import boolean2
import pylab
from boolean2 import util
#Define the initial conditions for each node in the network (either TRUE or FALSE)
text = """
ABCA1 = False
ABCB1 = False
ABCC3 = False
ABCG2 = False
ACAT1 = False
ACO2 = False
ACSF2 = False
ACTC1 = False
ACTR3 = False
ACVRL1 = False
ADAM10 = False
ADAM28 = False
ADAMDEC1 = False
ADAMTS10 = False
ADAMTS5 = False
ADAR = False
ADCY1 = False
ADGRE5 = False
ADH5 = False
ADIPOQ = False
ADORA1 = False
ADRA2B = False
ADRB2 = False
ADRBK1 = False
AES = False
AFG3L2 = False
AGAP7 = False
AGER = False
AHCTF1 = False
AHR = False
AIG1 = False
AKAP13 = False
AKR1C1 = False
AKR1C2 = False
AKT1 = False
AKT2 = False
ALAS1 = False
ALDH1A1 = False
ALOX12 = False
ALOX5 = False
ALX1 = False
AMH = False
AMICA1 = False
ANG = False
ANGPT = False
ANGPTL4 = False
ANKRD33B = False
ANPEP = False
AP1S2 = False
AP2A1 = False
AP2M1 = False
APAF1 = False
APBB3 = False
APC = False
APCDD1 = False
APEX1 = False
APOBEC3A = False
APOBEC3B = False
APOBEC3F = False
APOBEC3G = False
APOBEC3H = False
APOC3 = False
AQP1 = False
AQR = False
AR = False
ARC = False
AREG = False
ARF = False
ARG1 = False
ARHGEF16 = False
ARHGEF2 = False
ARID5A = False
ARSG = False
ASAP2 = False
ASCL1 = False
ASNS = False
ASS1 = False
ATF = False
ATG16L1 = False
ATG5 = False
ATG7 = False
ATM = False
ATP13A3 = False
ATP2C1 = False
ATP5A1 = False
ATP5B = False
ATXN2 = False
AVPR2 = False
AXIN = False
AXL = False
B2M = False
BACE1 = False
BAD = False
BAK1 = False
BAMBI = False
BAX = False
BBC3 = False
BCAR1 = False
BCAS4 = False
BCL11A = False
BCL2 = False
BCL2A1 = False
BCL2L1 = False
BCL2L11 = False
BCL3 = False
BCL6 = False
BCL9L = False
BCLXL = False
BCR = False
BDKRB2 = False
BECN1 = False
BEX1 = False
BGLAP = False
BHLHE41 = False
BIN1 = False
BIRC3 = False
BIRC5 = False
BLK = False
BMI1 = False
BMP2 = False
BMP2K = False
BRCA1 = False
BRCA2 = False
BRD7 = False
BST2 = False
BTG2 = False
BTNL9 = False
BTRC = False
C1QA = False
C1QL4 = False
C1S = False
C2orf91 = False
C3AR1 = False
C7orf29 = False
C9orf89 = False
CAD = False
CALD1 = False
CAMP = False
CAPNS1 = False
CASP1 = False
CASP3 = False
CASP7 = False
CASP8 = False
CASP9 = False
CAV1 = False
CAV2 = False
CBFB = False
CCK = False
CCL11 = False
CCL2 = False
CCL20 = False
CCL21 = False
CCL22 = False
CCL3 = False
CCL4 = False
CCL5 = False
CCNA1 = False
CCNA2 = False
CCNB1 = False
CCND1 = False
CCND2 = False
CCND3 = False
CCNE1 = False
CCNG2 = False
CCNI = False
CCNT1-CDK9 = False
CCR1 = False
CCR10 = False
CCR2 = False
CCR3 = False
CCR4 = False
CCR5 = False
CCR7 = False
CCRN4L = False
CD14 = False
CD151 = False
CD163 = False
CD19 = False
CD1D = False
CD207 = False
CD209 = False
CD22 = False
CD27 = False
CD274 = False
CD28 = True
CD2AP = False
CD300LB = False
CD36 = False
CD38 = False
CD3G = False
CD4 = False
CD40 = False
CD40LG = False
CD44 = False
CD46 = False
CD52 = False
CD58 = False
