_PTPN6 -| v_SYK +v_SYK -> v_PIK3AP1_phosphorylated +v_SEMA4_PLXNB2_MET_complex -> v_ARHGEF12 +v_RELA_NFKB1_complex_M2_macrophage_nucleus -> v_CXCL16 +v_CREB1_phosphorylated -> v_MIF +v_SEMA4A_M2_macrophage__secreted_components -> v_SEMA4A_M2_macrophage__extracellular_space +v_CREB1_phosphorylated -> v_ICOSLG +v_STAT3_STAT3_complex -> v_CD86 +v_PRL_PRLR_complex -> v_JAK2 +v_CCL21_CCR7_complex -> v_JAK2 +v_LIFR_IL6ST_CTF1_complex -> v_JAK1 +v_IL11Ra_IL6ST_IL11_complex -> v_JAK1 +v_ITGB1_ITGA1_col4a_complex -> v_PTK2 +v_IL17Ra_IL17Rc_IL17F_complex -> v_TRAF3IP2_phosphorylated +v_TRAF3IP2_phosphorylated -> v_TRAF6_ubiquitinated +v_CYLD -| v_TRAF6_ubiquitinated +v_IL15 -> v_proliferation_survival_signal_phenotype +v_PDGFC -> v_proliferation_survival_signal_phenotype +v_Vegfc_M2_macrophage__secreted_components -> v_proliferation_survival_signal_phenotype +v_Vegfb_M2_macrophage__secreted_components -> v_proliferation_survival_signal_phenotype +v_IL8_M2_macrophage__secreted_components -> v_proliferation_survival_signal_phenotype +v_VEGFa_M2_macrophage__secreted_components -> v_proliferation_survival_signal_phenotype +v_CSF1_M2_macrophage__secreted_components -> v_proliferation_survival_signal_phenotype +v_TGFB1_M2_macrophage__secreted_components -> v_proliferation_survival_signal_phenotype +v_FASL_M2_macrophage__secreted_components -> v_apoptosis_signal_phenotype +v_CCL20 -> v_Cell_chemotaxis_migration_signal_phenotype +v_FN1 -> v_Cell_chemotaxis_migration_signal_phenotype +v_CSF1_M2_macrophage__secreted_components -> v_Cell_chemotaxis_migration_signal_phenotype +v_IL8_M2_macrophage__secreted_components -> v_Cell_chemotaxis_migration_signal_phenotype +v_MMP3 -> v_Cell_chemotaxis_migration_signal_phenotype +v_MMP14 -> v_Cell_chemotaxis_migration_signal_phenotype +v_MMP9 -> v_Cell_chemotaxis_migration_signal_phenotype +v_FASL_M2_macrophage__secreted_components -> v_FASL_M2_macrophage__extracellular_space +v_p53_phosphorylated_M2_macrophage__cytoplasm -> v_p53_phosphorylated_M2_macrophage_nucleus +v_Mcl1_rna -> v_mcl1 +v_AKT1 -| v_GSK3B +v_MSK1_phosphorylated -| v_GSK3B +$v_AKT1: v_AKT1_phosphorylated +$v_AKT1_phosphorylated: v_PI3K +$v_ARHGEF12: v_SEMA4_PLXNB2_MET_complex +$v_ARRB2: v_CXCL13_ACKR4_complex +$v_ASK1: v_DAXX +$v_BAX: !v_BCL2_M2_macrophage_mitochondrion_membrane_active & !v_BCL2L1 & !v_mcl1 +$v_BCL2L1: !v_BAD & !v_Bim +$v_BCL2_M2_macrophage_mitochondrion_membrane: v_Bcl2_rna +$v_BCL2_M2_macrophage_mitochondrion_membrane_active: v_BCL2_M2_macrophage_mitochondrion_membrane & !v_BAD & !v_Bim & !v_RXRa_NUR77_complex +$v_BCL3_rna: v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_C_EBPb_phosphorylated & v_STAT3_STAT3_complex +$v_Bcl2_rna: v_RELA_NFKB1_complex_M2_macrophage_nucleus +$v_Bim: v_FOXO1 +$v_C5a_C5aR1_complex: v_c5a +$v_CASP3: v_CASP8 | v_CASP9 +$v_CASP7: v_CASP8 | v_CASP9 +$v_CASP8: v_FADD +$v_CASP9: v_BAX & !v_AKT1_phosphorylated & !v_XIAP +$v_CCL20: v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_C_EBPb_phosphorylated & v_CREB1_phosphorylated +$v_CCL21_CCR7_complex: v_CCl21 +$v_CD32a: v_STAT3_STAT3_complex +$v_CD32b_rna: v_STAT3_STAT3_complex +$v_CD84: v_C_EBPb_phosphorylated +$v_CD86: v_STAT3_STAT3_complex +$v_COX2_rna: v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_NFAT5_phosphorylated +$v_CREB1_phosphorylated: !v_GSK3B +$v_CSF1R_CSF1_complex: v_CSF1R & v_CSF1_M2_macrophage__extracellular_space +$v_CSF1_M2_macrophage__extracellular_space: v_CSF1_M2_macrophage__secreted_components +$v_CSF1_M2_macrophage__secreted_components: v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_C_EBPb_phosphorylated +$v_CSF2_rna: v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_CREB1_phosphorylated & v_C_EBPb_phosphorylated & v_NFAT5_phosphorylated +$v_CSFR1R_IL34_complex: v_IL34 & v_CSF1R +$v_CTNNB1: v_GSK3b_APC_AXIN1_CTNNB1_CK1A_complex & v_Dvl1 +$v_CTNNB1_TCF_LEF_complex: v_TCF_LEF & v_CTNNB1 +$v_CXCL13_ACKR4_complex: v_CXCL13 +$v_CXCL16: v_RELA_NFKB1_complex_M2_macrophage_nucleus +$v_CXCR1_IL8_complex: v_IL8_M2_macrophage__extracellular_space +$v_C_EBPb_phosphorylated: v_p38_MAP_KINASE_phosphorylated_M2_macrophage_nucleus | v_CREB1_phosphorylated | v_ERK1_phosphorylated_M2_macrophage__cytoplasm +$v_Cell_chemotaxis_migration_signal_phenotype: v_CCL20 | v_FN1 | v_CSF1_M2_macrophage__secreted_components | v_IL8_M2_macrophage__secreted_components | v_MMP3 | v_MMP14 | v_MMP9 +$v_DAG_simple_molecule: v_PIP2_simple_molecule & v_PLCG2 +$v_DAXX: v_TGFBR1_TGFBR2_TGFB1_complex | v_FASL_FAS_complex +$v_Dvl1: v_FZD5_LRP5_wnt5a_complex | v_WNT5B_FZD1_LRP5_complex +$v_EDA: v_CREB1_phosphorylated +$v_ERK1_phosphorylated_M2_macrophage__cytoplasm: v_MEK1_phosphorylated | v_MEK2_phosphorylated | v_C5a_C5aR1_complex +$v_ERK1_phosphorylated_M2_macrophage_nucleus: v_ERK1_phosphorylated_M2_macrophage__cytoplasm +$v_FADD: v_FASL_FAS_complex +$v_FAS: v_p53_phosphorylated_M2_macrophage_nucleus +$v_FASL_FAS_complex: v_FASL_M2_macrophage__extracellular_space & v_FAS +$v_FASL_M2_macrophage__extracellular_space: v_FASL_M2_macrophage__secreted_components +$v_FASL_M2_macrophage__secreted_components: v_FOXO1 +$v_FN1: v_CTNNB1_TCF_LEF_complex +$v_FOXO1: !v_AKT1_phosphorylated & !v_mcl1 +$v_GAB2_phosphorylated: v_HCK +$v_GAL_GALR2_complex: v_gal +$v_GAS6_MERTK_complex: v_GAS6 +$v_GNA12_GNA13_complex: v_GAL_GALR2_complex +$v_GNAI3: (v_CXCR1_IL8_complex | v_CCL21_CCR7_complex) & v_GNB_GNG_GNAI3_complex +$v_GNB_GNG_complex: (v_CXCR1_IL8_complex | v_CCL21_CCR7_complex) & v_GNB_GNG_GNAI3_complex +$v_GSK3B: !v_AKT1 & !v_MSK1_phosphorylated +$v_GSK3b_APC_AXIN1_CK1A_complex: v_GSK3b_APC_AXIN1_CTNNB1_CK1A_complex & v_Dvl1 +$v_Grb2: v_Shc_phosphorylated | v_CSF1R_CSF1_complex | v_CSFR1R_IL34_complex | v_vegfc_vegfr3_complex +$v_HRAS: v_SOS1 | v_EFNB1_EPHB1_complex | v_GAS6_MERTK_complex +$v_ICOSLG: v_CREB1_phosphorylated +$v_IFNa_rna: v_IRF7 +$v_IFNb_rna: v_IRF7 +$v_IKK1_IKK2_complex: v_IKK1_phosphorylated & v_IKK2_phosphorylated +$v_IKK2_phosphorylated: v_PRKCQ +$v_IKK_complex: v_AKT1_phosphorylated | v_TAK1_phosphorylated | v_TRAF6_ubiquitinated +$v_IL10R1_IL10R2_IL10_complex: v_IL10R1_IL10R2_complex & v_IL10_M2_macrophage__extracellular_space +$v_IL10_M2_macrophage__extracellular_space: v_IL10_M2_macrophage__secreted_components +$v_IL10_M2_macrophage__secreted_components: v_STAT3_STAT3_complex & v_klf4 & v_C_EBPb_phosphorylated & v_FOXO1 +$v_IL12_rna: v_RELA_NFKB1_complex_M2_macrophage_nucleus +$v_IL15: v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_CREB1_phosphorylated & v_C_EBPb_phosphorylated +$v_IL18_M2_macrophage__cytoplasm: v_NFAT5_phosphorylated +$v_IL18_M2_macrophage__cytoplasm_active: v_IL18_M2_macrophage__cytoplasm & v_NLRP3_INFLAMMASOME_complex +$v_IL1B: v_NLRP3_INFLAMMASOME_complex +$v_IL23R_IL12RB1_IL23_complex: v_IL23R_IL12RB1_complex & v_IL23_M2_macrophage__extracellular_space +$v_IL23_M2_macrophage__extracellular_space: v_IL23_M2_macrophage__secreted_components +$v_IL23_M2_macrophage__secreted_components: v_RELA_NFKB1_complex_M2_macrophage_nucleus +$v_IL4: v_STAT3_STAT3_complex & v_STAT6_STAT6_complex +$v_IL4R: v_STAT6_STAT6_complex +$v_IL4_IL4Ra_complex: v_IL4 & v_IL4R +$v_IL6_rna: v_klf4 & v_CREB1_phosphorylated & v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_NFAT5_phosphorylated +$v_IL8_M2_macrophage__extracellular_space: v_IL8_M2_macrophage__secreted_components +$v_IL8_M2_macrophage__secreted_components: v_RELA_NFKB1_complex_M2_macrophage_nucleus +$v_IP3_simple_molecule: v_PIP2_simple_molecule & v_PLCG2 +$v_IRF7: v_IKK_complex | v_OPN +$v_ITCH_phosphorylated: v_JNK1_phosphorylated_M2_macrophage__cytoplasm +$v_ITGB1_ITGA1_col4a_complex: (v_col4a4 & v_ITGB1_ITGA1_complex) | (v_col4a5 & v_ITGB1_ITGA1_complex) +$v_JAG1: v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_CREB1_phosphorylated & v_C_EBPb_phosphorylated +$v_JAK1: v_LIFR_IL6ST_CTF1_complex | v_IL11Ra_IL6ST_IL11_complex +$v_JAK1_TYK2_complex: v_IL23R_IL12RB1_IL23_complex | v_IL10R1_IL10R2_IL10_complex | v_IL4_IL4Ra_complex +$v_JAK2: v_PRL_PRLR_complex | v_CCL21_CCR7_complex +$v_JNK1_phosphorylated_M2_macrophage__cytoplasm: v_MKK7_phosphorylated | v_MKK4_phosphorylated | v_ASK1 | v_Rac1 +$v_JNK1_phosphorylated_M2_macrophage_nucleus: v_JNK1_phosphorylated_M2_macrophage__cytoplasm +$v_MDM2_phosphorylated: v_AKT1_phosphorylated +$v_MEK1_phosphorylated: v_TPL2 | v_RAF1 +$v_MEK2_phosphorylated: v_TPL2 | v_RAF1 +$v_MIF: v_CREB1_phosphorylated +$v_MKK3_phosphorylated: v_ASK1 +$v_MKK4_phosphorylated: v_ASK1 | v_MEKK1 +$v_MKK6_phosphorylated: v_ASK1 +$v_MKK7_phosphorylated: v_ASK1 +$v_MMP14: v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_CREB1_phosphorylated & v_C_EBPb_phosphorylated +$v_MMP3: v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_CREB1_phosphorylated & v_C_EBPb_phosphorylated +$v_MMP9: v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_CREB1_phosphorylated & v_C_EBPb_phosphorylated +$v_MSK1_phosphorylated: v_p38_MAP_KINASE_phosphorylated_M2_macrophage_nucleus +$v_Matrix_degradation_signal_phenotype: (v_MMP3 | v_MMP14 | v_MMP9 | v_PDGFC) & !v_col4a3 +$v_Mcl1_rna: v_CREB1_phosphorylated +$v_NFAT5_phosphorylated: v_ERK1_phosphorylated_M2_macrophage__cytoplasm | v_p38_MAP_KINASE_phosphorylated_M2_macrophage__cytoplasm +$v_NFKB1: v_NFKB1_TPL2_complex & v_IKK_complex +$v_NFKBIA_phosphorylated: (v_IKK_complex | v_Syk_phosphorylated) & v_NFKBIA_RELA_NFKB1_complex +$v_NFKBIE: v_RELA_NFKB1_NFKBIE_complex & v_IKK1_IKK2_complex +$v_NLK_phosphorylated: v_TAK1_phosphorylated +$v_NLRP3: v_RELA_NFKB1_complex_M2_macrophage_nucleus +$v_NLRP3_INFLAMMASOME_complex: v_NLRP3 & v_Casp1 & v_ASC +$v_PDGFC: v_C_EBPb_phosphorylated +$v_PI3K: (v_Syk_phosphorylated | v_C5a_C5aR1_complex | v_GAB2_phosphorylated | v_HRAS | v_CSF1R_CSF1_complex | v_VegfR1_vegfb_complex | v_VegfR1_Vegfa_complex | v_VegfR2_vegfc_nrp2_complex | v_TGFBR1_TGFBR2_TGFB1_complex | v_Src | v_GNB_GNG_complex | v_GAS6_MERTK_complex | v_PIK3AP1_phosphorylated | v_CD40LG_ITGB1_ITGA1_complex | v_PTK2 | v_JAK1_TYK2_complex | v_TRAF6_ubiquitinated) & !v_SHIP1 & !v_PTPN6 +$v_PIK3AP1_phosphorylated: v_SYK +$v_PLCG2: v_Syk_phosphorylated | v_PI3K | v_VegfR1_Vegfa_complex | v_VegfR1_vegfb_complex | v_GNB_GNG_complex +$v_PPARg_rna: v_C_EBPb_phosphorylated +$v_PRKCD: v_DAG_simple_molecule +$v_PRKCQ: v_SH2D1A +$v_PRL_PRLR_complex: v_PRL +$v_PTK2: v_ITGB1_ITGA1_col4a_complex +$v_PTPN6: v_HLA_B_LILRB1_complex | v_C5a_C5aR1_complex +$v_Prkcd: v_CSF1R_CSF1_complex | v_CSFR1R_IL34_complex +$v_RAF1: v_AKT1_phosphorylated | v_PRKCD | v_HRAS +$v_RBL1_E2F4_DP1_complex: v_SMAD2_SMAD4_complex +$v_RELA_NFKB1_complex_M2_macrophage__cytoplasm: ((v_IKK_complex | v_Syk_phosphorylated) & v_NFKBIA_RELA_NFKB1_complex) | (v_RELA_NFKB1_NFKBIE_complex & v_IKK1_IKK2_complex) +$v_RELA_NFKB1_complex_M2_macrophage_nucleus: v_RELA_NFKB1_complex_M2_macrophage__cytoplasm & v_Prkcd & !v_Sirt1 +$v_RHOA: v_GNA12_GNA13_complex | v_ARHGEF12 +$v_RXRa_NUR77_complex: !v_AKT1_phosphorylated +$v_Rac1: v_Dvl1 & !v_NRP1_PLXNA1_sema3A_complex & !v_RHOA & !v_SEMA4_PLXNB2_MET_complex +$v_SARA: v_SMAD2_SARA_complex & v_TGFBR1_TGFBR2_TGFB1_complex & !v_SMAD7 +$v_SEMA4A_M2_macrophage__extracellular_space: v_SEMA4A_M2_macrophage__secreted_components +$v_SEMA4A_M2_macrophage__secreted_components: v_C_EBPb_phosphorylated +$v_SEMA4_PLXNB2_MET_complex: (v_SEMA4D & v_PLXNB2_MET_complex) | (v_SEMA4A_M2_macrophage__extracellular_space & v_PLXNB2_MET_complex) +$v_SHIP1: v_immune_complex_CD32b_complex +$v_SMAD2_SMAD4_complex: v_SMAD2_phosphorylated & v_SMAD4 +$v_SMAD2_phosphorylated: v_SMAD2_SARA_complex & v_TGFBR1_TGFBR2_TGFB1_complex & !v_SMAD7 +$v_SOS1: v_Grb2 +$v_STAT3: v_JAK1 | v_JAK1_TYK2_complex | v_JAK2 +$v_STAT3_STAT3_complex: v_STAT3 +$v_STAT6: v_JAK1 | v_JAK1_TYK2_complex +$v_STAT6_STAT6_complex: v_STAT6 +$v_SYK: !v_PTPN6 +$v_Shc_phosphorylated: v_TGFBR1_TGFBR2_TGFB1_complex | v_VegfR2_vegfc_nrp2_complex | v_Src | v_JAK2 | v_JAK1_TYK2_complex +$v_Src: v_GNAI3 +$v_Syk_phosphorylated: v_HCK | v_immune_complex_CD16a_complex | v_immune_complex_CD32a_complex | v_immune_complex_CD64_complex +$v_TAK1_phosphorylated: v_TGFBR1_TGFBR2_TGFB1_complex +$v_TCF_LEF: !v_NLK_phosphorylated +$v_TGFB1_M2_macrophage__extracellular_space: v_TGFB1_M2_macrophage__secreted_components +$v_TGFBR1_TGFBR2_TGFB1_complex: v_TGFB1_M2_macrophage__extracellular_space & v_TGFBR1_TGFBR2_complex +$v_TNFAIP3_rna: v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_CREB1_phosphorylated & v_C_EBPb_phosphorylated +$v_TPL2: v_NFKB1_TPL2_complex & v_IKK_complex +$v_TRAF1_rna: v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_NFAT5_phosphorylated +$v_TRAF3IP2_phosphorylated: v_IL17Ra_IL17Rc_IL17F_complex +$v_TRAF6_ubiquitinated: v_TRAF3IP2_phosphorylated & !v_CYLD +$v_T_cells_activation_signal_phenotype: v_CSF1_M2_macrophage__secreted_components | v_CCL18 | v_CD86 +$v_VEGFa_M2_macrophage__extracellular_space: v_VEGFa_M2_macrophage__secreted_components +$v_VEGFa_M2_macrophage__secreted_components: v_Vegfa_rna +$v_VegfR1_Vegfa_complex: v_VEGFa_M2_macrophage__extracellular_space & v_VegfR1 +$v_VegfR1_vegfb_complex: v_Vegfb_M2_macrophage__extracellular_space & v_VegfR1 +$v_VegfR2_vegfc_nrp2_complex: v_Vegfc_M2_macrophage__extracellular_space +$v_Vegfa_rna: v_NFAT5_phosphorylated & v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_C_EBPb_phosphorylated & v_STAT3_STAT3_complex +$v_Vegfb_M2_macrophage__extracellular_space: v_Vegfb_M2_macrophage__secreted_components +$v_Vegfb_M2_macrophage__secreted_components: v_NFAT5_phosphorylated & v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_CREB1_phosphorylated & v_C_EBPb_phosphorylated & v_STAT3_STAT3_complex +$v_Vegfc_M2_macrophage__extracellular_space: v_Vegfc_M2_macrophage__secreted_components +$v_Vegfc_M2_macrophage__secreted_components: v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_C_EBPb_phosphorylated & v_NFAT5_phosphorylated & v_STAT3_STAT3_complex & v_CREB1_phosphorylated +$v_XIAP: v_RELA_NFKB1_complex_M2_macrophage_nucleus +$v_angiogenesis_signal_phenotype: v_OPN | v_Vegfc_M2_macrophage__secreted_components | v_VEGFa_M2_macrophage__secreted_components | v_Vegfb_M2_macrophage__secreted_components +$v_apoptosis_M2_macrophage_phenotype: (v_CASP8 | v_CASP3 | v_CASP7 | v_p53_phosphorylated_M2_macrophage__cytoplasm | v_Bim | v_FASL_M2_macrophage__secreted_components | v_NLRP3_INFLAMMASOME_complex | v_RXRa_NUR77_complex) & !v_BCL2_M2_macrophage_mitochondrion_membrane_active & !v_mcl1 & !v_BCL2L1 +$v_apoptosis_signal_phenotype: v_FASL_M2_macrophage__secreted_components +$v_cFLIP: v_RELA_NFKB1_complex_M2_macrophage_nucleus +$v_cFLIP_ubiquitinated: v_cFLIP & v_ITCH_phosphorylated +$v_cMyc: v_c_Myc_rna +$v_cMyc_phosphorylated: v_cMyc & v_ERK1_phosphorylated_M2_macrophage__cytoplasm +$v_c_Myc_rna: v_STAT3_STAT3_complex & !v_RBL1_E2F4_DP1_complex +$v_immune_complex_CD16a_complex: v_immune_complex_complex & v_C5a_C5aR1_complex +$v_immune_complex_CD32a_complex: v_immune_complex_complex & v_CD32a & v_C5a_C5aR1_complex +$v_immune_complex_CD32b_complex: v_immune_complex_complex +$v_immune_complex_CD64_complex: v_immune_complex_complex & v_C5a_C5aR1_complex +$v_inflammation_signal_phenotype: (v_C5a_C5aR1_complex | v_CCL20 | v_COX2_rna | v_IL15 | v_IRF7 | v_RELA_NFKB1_complex_M2_macrophage_nucleus | v_IL23_M2_macrophage__secreted_components | v_CCL18 | v_SEMA4A_M2_macrophage__secreted_components | v_sema7a) & !v_PPARg_rna & !v_TGFB1_M2_macrophage__secreted_components & !v_IL10_M2_macrophage__secreted_components & !v_ARRB2 +$v_klf4: v_STAT3_STAT3_complex +$v_mcl1: v_Mcl1_rna +$v_p15_rna: v_FOXO1 +$v_p300_SP1_complex: v_SMAD2_SMAD4_complex +$v_p38_MAP_KINASE_phosphorylated_M2_macrophage__cytoplasm: (v_MKK3_phosphorylated | v_MKK6_phosphorylated | v_C5a_C5aR1_complex) & !v_DUSP1 +$v_p38_MAP_KINASE_phosphorylated_M2_macrophage_nucleus: v_p38_MAP_KINASE_phosphorylated_M2_macrophage__cytoplasm +$v_p53: v_cMyc_phosphorylated +$v_p53_phosphorylated_M2_macrophage__cytoplasm: v_p53 & !v_MDM2_phosphorylated +$v_p53_phosphorylated_M2_macrophage_nucleus: v_p53_phosphorylated_M2_macrophage__cytoplasm +$v_proliferation_survival_M2_macrophage_phenotype: (v_XIAP | v_ERK1_phosphorylated_M2_macrophage_nucleus | v_p38_MAP_KINASE_phosphorylated_M2_macrophage_nucleus | v_BCL2L1 | v_MDM2_phosphorylated | v_CREB1_phosphorylated | v_TGFB1_M2_macrophage__secreted_components | v_cFLIP | v_BCL3_rna | v_Vegfc_M2_macrophage__secreted_components | v_CSF1_M2_macrophage__secreted_components | v_IL8_M2_macrophage__secreted_components | v_VEGFa_M2_macrophage__secreted_components | v_Vegfb_M2_macrophage__secreted_components | v_HBGEF | v_cMyc_phosphorylated) & !v_p15_rna +$v_proliferation_survival_signal_phenotype: v_IL15 | v_PDGFC | v_Vegfc_M2_macrophage__secreted_components | v_Vegfb_M2_macrophage__secreted_components | v_IL8_M2_macrophage__secreted_components | v_VEGFa_M2_macrophage__secreted_components | v_CSF1_M2_macrophage__secreted_components | v_TGFB1_M2_macrophage__secreted_components +$v_sema7a: v_C_EBPb_phosphorylated +$v_smad1_phosphorylated: v_ARI_ARII_bmp6_complex +$v_smad4_smad1_complex: v_smad1_phosphorylated & v_SMAD4 +$v_vegfc_vegfr3_complex: v_Vegfc_M2_macrophage__extracellular_space diff --git a/models/[id-240]__[var-197]__[in-52]__[M2-SYNOVIAL-MACROPHAGE]/model.bnet b/models/[id-240]__[var-197]__[in-52]__[M2-SYNOVIAL-MACROPHAGE]/model.bnet new file mode 100644 index 0000000..33e732c --- /dev/null +++ b/models/[id-240]__[var-197]__[in-52]__[M2-SYNOVIAL-MACROPHAGE]/model.bnet @@ -0,0 +1,198 @@ +targets,factors +v_AKT1, v_AKT1_phosphorylated +v_AKT1_phosphorylated, v_PI3K +v_ARHGEF12, v_SEMA4_PLXNB2_MET_complex +v_ARRB2, v_CXCL13_ACKR4_complex +v_ASK1, v_DAXX +v_BAX, ((!v_BCL2_M2_macrophage_mitochondrion_membrane_active & !v_BCL2L1) & !v_mcl1) +v_BCL2L1, (!v_BAD & !v_Bim) +v_BCL2_M2_macrophage_mitochondrion_membrane, v_Bcl2_rna +v_BCL2_M2_macrophage_mitochondrion_membrane_active, (((v_BCL2_M2_macrophage_mitochondrion_membrane & !v_BAD) & !v_Bim) & !v_RXRa_NUR77_complex) +v_BCL3_rna, ((v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_C_EBPb_phosphorylated) & v_STAT3_STAT3_complex) +v_Bcl2_rna, v_RELA_NFKB1_complex_M2_macrophage_nucleus +v_Bim, v_FOXO1 +v_C5a_C5aR1_complex, v_c5a +v_CASP3, (v_CASP8 | v_CASP9) +v_CASP7, (v_CASP8 | v_CASP9) +v_CASP8, v_FADD +v_CASP9, ((v_BAX & !v_AKT1_phosphorylated) & !v_XIAP) +v_CCL20, ((v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_C_EBPb_phosphorylated) & v_CREB1_phosphorylated) +v_CCL21_CCR7_complex, v_CCl21 +v_CD32a, v_STAT3_STAT3_complex +v_CD32b_rna, v_STAT3_STAT3_complex +v_CD84, v_C_EBPb_phosphorylated +v_CD86, v_STAT3_STAT3_complex +v_COX2_rna, (v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_NFAT5_phosphorylated) +v_CREB1_phosphorylated, !v_GSK3B +v_CSF1R_CSF1_complex, (v_CSF1R & v_CSF1_M2_macrophage__extracellular_space) +v_CSF1_M2_macrophage__extracellular_space, v_CSF1_M2_macrophage__secreted_components +v_CSF1_M2_macrophage__secreted_components, (v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_C_EBPb_phosphorylated) +v_CSF2_rna, (((v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_CREB1_phosphorylated) & v_C_EBPb_phosphorylated) & v_NFAT5_phosphorylated) +v_CSFR1R_IL34_complex, (v_IL34 & v_CSF1R) +v_CTNNB1, (v_GSK3b_APC_AXIN1_CTNNB1_CK1A_complex & v_Dvl1) +v_CTNNB1_TCF_LEF_complex, (v_TCF_LEF & v_CTNNB1) +v_CXCL13_ACKR4_complex, v_CXCL13 +v_CXCL16, v_RELA_NFKB1_complex_M2_macrophage_nucleus +v_CXCR1_IL8_complex, v_IL8_M2_macrophage__extracellular_space +v_C_EBPb_phosphorylated, ((v_p38_MAP_KINASE_phosphorylated_M2_macrophage_nucleus | v_CREB1_phosphorylated) | v_ERK1_phosphorylated_M2_macrophage__cytoplasm) +v_Cell_chemotaxis_migration_signal_phenotype, ((((((v_CCL20 | v_FN1) | v_CSF1_M2_macrophage__secreted_components) | v_IL8_M2_macrophage__secreted_components) | v_MMP3) | v_MMP14) | v_MMP9) +v_DAG_simple_molecule, (v_PIP2_simple_molecule & v_PLCG2) +v_DAXX, (v_TGFBR1_TGFBR2_TGFB1_complex | v_FASL_FAS_complex) +v_Dvl1, (v_FZD5_LRP5_wnt5a_complex | v_WNT5B_FZD1_LRP5_complex) +v_EDA, v_CREB1_phosphorylated +v_ERK1_phosphorylated_M2_macrophage__cytoplasm, ((v_MEK1_phosphorylated | v_MEK2_phosphorylated) | v_C5a_C5aR1_complex) +v_ERK1_phosphorylated_M2_macrophage_nucleus, v_ERK1_phosphorylated_M2_macrophage__cytoplasm +v_FADD, v_FASL_FAS_complex +v_FAS, v_p53_phosphorylated_M2_macrophage_nucleus +v_FASL_FAS_complex, (v_FASL_M2_macrophage__extracellular_space & v_FAS) +v_FASL_M2_macrophage__extracellular_space, v_FASL_M2_macrophage__secreted_components +v_FASL_M2_macrophage__secreted_components, v_FOXO1 +v_FN1, v_CTNNB1_TCF_LEF_complex +v_FOXO1, (!v_AKT1_phosphorylated & !v_mcl1) +v_GAB2_phosphorylated, v_HCK +v_GAL_GALR2_complex, v_gal +v_GAS6_MERTK_complex, v_GAS6 +v_GNA12_GNA13_complex, v_GAL_GALR2_complex +v_GNAI3, ((v_CXCR1_IL8_complex | v_CCL21_CCR7_complex) & v_GNB_GNG_GNAI3_complex) +v_GNB_GNG_complex, ((v_CXCR1_IL8_complex | v_CCL21_CCR7_complex) & v_GNB_GNG_GNAI3_complex) +v_GSK3B, (!v_AKT1 & !v_MSK1_phosphorylated) +v_GSK3b_APC_AXIN1_CK1A_complex, (v_GSK3b_APC_AXIN1_CTNNB1_CK1A_complex & v_Dvl1) +v_Grb2, (((v_Shc_phosphorylated | v_CSF1R_CSF1_complex) | v_CSFR1R_IL34_complex) | v_vegfc_vegfr3_complex) +v_HRAS, ((v_SOS1 | v_EFNB1_EPHB1_complex) | v_GAS6_MERTK_complex) +v_ICOSLG, v_CREB1_phosphorylated +v_IFNa_rna, v_IRF7 +v_IFNb_rna, v_IRF7 +v_IKK1_IKK2_complex, (v_IKK1_phosphorylated & v_IKK2_phosphorylated) +v_IKK2_phosphorylated, v_PRKCQ +v_IKK_complex, ((v_AKT1_phosphorylated | v_TAK1_phosphorylated) | v_TRAF6_ubiquitinated) +v_IL10R1_IL10R2_IL10_complex, (v_IL10R1_IL10R2_complex & v_IL10_M2_macrophage__extracellular_space) +v_IL10_M2_macrophage__extracellular_space, v_IL10_M2_macrophage__secreted_components +v_IL10_M2_macrophage__secreted_components, (((v_STAT3_STAT3_complex & v_klf4) & v_C_EBPb_phosphorylated) & v_FOXO1) +v_IL12_rna, v_RELA_NFKB1_complex_M2_macrophage_nucleus +v_IL15, ((v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_CREB1_phosphorylated) & v_C_EBPb_phosphorylated) +v_IL18_M2_macrophage__cytoplasm, v_NFAT5_phosphorylated +v_IL18_M2_macrophage__cytoplasm_active, (v_IL18_M2_macrophage__cytoplasm & v_NLRP3_INFLAMMASOME_complex) +v_IL1B, v_NLRP3_INFLAMMASOME_complex +v_IL23R_IL12RB1_IL23_complex, (v_IL23R_IL12RB1_complex & v_IL23_M2_macrophage__extracellular_space) +v_IL23_M2_macrophage__extracellular_space, v_IL23_M2_macrophage__secreted_components +v_IL23_M2_macrophage__secreted_components, v_RELA_NFKB1_complex_M2_macrophage_nucleus +v_IL4, (v_STAT3_STAT3_complex & v_STAT6_STAT6_complex) +v_IL4R, v_STAT6_STAT6_complex +v_IL4_IL4Ra_complex, (v_IL4 & v_IL4R) +v_IL6_rna, (((v_klf4 & v_CREB1_phosphorylated) & v_RELA_NFKB1_complex_M2_macrophage_nucleus) & v_NFAT5_phosphorylated) +v_IL8_M2_macrophage__extracellular_space, v_IL8_M2_macrophage__secreted_components +v_IL8_M2_macrophage__secreted_components, v_RELA_NFKB1_complex_M2_macrophage_nucleus +v_IP3_simple_molecule, (v_PIP2_simple_molecule & v_PLCG2) +v_IRF7, (v_IKK_complex | v_OPN) +v_ITCH_phosphorylated, v_JNK1_phosphorylated_M2_macrophage__cytoplasm +v_ITGB1_ITGA1_col4a_complex, ((v_col4a4 & v_ITGB1_ITGA1_complex) | (v_col4a5 & v_ITGB1_ITGA1_complex)) +v_JAG1, ((v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_CREB1_phosphorylated) & v_C_EBPb_phosphorylated) +v_JAK1, (v_LIFR_IL6ST_CTF1_complex | v_IL11Ra_IL6ST_IL11_complex) +v_JAK1_TYK2_complex, ((v_IL23R_IL12RB1_IL23_complex | v_IL10R1_IL10R2_IL10_complex) | v_IL4_IL4Ra_complex) +v_JAK2, (v_PRL_PRLR_complex | v_CCL21_CCR7_complex) +v_JNK1_phosphorylated_M2_macrophage__cytoplasm, (((v_MKK7_phosphorylated | v_MKK4_phosphorylated) | v_ASK1) | v_Rac1) +v_JNK1_phosphorylated_M2_macrophage_nucleus, v_JNK1_phosphorylated_M2_macrophage__cytoplasm +v_MDM2_phosphorylated, v_AKT1_phosphorylated +v_MEK1_phosphorylated, (v_TPL2 | v_RAF1) +v_MEK2_phosphorylated, (v_TPL2 | v_RAF1) +v_MIF, v_CREB1_phosphorylated +v_MKK3_phosphorylated, v_ASK1 +v_MKK4_phosphorylated, (v_ASK1 | v_MEKK1) +v_MKK6_phosphorylated, v_ASK1 +v_MKK7_phosphorylated, v_ASK1 +v_MMP14, ((v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_CREB1_phosphorylated) & v_C_EBPb_phosphorylated) +v_MMP3, ((v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_CREB1_phosphorylated) & v_C_EBPb_phosphorylated) +v_MMP9, ((v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_CREB1_phosphorylated) & v_C_EBPb_phosphorylated) +v_MSK1_phosphorylated, v_p38_MAP_KINASE_phosphorylated_M2_macrophage_nucleus +v_Matrix_degradation_signal_phenotype, ((((v_MMP3 | v_MMP14) | v_MMP9) | v_PDGFC) & !v_col4a3) +v_Mcl1_rna, v_CREB1_phosphorylated +v_NFAT5_phosphorylated, (v_ERK1_phosphorylated_M2_macrophage__cytoplasm | v_p38_MAP_KINASE_phosphorylated_M2_macrophage__cytoplasm) +v_NFKB1, (v_NFKB1_TPL2_complex & v_IKK_complex) +v_NFKBIA_phosphorylated, ((v_IKK_complex | v_Syk_phosphorylated) & v_NFKBIA_RELA_NFKB1_complex) +v_NFKBIE, (v_RELA_NFKB1_NFKBIE_complex & v_IKK1_IKK2_complex) +v_NLK_phosphorylated, v_TAK1_phosphorylated +v_NLRP3, v_RELA_NFKB1_complex_M2_macrophage_nucleus +v_NLRP3_INFLAMMASOME_complex, ((v_NLRP3 & v_Casp1) & v_ASC) +v_PDGFC, v_C_EBPb_phosphorylated +v_PI3K, ((((((((((((((((((v_Syk_phosphorylated | v_C5a_C5aR1_complex) | v_GAB2_phosphorylated) | v_HRAS) | v_CSF1R_CSF1_complex) | v_VegfR1_vegfb_complex) | v_VegfR1_Vegfa_complex) | v_VegfR2_vegfc_nrp2_complex) | v_TGFBR1_TGFBR2_TGFB1_complex) | v_Src) | v_GNB_GNG_complex) | v_GAS6_MERTK_complex) | v_PIK3AP1_phosphorylated) | v_CD40LG_ITGB1_ITGA1_complex) | v_PTK2) | v_JAK1_TYK2_complex) | v_TRAF6_ubiquitinated) & !v_SHIP1) & !v_PTPN6) +v_PIK3AP1_phosphorylated, v_SYK +v_PLCG2, ((((v_Syk_phosphorylated | v_PI3K) | v_VegfR1_Vegfa_complex) | v_VegfR1_vegfb_complex) | v_GNB_GNG_complex) +v_PPARg_rna, v_C_EBPb_phosphorylated +v_PRKCD, v_DAG_simple_molecule +v_PRKCQ, v_SH2D1A +v_PRL_PRLR_complex, v_PRL +v_PTK2, v_ITGB1_ITGA1_col4a_complex +v_PTPN6, (v_HLA_B_LILRB1_complex | v_C5a_C5aR1_complex) +v_Prkcd, (v_CSF1R_CSF1_complex | v_CSFR1R_IL34_complex) +v_RAF1, ((v_AKT1_phosphorylated | v_PRKCD) | v_HRAS) +v_RBL1_E2F4_DP1_complex, v_SMAD2_SMAD4_complex +v_RELA_NFKB1_complex_M2_macrophage__cytoplasm, (((v_IKK_complex | v_Syk_phosphorylated) & v_NFKBIA_RELA_NFKB1_complex) | (v_RELA_NFKB1_NFKBIE_complex & v_IKK1_IKK2_complex)) +v_RELA_NFKB1_complex_M2_macrophage_nucleus, ((v_RELA_NFKB1_complex_M2_macrophage__cytoplasm & v_Prkcd) & !v_Sirt1) +v_RHOA, (v_GNA12_GNA13_complex | v_ARHGEF12) +v_RXRa_NUR77_complex, !v_AKT1_phosphorylated +v_Rac1, (((v_Dvl1 & !v_NRP1_PLXNA1_sema3A_complex) & !v_RHOA) & !v_SEMA4_PLXNB2_MET_complex) +v_SARA, ((v_SMAD2_SARA_complex & v_TGFBR1_TGFBR2_TGFB1_complex) & !v_SMAD7) +v_SEMA4A_M2_macrophage__extracellular_space, v_SEMA4A_M2_macrophage__secreted_components +v_SEMA4A_M2_macrophage__secreted_components, v_C_EBPb_phosphorylated +v_SEMA4_PLXNB2_MET_complex, ((v_SEMA4D & v_PLXNB2_MET_complex) | (v_SEMA4A_M2_macrophage__extracellular_space & v_PLXNB2_MET_complex)) +v_SHIP1, v_immune_complex_CD32b_complex +v_SMAD2_SMAD4_complex, (v_SMAD2_phosphorylated & v_SMAD4) +v_SMAD2_phosphorylated, ((v_SMAD2_SARA_complex & v_TGFBR1_TGFBR2_TGFB1_complex) & !v_SMAD7) +v_SOS1, v_Grb2 +v_STAT3, ((v_JAK1 | v_JAK1_TYK2_complex) | v_JAK2) +v_STAT3_STAT3_complex, v_STAT3 +v_STAT6, (v_JAK1 | v_JAK1_TYK2_complex) +v_STAT6_STAT6_complex, v_STAT6 +v_SYK, !v_PTPN6 +v_Shc_phosphorylated, ((((v_TGFBR1_TGFBR2_TGFB1_complex | v_VegfR2_vegfc_nrp2_complex) | v_Src) | v_JAK2) | v_JAK1_TYK2_complex) +v_Src, v_GNAI3 +v_Syk_phosphorylated, (((v_HCK | v_immune_complex_CD16a_complex) | v_immune_complex_CD32a_complex) | v_immune_complex_CD64_complex) +v_TAK1_phosphorylated, v_TGFBR1_TGFBR2_TGFB1_complex +v_TCF_LEF, !v_NLK_phosphorylated +v_TGFB1_M2_macrophage__extracellular_space, v_TGFB1_M2_macrophage__secreted_components +v_TGFBR1_TGFBR2_TGFB1_complex, (v_TGFB1_M2_macrophage__extracellular_space & v_TGFBR1_TGFBR2_complex) +v_TNFAIP3_rna, ((v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_CREB1_phosphorylated) & v_C_EBPb_phosphorylated) +v_TPL2, (v_NFKB1_TPL2_complex & v_IKK_complex) +v_TRAF1_rna, (v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_NFAT5_phosphorylated) +v_TRAF3IP2_phosphorylated, v_IL17Ra_IL17Rc_IL17F_complex +v_TRAF6_ubiquitinated, (v_TRAF3IP2_phosphorylated & !v_CYLD) +v_T_cells_activation_signal_phenotype, ((v_CSF1_M2_macrophage__secreted_components | v_CCL18) | v_CD86) +v_VEGFa_M2_macrophage__extracellular_space, v_VEGFa_M2_macrophage__secreted_components +v_VEGFa_M2_macrophage__secreted_components, v_Vegfa_rna +v_VegfR1_Vegfa_complex, (v_VEGFa_M2_macrophage__extracellular_space & v_VegfR1) +v_VegfR1_vegfb_complex, (v_Vegfb_M2_macrophage__extracellular_space & v_VegfR1) +v_VegfR2_vegfc_nrp2_complex, v_Vegfc_M2_macrophage__extracellular_space +v_Vegfa_rna, (((v_NFAT5_phosphorylated & v_RELA_NFKB1_complex_M2_macrophage_nucleus) & v_C_EBPb_phosphorylated) & v_STAT3_STAT3_complex) +v_Vegfb_M2_macrophage__extracellular_space, v_Vegfb_M2_macrophage__secreted_components +v_Vegfb_M2_macrophage__secreted_components, ((((v_NFAT5_phosphorylated & v_RELA_NFKB1_complex_M2_macrophage_nucleus) & v_CREB1_phosphorylated) & v_C_EBPb_phosphorylated) & v_STAT3_STAT3_complex) +v_Vegfc_M2_macrophage__extracellular_space, v_Vegfc_M2_macrophage__secreted_components +v_Vegfc_M2_macrophage__secreted_components, ((((v_RELA_NFKB1_complex_M2_macrophage_nucleus & v_C_EBPb_phosphorylated) & v_NFAT5_phosphorylated) & v_STAT3_STAT3_complex) & v_CREB1_phosphorylated) +v_XIAP, v_RELA_NFKB1_complex_M2_macrophage_nucleus +v_angiogenesis_signal_phenotype, (((v_OPN | v_Vegfc_M2_macrophage__secreted_components) | v_VEGFa_M2_macrophage__secreted_components) | v_Vegfb_M2_macrophage__secreted_components) +v_apoptosis_M2_macrophage_phenotype, ((((((((((v_CASP8 | v_CASP3) | v_CASP7) | v_p53_phosphorylated_M2_macrophage__cytoplasm) | v_Bim) | v_FASL_M2_macrophage__secreted_components) | v_NLRP3_INFLAMMASOME_complex) | v_RXRa_NUR77_complex) & !v_BCL2_M2_macrophage_mitochondrion_membrane_active) & !v_mcl1) & !v_BCL2L1) +v_apoptosis_signal_phenotype, v_FASL_M2_macrophage__secreted_components +v_cFLIP, v_RELA_NFKB1_complex_M2_macrophage_nucleus +v_cFLIP_ubiquitinated, (v_cFLIP & v_ITCH_phosphorylated) +v_cMyc, v_c_Myc_rna +v_cMyc_phosphorylated, (v_cMyc & v_ERK1_phosphorylated_M2_macrophage__cytoplasm) +v_c_Myc_rna, (v_STAT3_STAT3_complex & !v_RBL1_E2F4_DP1_complex) +v_immune_complex_CD16a_complex, (v_immune_complex_complex & v_C5a_C5aR1_complex) +v_immune_complex_CD32a_complex, ((v_immune_complex_complex & v_CD32a) & v_C5a_C5aR1_complex) +v_immune_complex_CD32b_complex, v_immune_complex_complex +v_immune_complex_CD64_complex, (v_immune_complex_complex & v_C5a_C5aR1_complex) +v_inflammation_signal_phenotype, (((((((((((((v_C5a_C5aR1_complex | v_CCL20) | v_COX2_rna) | v_IL15) | v_IRF7) | v_RELA_NFKB1_complex_M2_macrophage_nucleus) | v_IL23_M2_macrophage__secreted_components) | v_CCL18) | v_SEMA4A_M2_macrophage__secreted_components) | v_sema7a) & !v_PPARg_rna) & !v_TGFB1_M2_macrophage__secreted_components) & !v_IL10_M2_macrophage__secreted_components) & !v_ARRB2) +v_klf4, v_STAT3_STAT3_complex +v_mcl1, v_Mcl1_rna +v_p15_rna, v_FOXO1 +v_p300_SP1_complex, v_SMAD2_SMAD4_complex +v_p38_MAP_KINASE_phosphorylated_M2_macrophage__cytoplasm, (((v_MKK3_phosphorylated | v_MKK6_phosphorylated) | v_C5a_C5aR1_complex) & !v_DUSP1) +v_p38_MAP_KINASE_phosphorylated_M2_macrophage_nucleus, v_p38_MAP_KINASE_phosphorylated_M2_macrophage__cytoplasm +v_p53, v_cMyc_phosphorylated +v_p53_phosphorylated_M2_macrophage__cytoplasm, (v_p53 & !v_MDM2_phosphorylated) +v_p53_phosphorylated_M2_macrophage_nucleus, v_p53_phosphorylated_M2_macrophage__cytoplasm +v_proliferation_survival_M2_macrophage_phenotype, ((((((((((((((((v_XIAP | v_ERK1_phosphorylated_M2_macrophage_nucleus) | v_p38_MAP_KINASE_phosphorylated_M2_macrophage_nucleus) | v_BCL2L1) | v_MDM2_phosphorylated) | v_CREB1_phosphorylated) | v_TGFB1_M2_macrophage__secreted_components) | v_cFLIP) | v_BCL3_rna) | v_Vegfc_M2_macrophage__secreted_components) | v_CSF1_M2_macrophage__secreted_components) | v_IL8_M2_macrophage__secreted_components) | v_VEGFa_M2_macrophage__secreted_components) | v_Vegfb_M2_macrophage__secreted_components) | v_HBGEF) | v_cMyc_phosphorylated) & !v_p15_rna) +v_proliferation_survival_signal_phenotype, (((((((v_IL15 | v_PDGFC) | v_Vegfc_M2_macrophage__secreted_components) | v_Vegfb_M2_macrophage__secreted_components) | v_IL8_M2_macrophage__secreted_components) | v_VEGFa_M2_macrophage__secreted_components) | v_CSF1_M2_macrophage__secreted_components) | v_TGFB1_M2_macrophage__secreted_components) +v_sema7a, v_C_EBPb_phosphorylated +v_smad1_phosphorylated, v_ARI_ARII_bmp6_complex +v_smad4_smad1_complex, (v_smad1_phosphorylated & v_SMAD4) +v_vegfc_vegfr3_complex, v_Vegfc_M2_macrophage__extracellular_space diff --git a/models/[id-240]__[var-197]__[in-52]__[M2-SYNOVIAL-MACROPHAGE]/model.sbml b/models/[id-240]__[var-197]__[in-52]__[M2-SYNOVIAL-MACROPHAGE]/model.sbml new file mode 100644 index 0000000..e438130 --- /dev/null +++ b/models/[id-240]__[var-197]__[in-52]__[M2-SYNOVIAL-MACROPHAGE]/model.sbml @@ -0,0 +1 @@ +v_AKT1_phosphorylated1v_PI3K1v_SEMA4_PLXNB2_MET_complex1v_CXCL13_ACKR4_complex1v_DAXX1v_BCL2_M2_macrophage_mitochondrion_membrane_active1v_BCL2L11v_mcl11v_BAD1v_Bim1v_Bcl2_rna1v_BCL2_M2_macrophage_mitochondrion_membrane1v_BAD1v_Bim1v_RXRa_NUR77_complex1v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_C_EBPb_phosphorylated1v_STAT3_STAT3_complex1v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_FOXO11v_c5a1v_CASP81v_CASP91v_CASP81v_CASP91v_FADD1v_BAX1v_AKT1_phosphorylated1v_XIAP1v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_C_EBPb_phosphorylated1v_CREB1_phosphorylated1v_CCl211v_STAT3_STAT3_complex1v_STAT3_STAT3_complex1v_C_EBPb_phosphorylated1v_STAT3_STAT3_complex1v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_NFAT5_phosphorylated1v_GSK3B1v_CSF1R1v_CSF1_M2_macrophage__extracellular_space1v_CSF1_M2_macrophage__secreted_components1v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_C_EBPb_phosphorylated1v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_CREB1_phosphorylated1v_C_EBPb_phosphorylated1v_NFAT5_phosphorylated1v_IL341v_CSF1R1v_GSK3b_APC_AXIN1_CTNNB1_CK1A_complex1v_Dvl11v_TCF_LEF1v_CTNNB11v_CXCL131v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_IL8_M2_macrophage__extracellular_space1v_p38_MAP_KINASE_phosphorylated_M2_macrophage_nucleus1v_CREB1_phosphorylated1v_ERK1_phosphorylated_M2_macrophage__cytoplasm1v_CCL201v_FN11v_CSF1_M2_macrophage__secreted_components1v_IL8_M2_macrophage__secreted_components1v_MMP31v_MMP141v_MMP91v_PIP2_simple_molecule1v_PLCG21v_TGFBR1_TGFBR2_TGFB1_complex1v_FASL_FAS_complex1v_FZD5_LRP5_wnt5a_complex1v_WNT5B_FZD1_LRP5_complex1v_CREB1_phosphorylated1v_MEK1_phosphorylated1v_MEK2_phosphorylated1v_C5a_C5aR1_complex1v_ERK1_phosphorylated_M2_macrophage__cytoplasm1v_FASL_FAS_complex1v_p53_phosphorylated_M2_macrophage_nucleus1v_FASL_M2_macrophage__extracellular_space1v_FAS1v_FASL_M2_macrophage__secreted_components1v_FOXO11v_CTNNB1_TCF_LEF_complex1v_AKT1_phosphorylated1v_mcl11v_HCK1v_gal1v_GAS61v_GAL_GALR2_complex1v_CXCR1_IL8_complex1v_CCL21_CCR7_complex1v_GNB_GNG_GNAI3_complex1v_CXCR1_IL8_complex1v_CCL21_CCR7_complex1v_GNB_GNG_GNAI3_complex1v_AKT11v_MSK1_phosphorylated1v_GSK3b_APC_AXIN1_CTNNB1_CK1A_complex1v_Dvl11v_Shc_phosphorylated1v_CSF1R_CSF1_complex1v_CSFR1R_IL34_complex1v_vegfc_vegfr3_complex1v_SOS11v_EFNB1_EPHB1_complex1v_GAS6_MERTK_complex1v_CREB1_phosphorylated1v_IRF71v_IRF71v_IKK1_phosphorylated1v_IKK2_phosphorylated1v_PRKCQ1v_AKT1_phosphorylated1v_TAK1_phosphorylated1v_TRAF6_ubiquitinated1v_IL10R1_IL10R2_complex1v_IL10_M2_macrophage__extracellular_space1v_IL10_M2_macrophage__secreted_components1v_STAT3_STAT3_complex1v_klf41v_C_EBPb_phosphorylated1v_FOXO11v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_CREB1_phosphorylated1v_C_EBPb_phosphorylated1v_NFAT5_phosphorylated1v_IL18_M2_macrophage__cytoplasm1v_NLRP3_INFLAMMASOME_complex1v_NLRP3_INFLAMMASOME_complex1v_IL23R_IL12RB1_complex1v_IL23_M2_macrophage__extracellular_space1v_IL23_M2_macrophage__secreted_components1v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_STAT3_STAT3_complex1v_STAT6_STAT6_complex1v_STAT6_STAT6_complex1v_IL41v_IL4R1v_klf41v_CREB1_phosphorylated1v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_NFAT5_phosphorylated1v_IL8_M2_macrophage__secreted_components1v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_PIP2_simple_molecule1v_PLCG21v_IKK_complex1v_OPN1v_JNK1_phosphorylated_M2_macrophage__cytoplasm1v_col4a41v_ITGB1_ITGA1_complex1v_col4a51v_ITGB1_ITGA1_complex1v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_CREB1_phosphorylated1v_C_EBPb_phosphorylated1v_LIFR_IL6ST_CTF1_complex1v_IL11Ra_IL6ST_IL11_complex1v_IL23R_IL12RB1_IL23_complex1v_IL10R1_IL10R2_IL10_complex1v_IL4_IL4Ra_complex1v_PRL_PRLR_complex1v_CCL21_CCR7_complex1v_MKK7_phosphorylated1v_MKK4_phosphorylated1v_ASK11v_Rac11v_JNK1_phosphorylated_M2_macrophage__cytoplasm1v_AKT1_phosphorylated1v_TPL21v_RAF11v_TPL21v_RAF11v_CREB1_phosphorylated1v_ASK11v_ASK11v_MEKK11v_ASK11v_ASK11v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_CREB1_phosphorylated1v_C_EBPb_phosphorylated1v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_CREB1_phosphorylated1v_C_EBPb_phosphorylated1v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_CREB1_phosphorylated1v_C_EBPb_phosphorylated1v_p38_MAP_KINASE_phosphorylated_M2_macrophage_nucleus1v_MMP31v_MMP141v_MMP91v_PDGFC1v_col4a31v_CREB1_phosphorylated1v_ERK1_phosphorylated_M2_macrophage__cytoplasm1v_p38_MAP_KINASE_phosphorylated_M2_macrophage__cytoplasm1v_NFKB1_TPL2_complex1v_IKK_complex1v_IKK_complex1v_Syk_phosphorylated1v_NFKBIA_RELA_NFKB1_complex1v_RELA_NFKB1_NFKBIE_complex1v_IKK1_IKK2_complex1v_TAK1_phosphorylated1v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_NLRP31v_Casp11v_ASC1v_C_EBPb_phosphorylated1v_Syk_phosphorylated1v_C5a_C5aR1_complex1v_GAB2_phosphorylated1v_HRAS1v_CSF1R_CSF1_complex1v_VegfR1_vegfb_complex1v_VegfR1_Vegfa_complex1v_VegfR2_vegfc_nrp2_complex1v_TGFBR1_TGFBR2_TGFB1_complex1v_Src1v_GNB_GNG_complex1v_GAS6_MERTK_complex1v_PIK3AP1_phosphorylated1v_CD40LG_ITGB1_ITGA1_complex1v_PTK21v_JAK1_TYK2_complex1v_TRAF6_ubiquitinated1v_SHIP11v_PTPN61v_SYK1v_Syk_phosphorylated1v_PI3K1v_VegfR1_Vegfa_complex1v_VegfR1_vegfb_complex1v_GNB_GNG_complex1v_C_EBPb_phosphorylated1v_DAG_simple_molecule1v_SH2D1A1v_PRL1v_ITGB1_ITGA1_col4a_complex1v_HLA_B_LILRB1_complex1v_C5a_C5aR1_complex1v_CSF1R_CSF1_complex1v_CSFR1R_IL34_complex1v_AKT1_phosphorylated1v_PRKCD1v_HRAS1v_SMAD2_SMAD4_complex1v_IKK_complex1v_Syk_phosphorylated1v_NFKBIA_RELA_NFKB1_complex1v_RELA_NFKB1_NFKBIE_complex1v_IKK1_IKK2_complex1v_RELA_NFKB1_complex_M2_macrophage__cytoplasm1v_Prkcd1v_Sirt11v_GNA12_GNA13_complex1v_ARHGEF121v_AKT1_phosphorylated1v_Dvl11v_NRP1_PLXNA1_sema3A_complex1v_RHOA1v_SEMA4_PLXNB2_MET_complex1v_SMAD2_SARA_complex1v_TGFBR1_TGFBR