CD59 = False
CD79A = False
CD80 = False
CD81 = False
CD82 = False
CD83 = False
CD86 = False
CD9 = False
CD97 = False
CD99 = False
CDA = False
CDC25C = False
CDC40 = False
CDC42 = False
CDC42EP3 = False
CDH1 = False
CDH15 = False
CDH26 = False
CDK1 = False
CDK16 = False
CDK18 = False
CDK2 = False
CDK4 = False
CDK6 = False
CDKN1A = False
CDKN1B = False
CDKN1C = False
CDKN2A = False
CDKN2B = False
CDO1 = False
CDR2L = False
CEACAM1 = False
CEACAM6 = False
CEBP = False
CECR1 = False
CERS2 = False
CETP = False
CFLAR = False
CFP = False
CFTR = False
CHCHD10 = False
CHEK1 = False
CHEK2 = False
CHGA = False
CHN2 = False
CHRNE = False
CHUK = False
CIITA = False
CISH = False
CITED4 = False
CKM = False
CLDN2 = False
CLDN3 = False
CLDN7 = False
CLEC5A = False
CLIP4 = False
CLMN = False
CLTA = False
CLUHP3 = False
CNR1 = False
COL10A1 = False
COL11A2 = False
COL1A1 = False
COL1A2 = False
COL2A1 = False
COPS5 = False
CORO1A = False
CORO2B = False
COX6B1 = False
COX6B2 = False
CPT1A = False
CPT1B = False
CPZ = False
CREB3 = False
CREBBP = False
CREM = False
CRHR1 = False
CRISPLD2 = False
CRP = False
CRYAB = False
CSF1 = False
CSF3R = False
CSNK1A1 = False
CSRP1 = False
CST5 = False
CST7 = False
CSTB = False
CTBP1 = False
CTCF = False
CTGF = False
CTNNB1 = False
CTPS1 = False
CTSB = False
CTSD = False
CTSL = False
CTSS = False
CTSZ = False
CXADR = False
CXCL1 = False
CXCL10 = False
CXCL12 = False
CXCL14 = False
CXCL5 = False
CXCL8 = False
CXCL9 = False
CXCR1 = False
CXCR2 = False
CXCR4 = False
CXCR5 = False
CXorf21 = False
CYBB = False
CYCS = False
CYFIP2 = False
CYLD = False
CYP17A1 = False
CYP19A1 = False
CYP1B1 = False
CYP24A1 = False
CYP26B1 = False
CYP27A1 = False
CYP27B1 = False
CYP2C8 = False
CYP2E1 = False
CYP3A4 = False
CYP7A1 = False
DAPK2 = False
DBF4 = False
DBH = False
DDB2 = False
DDIT4 = False
DDX26B = False
DDX58 = False
DEFA1 = False
DEFA3 = False
DEFA4 = False
DEFB1 = False
DEFB103B = False
DEFB4A = False
DEFB4B = False
DENND6B = False
DEPTOR = False
DFNB31 = False
DHFR = False
DICER1 = False
DKK1 = False
DLL1 = False
DNAH10 = False
DNAJB4 = False
DNASE2 = False
DNM2 = False
DNM3 = False
DNMT1 = False
DNMT3A = False
DOCK10 = False
DPF3 = False
DR1 = False
DRAM1 = False
DROSHA = False
DST = False
DTX4 = False
DUSP1 = False
DVL1 = False
DVL2 = False
E2F1 = False
E2F3 = False
E2F6 = False
E2F7 = False
EAF2 = False
EAPP = False
EBI3 = False
EBNA1BP2 = False
EDN1 = False
EDNRB = False
EEF2 = False
EFCAB12 = False
EFNB1 = False
EGF = False
EGFR = False
EGLN1 = False
EGLN3 = False
EGR1 = False
EGR3 = False
EIF2AK1 = False
EIF2AK2 = False
EIF2B5 = False
EIF4G1 = False
ELF = False
ELFN2 = False
ELL = False
EMID1 = False
EN2 = False
EP300 = False
EPAS1 = False
EPB41L1 = False
EPCAM = False
EPO = False
ERBB2 = False
ERBB3 = False
ERCC1 = False
ERCC5 = False
ERG = False
ERICD = False
ESR = False
ESRRA = False
ETF1 = False
ETS1 = False
ETS2 = False
ETV1 = False
ETV3 = False
ETV4 = False
ETV6 = False
EXT1 = False
EZH2 = False
EZR = False
F11R = False
F13A1 = False
F2R = False
F3 = False
FABP1 = False
FABP3 = False
FADS3 = False
FAF1 = False
FAIM3 = False
FAM116B = False
FAM179A = False
FAM200B = False
FANCE = False
FANCM = False
FAS = False
FASLG = False
FBP1 = False
FCER1A = False
FCER2 = False
FCN2 = False
FENDRR = False
FFAR2 = False
FGF2 = False
FGF7 = False
FGF8 = False
FGFR1 = False
FGFR3 = False
FGR = False
FLI1 = False
FLJ34208 = False
FLJ44511 = False
FLT1 = False
FLT3 = False
FMNL2 = False
FMR1 = False
FN1 = False
FOS = False
FOSL1 = False
FOSL2 = False
FOXC1 = False
FOXD3 = False
FOXF1 = False
FOXM1 = False
FOXO = False
FOXP3 = False
FRIZZLED = False
FST = False
FTH1P18 = False
FUCA1 = False
FXR2 = False
FXYD6 = False
FZD6 = False
G6PD = False
GABARAP = False
GABARAPL2 = False
GAD1 = False
GADD45A = False
GADD45B = False
GALT = False
GAPDH = False
GAPVD1 = False
GAST = False
GATA1 = False
GATA2 = False
GATA3 = False
GATA6 = False
GCK = False
GDF15 = False
GEMIN2 = False
GFAP = False
GFER = False
GH2 = False
GJA1 = False
GJD3 = False
GLIPR1 = False
GM2A = False
GML = False
GMPR = False
GNAI1 = False
GNLY = False
GOLPH3 = False
GOT1 = False
GP1BB = False
GPA33 = False
GPER = False
GPLD1 = False
GPR114 = False
GPR65 = False
GPR84 = False
GPT2 = False
GRIA2 = False
GRIN2B = False
GRK5 = False
GSK3B = False
GSN = False
GSTP1 = False
GTF2B = False
H19 = False
HAMP = False
HAP1 = False
HAS2 = False
HAVCR2 = False
HBEGF = False
HDAC1 = False
HDAC2 = False
HDAC3 = False
HDAC4 = False
HDAC7 = False
HES1 = False
HEXIM1 = False
HEY1 = False
HGF = False
HGS = False
HHLA2 = False
HIC1 = False
HIF1A = False
HIPK2 = False
HIST1H2AC = False
HIV = True
HLA-A = False
HLA-B = False
HLA-C = False
HLA-DOA = False
HLA-DRA = False
HLA-DRB1 = False
HMGA1 = False
HMGA2 = False
HMGB1 = False
HMGCS1 = False
HMOX1 = False
HMSD = False
HNF4A = False
HNRNPA2B1 = False
HOXA10 = False
HOXA9 = False
HOXB13 = False
HP = False
HPSE = False
HSD11B1 = False
HSD17B1 = False
HSD17B11 = False
HSD17B2 = False
HSF1 = False
HSP90AA1 = False
HSPA4 = False
HSPA5 = False
HSPD1 = False
HTR1A = False
HTT = False
HYAL1 = False
ICAM1 = False
ICAM2 = False
ID = False
IDO1 = False
IFI16 = False
IFI27 = False
IFI44 = False
IFI44L = False
IFIT1 = False
IFIT3 = False
IFITM = False
IFNA = False
IFNAR1 = False
IFNB1 = False
IFNG = False
IFNGR1 = False
IGF1 = False
IGF1R = False
IGF2 = False
IGFBP3 = False
IGFBP7 = False
IGK = False
IGLV6-57 = False
IGSF9 = False
IKBKB = False
IKBKE = False
IL10 = False
IL12 = False
IL12A = False
IL12B = False
IL13 = False
IL15 = False
IL17 = False
IL17A = False
IL17C = False
IL18 = False
IL18R1 = False
IL1A = False
IL1B = False
IL1RL1 = False
IL1RN = False
IL2 = False
IL21 = False
IL22 = False
IL22RA1 = False
IL23A = False
IL23R = False
IL27 = False
IL27RA = False
IL2RA = False
IL2RB = False
IL2RG = False