2_TGFB1_complex1v_SMAD71v_SEMA4A_M2_macrophage__secreted_components1v_C_EBPb_phosphorylated1v_SEMA4D1v_PLXNB2_MET_complex1v_SEMA4A_M2_macrophage__extracellular_space1v_PLXNB2_MET_complex1v_immune_complex_CD32b_complex1v_SMAD2_phosphorylated1v_SMAD41v_SMAD2_SARA_complex1v_TGFBR1_TGFBR2_TGFB1_complex1v_SMAD71v_Grb21v_JAK11v_JAK1_TYK2_complex1v_JAK21v_STAT31v_JAK11v_JAK1_TYK2_complex1v_STAT61v_PTPN61v_TGFBR1_TGFBR2_TGFB1_complex1v_VegfR2_vegfc_nrp2_complex1v_Src1v_JAK21v_JAK1_TYK2_complex1v_GNAI31v_HCK1v_immune_complex_CD16a_complex1v_immune_complex_CD32a_complex1v_immune_complex_CD64_complex1v_TGFBR1_TGFBR2_TGFB1_complex1v_NLK_phosphorylated1v_TGFB1_M2_macrophage__secreted_components1v_TGFB1_M2_macrophage__extracellular_space1v_TGFBR1_TGFBR2_complex1v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_CREB1_phosphorylated1v_C_EBPb_phosphorylated1v_NFKB1_TPL2_complex1v_IKK_complex1v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_NFAT5_phosphorylated1v_IL17Ra_IL17Rc_IL17F_complex1v_TRAF3IP2_phosphorylated1v_CYLD1v_CSF1_M2_macrophage__secreted_components1v_CCL181v_CD861v_VEGFa_M2_macrophage__secreted_components1v_Vegfa_rna1v_VEGFa_M2_macrophage__extracellular_space1v_VegfR11v_Vegfb_M2_macrophage__extracellular_space1v_VegfR11v_Vegfc_M2_macrophage__extracellular_space1v_NFAT5_phosphorylated1v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_C_EBPb_phosphorylated1v_STAT3_STAT3_complex1v_Vegfb_M2_macrophage__secreted_components1v_NFAT5_phosphorylated1v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_CREB1_phosphorylated1v_C_EBPb_phosphorylated1v_STAT3_STAT3_complex1v_Vegfc_M2_macrophage__secreted_components1v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_C_EBPb_phosphorylated1v_NFAT5_phosphorylated1v_STAT3_STAT3_complex1v_CREB1_phosphorylated1v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_OPN1v_Vegfc_M2_macrophage__secreted_components1v_VEGFa_M2_macrophage__secreted_components1v_Vegfb_M2_macrophage__secreted_components1v_CASP81v_CASP31v_CASP71v_p53_phosphorylated_M2_macrophage__cytoplasm1v_Bim1v_FASL_M2_macrophage__secreted_components1v_NLRP3_INFLAMMASOME_complex1v_RXRa_NUR77_complex1v_BCL2_M2_macrophage_mitochondrion_membrane_active1v_mcl11v_BCL2L11v_FASL_M2_macrophage__secreted_components1v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_cFLIP1v_ITCH_phosphorylated1v_c_Myc_rna1v_cMyc1v_ERK1_phosphorylated_M2_macrophage__cytoplasm1v_STAT3_STAT3_complex1v_RBL1_E2F4_DP1_complex1v_immune_complex_complex1v_C5a_C5aR1_complex1v_immune_complex_complex1v_CD32a1v_C5a_C5aR1_complex1v_immune_complex_complex1v_immune_complex_complex1v_C5a_C5aR1_complex1v_C5a_C5aR1_complex1v_CCL201v_COX2_rna1v_IL151v_IRF71v_RELA_NFKB1_complex_M2_macrophage_nucleus1v_IL23_M2_macrophage__secreted_components1v_CCL181v_SEMA4A_M2_macrophage__secreted_components1v_sema7a1v_PPARg_rna1v_TGFB1_M2_macrophage__secreted_components1v_IL10_M2_macrophage__secreted_components1v_ARRB21v_STAT3_STAT3_complex1v_Mcl1_rna1v_FOXO11v_SMAD2_SMAD4_complex1v_MKK3_phosphorylated1v_MKK6_phosphorylated1v_C5a_C5aR1_complex1v_DUSP11v_p38_MAP_KINASE_phosphorylated_M2_macrophage__cytoplasm1v_cMyc_phosphorylated1v_p531v_MDM2_phosphorylated1v_p53_phosphorylated_M2_macrophage__cytoplasm1v_XIAP1v_ERK1_phosphorylated_M2_macrophage_nucleus1v_p38_MAP_KINASE_phosphorylated_M2_macrophage_nucleus1v_BCL2L11v_MDM2_phosphorylated1v_CREB1_phosphorylated1v_TGFB1_M2_macrophage__secreted_components1v_cFLIP1v_BCL3_rna1v_Vegfc_M2_macrophage__secreted_components1v_CSF1_M2_macrophage__secreted_components1v_IL8_M2_macrophage__secreted_components1v_VEGFa_M2_macrophage__secreted_components1v_Vegfb_M2_macrophage__secreted_components1v_HBGEF1v_cMyc_phosphorylated1v_p15_rna1v_IL151v_PDGFC1v_Vegfc_M2_macrophage__secreted_components1v_Vegfb_M2_macrophage__secreted_components1v_IL8_M2_macrophage__secreted_components1v_VEGFa_M2_macrophage__secreted_components1v_CSF1_M2_macrophage__secreted_components1v_TGFB1_M2_macrophage__secreted_components1v_C_EBPb_phosphorylated1v_ARI_ARII_bmp6_complex1v_smad1_phosphorylated1v_SMAD41v_Vegfc_M2_macrophage__extracellular_space1 \ No newline at end of file diff --git a/models/summary.csv b/models/summary.csv index 7a86eb1..b66ca2e 100644 --- a/models/summary.csv +++ b/models/summary.csv @@ -237,3 +237,5 @@ ID, name, variables, inputs, regulations 236, BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE, 109, 8, 263 237, COLORECTAL-TUMORIGENESIS-REVERSION-SWITCH, 17, 0, 44 238, DNA-DAMAGE-INDUCED-FERROPTOSIS, 33, 1, 89 +239, M1-SYNOVIAL-MACROPHAGE, 234, 69, 562 +240, M2-SYNOVIAL-MACROPHAGE, 197, 52, 430 diff --git a/sources/239_M1-SYNOVIAL-MACROPHAGE/citation.bib b/sources/239_M1-SYNOVIAL-MACROPHAGE/citation.bib new file mode 100644 index 0000000..97af942 --- /dev/null +++ b/sources/239_M1-SYNOVIAL-MACROPHAGE/citation.bib @@ -0,0 +1,10 @@ +@article{bbm-239, + title={Large-scale computational modelling of the M1 and M2 synovial macrophages in rheumatoid arthritis}, + author={Zerrouk, Naouel and Alcraft, Rachel and Hall, Benjamin A and Aug{\'e}, Franck and Niarakis, Anna}, + journal={npj Systems Biology and Applications}, + volume={10}, + number={1}, + pages={10}, + year={2024}, + publisher={Nature Publishing Group UK London} +} \ No newline at end of file diff --git a/sources/239_M1-SYNOVIAL-MACROPHAGE/metadata.json b/sources/239_M1-SYNOVIAL-MACROPHAGE/metadata.json new file mode 100644 index 0000000..95340d8 --- /dev/null +++ b/sources/239_M1-SYNOVIAL-MACROPHAGE/metadata.json @@ -0,0 +1,7 @@ +{ + "id": 239, + "name": "M1-SYNOVIAL-MACROPHAGE", + "url-publication": "https://doi.org/10.1038/s41540-024-00337-5", + "url-model": "https://www.ebi.ac.uk/biomodels/MODEL2307180001", + "keywords": ["biomodels", "curated", "casq", "repaired"] +} \ No newline at end of file diff --git a/sources/239_M1-SYNOVIAL-MACROPHAGE/notes.md b/sources/239_M1-SYNOVIAL-MACROPHAGE/notes.md new file mode 100644 index 0000000..df73bd0 --- /dev/null +++ b/sources/239_M1-SYNOVIAL-MACROPHAGE/notes.md @@ -0,0 +1,3 @@ +### Modifications + +Removed unused variables: `EDA`, `HLA_DP_DQ_DR`, `ICOSLG`, `LGALS9`, `LILRB1`, `notch1`. \ No newline at end of file diff --git a/sources/239_M1-SYNOVIAL-MACROPHAGE/source.raw.sbml b/sources/239_M1-SYNOVIAL-MACROPHAGE/source.raw.sbml new file mode 100644 index 0000000..7f826cc --- /dev/null +++ b/sources/239_M1-SYNOVIAL-MACROPHAGE/source.raw.sbml @@ -0,0 +1,23399 @@ + + + + + + +

Created by CaSQ 1.3.0