IL3 = False
IL33 = False
IL4 = False
IL5 = False
IL6 = False
IL6ST = False
IL7 = False
IL7R = False
IL8 = False
ILK = False
INS = False
INSR = False
IPO7 = False
IRF1 = False
IRF2 = False
IRF3 = False
IRF4 = False
IRF5 = False
IRF7 = False
IRF8 = False
IRF9 = False
IRS1 = False
ITGA2B = False
ITGA4 = False
ITGA5 = False
ITGAD = False
ITGAV = False
ITGAX = False
ITGB2 = False
ITGB7 = False
JAG1 = False
JAK = True
JUN = False
JUNB = False
KALRN = False
KAT2A = False
KAT6A = False
KCNA3 = False
KCNF1 = False
KCNK5 = False
KCNQ2 = False
KCNQ3 = False
KCTD12 = False
KCTD17 = False
KDM6B = False
KHDRBS3 = False
KIAA0040 = False
KIAA1211L = False
KIAA1324L = False
KIF17 = False
KIF2B = False
KIR3DL1 = False
KIR3DS1 = False
KIT = False
KLF = False
KLK3 = False
KPNB1 = False
KRAS = False
KRT16 = False
KRT17 = False
KRT4 = False
KRT7 = False
LAG3 = False
LAMA1 = False
LAMA3 = False
LC3 = False
LCK = False
LCP2 = False
LDHA = False
LDLR = False
LDLRAD3 = False
LEF1 = False
LEFTY1 = False
LEP = False
LFNG = False
LGALS3 = False
LGALS3BP = False
LGALS9 = False
LILRA1 = False
LILRB4 = False
LIMK2 = False
LINC00086 = False
LIPE = False
LMO2 = False
LMP1 = False
LNX1 = False
LOR = False
LPAR = False
LPGAT1 = False
LPL = False
LPO = False
LRP1 = False
LRP4 = False
LRP5 = False
LRP6 = False
LRRC3B = False
LRRC8A = False
LRRC8D = False
LSP1 = False
LTBP1 = False
LTC4S = False
LTF = False
LTK = False
LY96 = False
MAD2L1 = False
MAP2K1 = False
MAP3K2 = False
MAP3K7 = False
MAP4 = False
MAPK1 = False
MAPK13 = False
MAPK14 = False
MAPK3 = False
MAPK3_2 = False
MAPK7 = False
MAPK8 = False
MAPK9 = False
MARCKS = False
MAT2A = False
MAT2B = False
MBP = False
MCHR1 = False
MCL1 = False
MDM2 = False
MECOM = False
MEF2C = False
MEF2D = False
MET = False
MICA = False
MICA_SP1 = False
MITF = False
MKI67 = False
MLC = False
MLC1 = False
MLPH = False
MMP1 = False
MMP13 = False
MMP14 = False
MMP2 = False
MMP3 = False
MMP7 = False
MMP9 = False
MPEG1 = False
MPO = False
MPP3 = False
MPZL1 = False
MRC1 = False
MRS2 = False
MS4A14 = False
MS4A7 = False
MSC = False
MSN = False
MSR1 = False
MST1 = False
MT2A = False
MTA1 = False
MTOR = False
MUC1 = False
MUC2 = False
MUC4 = False
MX1 = False
MX2 = False
MXI1 = False
MYB = False
MYBL2 = False
MYBPH = False
MYC = False
MYCN = False
MYLK = False
MYOZ1 = False
NAB2 = False
NACC2 = False
NAMPT = False
NANOG = False
NAPSB = False
NBEAL2 = False
NCAM1 = False
NCF1 = False
NCF1B = False
NCF1C = False
NCOR1 = False
NCOR2 = False
NCR3LG1 = False
NDST3 = False
NDUFA10 = False
NDUFA6 = False
NDUFAF4 = False
NDUFB7 = False
NDUFS6 = False
NDUFS7 = False
NDUFV1 = False
NDUFV2 = False
NECTIN1 = False
NEDD4L = False
NEFL = False
NEGR1 = False
NEO1 = False
NEUROG3 = False
NF1 = False
NFAT = False
NFATC1 = False
NFE2 = False
NFKB = False
NFKBIA = False
NGEF = False
NIM1 = False
NINJ1 = False
NKX3-1 = False
NLRP12 = False
NME1 = False
NMNAT2 = False
NOD2 = False
NOG = False
NOL7 = False
NOS2 = False
NOS3 = False
NOTCH1 = False
NOX4 = False
NOX5 = False
NPAS4 = False
NPTX1 = False
NPTX2 = False
NR0B2 = False
NR1H4 = False
NR1I2 = False
NR2F1 = False
NR3C1 = False
NR4A1 = False
NR4A2 = False
NRAS = False
NREP = False
NRF1 = False
NRIP1 = False
NRXN1 = False
NTN1 = False
NTNG2 = False
NUP = False
NXF1 = False
OCEL1 = False
OCLN = False
ODC1 = False
OGDHL = False
OLFML3 = False
OPRM1 = False
OPTN = False
ORM1 = False
OSM = False
OTOF = False
OTUD1 = False
OXTR = False
PARD6A = False
PARP1 = False
PAX = False
PCDH9 = False
PCK1 = False
PCK2 = False
PCNA = False
PCSK6 = False
PCTP = False
PDCD1LG2 = False
PDE5A = False
PDGFA = False
PDGFRL = False
PDIA2 = False
PDIA6 = False
PDK2 = False
PDK4 = False
PDLIM4 = False
PDPN = False
PDZD2 = False
PEBP1 = False
PER1 = False
PER2 = False
PERP = False
PEX5L = False
PF4 = False
PFKFB4 = False
PFKL = False
PFKM = False
PGAM2 = False
PGR = False
PHACTR1 = False
PHGDH = False
PI3 = False
PI3K = False
PIAS3 = False
PIK3C = False
PINX1 = False
PIP5K1C = False
PKIB = False
PLAU = False
PLAUR = False
PLCG1 = False
PLD1 = False
PLIN2 = False
PLK1 = False
PLOD157812 = False
PLOD162749 = False
PMAIP1 = False
PMEPA1 = False
PML = False
PMP22 = False
PNOC = False
PNPLA1 = False
POLB = False
POLR2A = False
POLR2C = False
POLR2H = False
POLR2I = False
POLR2K = False
POLR2L = False
POU = False
PPARA = False
PPARD = False
PPARG = False
PPFIBP1 = False
PPIA = False
PPP1R13B = False
PPP1R16B = False
PPP2R = False
PPP2R2B = False
PRDM1 = False
PRDM2 = False
PRDX3 = False
PRDX5 = False
PRF1 = False
PRICKLE1 = False
PRKACA = False
PRKC = False
PRKCE = False
PRKCH = False
PRKD1 = False
PRNP = False
PRODH = False
PROX1 = False
PRSS50 = False
PRUNE2 = False
PSMC5 = False
PTAFR = False
PTEN = False
PTGDS = False
PTGES = False
PTGIR = False
PTGS2 = False
PTH = False
PTHLH = False
PTK2B = False
PTMA = False
PTPN11 = False
PTPN14 = False
PTPN6 = False
PTPRE = False
PTPRF = False
PTPRK = False
PTPRN2 = False
PTPRS = False
PTTG1 = False
PTX3 = False
PURA = False
QPCT = False
RAB11FIP1 = False
RAB27A = False
RAB37 = False
RAB3A = False
RAC1 = False
RAF1 = False
RALB = False
RANBP1 = False
RANBP2 = False
RAP1A = False
RAP1B = False
RAPGEF1 = False
RARA_B = False
RARG = False
RAS = False
RASA4CP = False
RASGEF1A = False
RASGRP1 = False
RASSF1 = False
RB1 = False
RBL1 = False
RBL2 = False
RECQL4 = False
RELT = False
REPIN1 = False
RETN = False
RFC3 = False
RGS16 = False
RGS4 = False
RHOB = False
RHOH = False
RIPK2 = False
RNASE1 = False
RNASE2 = False
RNASE4 = False
RNASE7 = False
RNASEL = False
RND3 = False
RNPS1 = False
ROCK1 = False
ROR2 = False
RORC = False
RPRD2 = False
RPS27 = False
RPS6KA3 = False
RPS6KB1 = False
RRAGB = False
RRAS2 = False
RREB1 = False
RUNX = False
RXRA = False
S100A10 = False
S100A6 = False
S100A9 = False
SAA2 = False
SALL4 = False
SAMHD1 = False