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<apply> + <eq/> + <ci> sa2444 </ci> + <cn type="integer"> 1 </cn> + </apply> + <apply> + <eq/> + <ci> sa2442 </ci> + <cn type="integer"> 1 </cn> + </apply> + <apply> + <eq/> + <ci> sa2443 </ci> + <cn type="integer"> 1 </cn> + </apply> + <apply> + <eq/> + <ci> sa2441 </ci> + <cn type="integer"> 1 </cn> + </apply> + <apply> + <eq/> + <ci> sa3184 </ci> + <cn type="integer"> 1 </cn> + </apply> + </apply> + </math> + </qual:functionTerm> + </qual:listOfFunctionTerms> + </qual:transition> + <qual:transition qual:id="tr_sa3801"> + <qual:listOfInputs> + <qual:input qual:id="tr_sa3801_in_0" qual:qualitativeSpecies="sa2439" qual:sign="positive" qual:transitionEffect="none"/> + </qual:listOfInputs> + <qual:listOfOutputs> + <qual:output qual:id="tr_sa3801_out" qual:qualitativeSpecies="sa3801" qual:transitionEffect="assignmentLevel"/> + </qual:listOfOutputs> + <qual:listOfFunctionTerms> + <qual:defaultTerm qual:resultLevel="0"> + </qual:defaultTerm> + <qual:functionTerm qual:resultLevel="1"> + <math xmlns="http://www.w3.org/1998/Math/MathML"> + <apply> + <eq/> + <ci> sa2439 </ci> + <cn type="integer"> 1 </cn> + </apply> + </math> + </qual:functionTerm> + </qual:listOfFunctionTerms> + </qual:transition> + <qual:transition qual:id="tr_sa3802"> + <qual:listOfInputs> + <qual:input qual:id="tr_sa3802_in_0" qual:qualitativeSpecies="sa2106" qual:sign="positive" qual:transitionEffect="none"/> + <qual:input qual:id="tr_sa3802_in_1" qual:qualitativeSpecies="sa2279" qual:sign="positive" qual:transitionEffect="none"/> + <qual:input qual:id="tr_sa3802_in_2" qual:qualitativeSpecies="sa2441" qual:sign="positive" qual:transitionEffect="none"/> + <qual:input qual:id="tr_sa3802_in_3" qual:qualitativeSpecies="sa2442" qual:sign="positive" qual:transitionEffect="none"/> + <qual:input qual:id="tr_sa3802_in_4" qual:qualitativeSpecies="sa2103" qual:sign="positive" qual:transitionEffect="none"/> + <qual:input qual:id="tr_sa3802_in_5" qual:qualitativeSpecies="sa2065" qual:sign="positive" qual:transitionEffect="none"/> + <qual:input qual:id="tr_sa3802_in_6" qual:qualitativeSpecies="sa2060" qual:sign="positive" qual:transitionEffect="none"/> + </qual:listOfInputs> + <qual:listOfOutputs> + <qual:output qual:id="tr_sa3802_out" qual:qualitativeSpecies="sa3802" qual:transitionEffect="assignmentLevel"/> + </qual:listOfOutputs> + <qual:listOfFunctionTerms> + <qual:defaultTerm qual:resultLevel="0"> + </qual:defaultTerm> + <qual:functionTerm qual:resultLevel="1"> + <math xmlns="http://www.w3.org/1998/Math/MathML"> + <apply> + <or/> + <apply> + <eq/> + <ci> sa2106 </ci> + <cn type="integer"> 1 </cn> + </apply> + <apply> + <eq/> + <ci> sa2279 </ci> + <cn type="integer"> 1 </cn> + </apply> + <apply> + <eq/> + <ci> sa2441 </ci> + <cn type="integer"> 1 </cn> + </apply> + <apply> + <eq/> + <ci> sa2442 </ci> + <cn type="integer"> 1 </cn> + </apply> + <apply> + <eq/> + <ci> sa2103 </ci> + <cn type="integer"> 1 </cn> + </apply> + <apply> + <eq/> + <ci> sa2065 </ci> + <cn type="integer"> 1 </cn> + </apply> + <apply> + <eq/> + <ci> sa2060 </ci> + <cn type="integer"> 1 </cn> + </apply> + </apply> + </math> + </qual:functionTerm> + </qual:listOfFunctionTerms> + </qual:transition> + <qual:transition qual:id="tr_sa3803"> + <qual:listOfInputs> + <qual:input qual:id="tr_sa3803_in_0" qual:qualitativeSpecies="sa2439" qual:sign="positive" qual:transitionEffect="none"/> + </qual:listOfInputs> + <qual:listOfOutputs> + <qual:output qual:id="tr_sa3803_out" qual:qualitativeSpecies="sa3803" qual:transitionEffect="assignmentLevel"/> + </qual:listOfOutputs> + <qual:listOfFunctionTerms> + <qual:defaultTerm qual:resultLevel="0"> + </qual:defaultTerm> + <qual:functionTerm qual:resultLevel="1"> + <math xmlns="http://www.w3.org/1998/Math/MathML"> + <apply> + <eq/> + <ci> sa2439 </ci> + <cn type="integer"> 1 </cn> + </apply> + </math> + </qual:functionTerm> + </qual:listOfFunctionTerms> + </qual:transition> + <qual:transition qual:id="tr_sa3808"> + <qual:listOfInputs> + <qual:input qual:id="tr_sa3808_in_0" qual:qualitativeSpecies="sa2127" qual:sign="positive" qual:transitionEffect="none"/> + </qual:listOfInputs> + <qual:listOfOutputs> + <qual:output qual:id="tr_sa3808_out" qual:qualitativeSpecies="sa3808" qual:transitionEffect="assignmentLevel"/> + </qual:listOfOutputs> + <qual:listOfFunctionTerms> + <qual:defaultTerm qual:resultLevel="0"> + </qual:defaultTerm> + <qual:functionTerm qual:resultLevel="1"> + <math xmlns="http://www.w3.org/1998/Math/MathML"> + <apply> + <eq/> + <ci> sa2127 </ci> + <cn type="integer"> 1 </cn> + </apply> + </math> + </qual:functionTerm> + </qual:listOfFunctionTerms> + </qual:transition> + <qual:transition qual:id="tr_sa3809"> + <qual:listOfInputs> + <qual:input qual:id="tr_sa3809_in_0" qual:qualitativeSpecies="sa2132" qual:sign="positive" qual:transitionEffect="none"/> + </qual:listOfInputs> + <qual:listOfOutputs> + <qual:output qual:id="tr_sa3809_out" qual:qualitativeSpecies="sa3809" qual:transitionEffect="assignmentLevel"/> + </qual:listOfOutputs> + <qual:listOfFunctionTerms> + <qual:defaultTerm qual:resultLevel="0"> + </qual:defaultTerm> + <qual:functionTerm qual:resultLevel="1"> + <math xmlns="http://www.w3.org/1998/Math/MathML"> + <apply> + <eq/> + <ci> sa2132 </ci> + <cn type="integer"> 1 </cn> + </apply> + </math> + </qual:functionTerm> + </qual:listOfFunctionTerms> + </qual:transition> + <qual:transition qual:id="tr_sa3812"> + <qual:listOfInputs> + <qual:input qual:id="tr_sa3812_in_0" qual:qualitativeSpecies="sa2029" qual:sign="negative" qual:transitionEffect="none"/> + <qual:input qual:id="tr_sa3812_in_1" qual:qualitativeSpecies="sa2038" qual:sign="negative" qual:transitionEffect="none"/> + </qual:listOfInputs> + <qual:listOfOutputs> + <qual:output qual:id="tr_sa3812_out" qual:qualitativeSpecies="sa3812" qual:transitionEffect="assignmentLevel"/> + </qual:listOfOutputs> + <qual:listOfFunctionTerms> + <qual:defaultTerm qual:resultLevel="0"> + </qual:defaultTerm> + <qual:functionTerm qual:resultLevel="1"> + <math xmlns="http://www.w3.org/1998/Math/MathML"> + <apply> + <and/> + <apply> + <eq/> + <ci> sa2029 </ci> + <cn type="integer"> 0 </cn> + </apply> + <apply> + <eq/> + <ci> sa2038 </ci> + <cn type="integer"> 0 </cn> + </apply> + </apply> + </math> + </qual:functionTerm> + </qual:listOfFunctionTerms> + </qual:transition> + </qual:listOfTransitions> + <listOfCompartments> + <compartment constant="true" id="comp1"/> + </listOfCompartments> + </model> +</sbml> \ No newline at end of file