SARDH = False
SARNP = False
SAT1 = False
SATB1 = False
SATB2 = False
SCARB1 = False
SCD = False
SCPEP1 = False
SDC1 = False
SDHD = False
SDS = False
SELE = False
SELPLG = False
SEMA4D = False
SEMA6A = False
SERINC3 = False
SERINC5 = False
SERPINA1 = False
SERPINA3 = False
SERPINB1 = False
SERPINB5 = False
SERPINB6 = False
SERPINC1 = False
SERPINE1 = False
SFT2D1 = False
SFTPD = False
SFXN3 = False
SFXN4 = False
SGK1 = False
SHANK1 = False
SHE = False
SHH = False
SIGIRR = False
SIGLEC1 = False
SIGLEC6 = False
SIK1 = False
SIM1 = False
SIRPG = False
SIRT1 = False
SIRT4 = False
SIVA = False
SKP2 = False
SLC17A7 = False
SLC19A1 = False
SLC20A1 = False
SLC22A23 = False
SLC25A20 = False
SLC25A27 = False
SLC25A4 = False
SLC29A1 = False
SLC2A1 = False
SLC2A3 = False
SLC31A1 = False
SLC37A2 = False
SLC46A1 = False
SLC4A7 = False
SLC51A = False
SLC5A5 = False
SLC5A8 = False
SLC6A12 = False
SLC6A6 = False
SLC7A1 = False
SLC7A2 = False
SLC9A1 = False
SLC9A3 = False
SLC9A9 = False
SLC9C2 = False
SLCO4C1 = False
SLPI = False
SLU7 = False
SMAD2 = False
SMAD3 = False
SMAD4 = False
SMAD7 = False
SMO = False
SNAI = False
SNRPA = False
SNRPC = False
SNRPD3 = False
SOCS = False
SOD1 = False
SOD2 = False
SOS1 = False
SOX7 = False
SOX9 = False
SP = False
SPARC = False
SPAST = False
SPI1 = False
SPN = False
SPP1 = False
SPRR1B = False
SPRY4 = False
SQSTM1 = False
SRC = False
SREBF1 = False
SRR = False
SRRM3 = False
SRSF1 = False
SRSF2 = False
SRSF6 = False
SSB = False
SSTR1 = False
SSTR2 = False
ST3GAL1 = False
ST3GAL3 = False
ST3GAL4 = False
ST3GAL5 = False
STAR = False
STARD7 = False
STAT1 = False
STAT2 = False
STAT3 = False
STAT4 = False
STAT5B = False
STAT6 = False
STEAP3 = False
STIM1 = False
STMN1 = False
STS = False
SUB1 = False
SULF2 = False
SULT1C2 = False
SUMO1 = False
SUMO2 = False
SURF1 = False
SURF2 = False
SUZ12 = False
SYCP2 = False
SYN1 = False
SYT3 = False
TAB2 = False
TAF7 = False
TAOK1 = False
TAP1 = False
TBC1D2 = False
TBL1X = False
TBP = False
TBX15 = False
TBX21 = False
TBX3 = False
TBXA2R = False
TBXAS1 = False
TCF4 = False
TCF7L2 = False
TCF7L2_LEF = False
TCFL5 = False
TCN1 = False
TDRD10 = False
TERF2 = False
TERT = False
TESPA1 = False
TFAP2A = False
TFAP4 = False
TFDP1 = False
TFE3 = False
TFEB = False
TFF1 = False
TGFB1 = False
TGFB3 = False
TGM2 = False
TGM5 = False
THBD = False
THBS1 = False
THEM4 = False
THEMIS2 = False
THOC2 = False
THOC6 = False
TIAM2 = False
TICAM1 = False
TIMP1 = False
TIMP3 = False
TJP1 = False
TK1 = False
TLE6 = False
TLR1 = True
TLR2 = True
TLR3 = True
TLR4 = True
TLR7 = True
TLR8 = True
TLR9 = True
TMEM136 = False
TMEM255A = False
TMEM37 = False
TMEM86A = False
TMPO = False
TNC = False
TNF = False
TNFA = False
TNFAIP3 = False
TNFAIP6 = False
TNFRSF10A = False
TNFRSF10B = False
TNFRSF10D = False
TNFRSF12A = False
TNFRSF13C = False
TNFRSF1A = False
TNFRSF1B = False
TNFRSF21 = False
TNFSF10 = False
TNFSF11 = False
TNFSF14 = False
TOMM40 = False
TOP2A = False
TP53 = False
TP53I3 = False
TP53INP1 = False
TP63 = False
TP73 = False
TPR = False
TPT1 = False
TRAF1 = False
TRAF2 = False
TRAF3IP3 = False
TREM1 = False
TRIM2 = False
TRIM22 = False
TRIM25 = False
TRIM28 = False
TRIM35 = False
TRIM5 = False
TRPV6 = False
TSC1 = False
TSC2 = False
TSG101 = False
TSHB = False
TSPAN5 = False
TSPAN7 = False
TTC39A = False
TUBB3 = False
TUBB4A = False
TWIST = False
TXLNB = False
TXNIP = False
TYK2 = False
TYMS = False
UBA7 = False
UBE2C = False
UBE2D3 = False
UBE2I = False
UBE2S = False
UBXN11 = False
UCP2 = False
UGT1A1 = False
UGT2B15 = False
UGT3A2 = False
UHRF1 = False
UMPS = False
UPF3B = False
UPK3A = False
UPP1 = False
UQCRC1 = False
UQCRFS1 = False
UVRAG = False
VAMP2 = False
VAT1L = False
VCAM1 = False
VDR = False
VEGFA = False
VIM = False
VitD = True
VLDLR = False
VMP1 = False
VWF = False
WASF2 = False
WDR91 = False
WLS = False
WNK2 = False
WNT = False
WRN = False
WT1 = False
XBP1 = False
XIAP = False
XKR8 = False
XPO1 = False
YBX1 = False
YWHAB = False
YY1 = False
ZAP70 = True
ZCCHC24 = False
ZDHHC18 = False
ZEB1 = False
ZFP36 = False
ZNF = False
ZNRD1 = False
ZYX = False

Define the network using Boolean formalism


ABCA1* = not NFKB
ABCB1* = not TP53
ABCC3* = not RXRA
ABCG2* = NFKB
ACAT1* = PPARG
ACO2* = (VDR and VitD)
ACSF2* = (VDR and VitD)
ACTC1* = not YY1
ACTR3* = CYFIP2
ACVRL1* = (VDR and VitD)
ADAM10* = TNFSF11
ADAM28* = (VDR and VitD)
ADAMDEC1* = (VDR and VitD)
ADAMTS10* = (VDR and VitD)
ADAMTS5* = not SIRT1
ADAR* = FRIZZLED
ADCY1* = (VDR and VitD)
ADGRE5* = WT1
ADH5* = (VDR and VitD)
ADIPOQ* = SP
ADORA1* = NFKB
ADRA2B* = not (VDR and VitD)
ADRB2* = not (VDR and VitD)
ADRBK1* = not CXCR4
AES* = HDAC1
AFG3L2* = (VDR and VitD)
AGAP7* = (VDR and VitD)
AGER* = not PPARG
AHCTF1* = XPO1
AHR* = not (VDR and VitD)
AIG1* = (VDR and VitD)
AKAP13* = LPAR
AKR1C1* = not (VDR and VitD)
AKR1C2* = not (VDR and VitD)
AKT1* = not THEM4
AKT2* = not NFKB
ALAS1* = RXRA
ALDH1A1* = not EZH2
ALOX12* = SP
ALOX5* = not NFKB
ALX1* = not (VDR and VitD)
AMH* = NFKB
AMICA1* = not (VDR and VitD)
ANG* = not PPARD
ANGPT* = not (VDR and VitD)
ANGPTL4* = PPARG
ANKRD33B* = not (VDR and VitD)
ANPEP* = not (VDR and VitD)
AP1S2* = (VDR and VitD)
AP2M1* = ARF
APAF1* = E2F1
APBB3* = (VDR and VitD)
APC* = not LRP6
APCDD1* = (VDR and VitD)
APEX1* = not HIF1A
APOBEC3A* = IFNA
APOBEC3B* = MYBL2
APOBEC3F* = IFNA
APOBEC3G* = CCL3 or MAPK1
APOBEC3H* = ZAP70
APOC3* = JUN
AQP1* = not (VDR and VitD)
AQR* = ELL
AR* = not PURA
ARC* = not (VDR and VitD)
AREG* = not BRCA1
ARF* = ADRB2
ARG1* = not TNF
ARHGEF16* = (VDR and VitD)
ARHGEF2* = (VDR and VitD)
ARID5A* = not (VDR and VitD)
ARSG* = (VDR and VitD)
ASAP2* = (VDR and VitD)
ASCL1* = not HES1
ASNS* = ATF
ASS1* = MYC
ATF* = MEF2D or not (VDR and VitD)
ATG16L1* = (VDR and VitD)
ATG5* = E2F1
ATG7* = HSF1
ATM* = TWIST
ATP13A3* = not HIV
ATP2C1* = SP
ATP5A1* = (VDR and VitD)
ATP5B* = (VDR and VitD)
ATXN2* = ZNF
AVPR2* = (VDR and VitD)
AXIN* = (VDR and VitD)
AXL* = not (VDR and VitD)
B2M* = NFKB
BACE1* = not NFKB
BAD* = not (VDR and VitD)
BAK1* = (VDR and VitD)
BAMBI* = not HDAC1
BAX* = not PER1
BBC3* = TP53
BCAR1* = EGR1
BCAS4* = (VDR and VitD)
BCL11A* = not SIRT1
BCL2* = CTSB or not DDB2 or PRNP or ZNRD1
BCL2A1* = NFKB
BCL2L1* = not BCL6
BCL2L11* = not NFKB
BCL3* = (VDR and VitD)
BCL6* = not CTCF or not IRF4
BCL9L* = (VDR and VitD)
BCLXL* = STAT3
BCR* = TP53
BDKRB2* = TP53
BECN1* = CAMP or not MCL1
BEX1* = not (VDR and VitD)
BGLAP* = TP53
BIN1* = not (VDR and VitD)
BIRC3* = NFKB
BIRC5* = not TP53
BLK* = PTK2B
BMI1* = MYC
BMP2* = not (VDR and VitD)
BMP2K* = not (VDR and VitD)
BRCA1* = not RBL1 or not RBL2
BRCA2* = not (VDR and VitD)
BRD7* = not MYC
BST2* = GATA1
BTG2* = FOXM1
BTNL9* = (VDR and VitD)
BTRC* = not COPS5
C1QA* = not (VDR and VitD)
C1QL4* = not (VDR and VitD)
C1S* = not (VDR and VitD)
C2orf91* = (VDR and VitD)
C3AR1* = not (VDR and VitD)
C7orf29* = (VDR and VitD)
C9orf89* = (VDR and VitD)
CAD* = MYC
CALD1* = NR3C1
CAMP* = (VDR and VitD)
CAPNS1* = NRF1
CASP1* = ETS1
CASP3* = not BCL2 or CASP8 or CASP9 or not XIAP
CASP7* = not XIAP
CASP8* = FAS
CASP9* = not BCLXL
CAV1* = not SREBF1
CAV2* = not SRC
CBFB* = not GATA1
CCK* = JUN
CCL11* = (VDR and VitD)
CCL2* = not CCR2
CCL20* = not IL10
CCL21* = NFKB
CCL22* = NFKB
CCL3* = not IL13
CCL4* = not CREM
CCL5* = CD40LG
CCNA1* = MYB
CCNA2* = not SP
CCNB1* = not TP53
CCND1* = not BHLHE41 or not HEXIM1
CCND2* = not BCL6
CCND3* = ETV4
CCNE1* = not PPARG
CCNG2* = not (VDR and VitD)
CCNI* = not CDK16 or not CDK2 or not CDK6
CCNT1-CDK9* = ZAP70
CCR1* = STAT1
CCR10* = (VDR and VitD)
CCR2* = not CCR5
CCR3* = NFKB
CCR4* = FOXP3
CCR5* = STAT4
CCR7* = not HIV
CCRN4L* = (VDR and VitD)
CD14* = DNM3
CD151* = SP
CD163* = IL10
CD19* = APEX1
CD1D* = not LEF1
CD207* = TGFB1
CD209* = IL10
CD22* = STAT1
CD27* = not IL10
CD274* = TNF
CD28* = HLA-DRB1
CD2AP* = SP
CD300LB* = (VDR and VitD)
CD36* = not (VDR and VitD)
CD38* = not IL4
CD3G* = NFKB
CD4* = not HES1
CD40* = not NFKBIA
CD40LG* = GATA3
CD44* = not (VDR and VitD)
CD46* = not HIV
CD52* = (VDR and VitD)
CD58* = not NFKBIA
CD79A* = not PTPN6
CD80* = not BCL6
CD81* = IFITM
CD82* = not HIV
CD83* = IL10
CD86* = NFKB
CD9* = not (VDR and VitD)
CD97* = (VDR and VitD)
CD99* = not HIV
CDA* = GATA1
CDC25C* = MYC
CDC40* = TPR
CDC42* = DVL1 or PTTG1
CDC42EP3* = not (VDR and VitD)
CDH1* = not ILK or NECTIN1 or PCK1 or PIP5K1C
CDH15* = (VDR and VitD)
CDH26* = (VDR and VitD)
CDK1* = not TP53
CDK16* = not CCNG2
CDK18* = (VDR and VitD)
CDK2* = not CDKN1A
CDK4* = not IRF1
CDK6* = not CDKN1C
CDKN1A* = ETV6 or not TBX3 or TP73
CDKN1B* = not COPS5
CDKN1C* = not HOXA10
CDKN2A* = not HDAC3
CDKN2B* = not BCL6
CDO1* = MYB
CDR2L* = (VDR and VitD)
CEACAM1* = not (VDR and VitD)
CEACAM6* = not (VDR and VitD)
CEBP* = MYB or (VDR and VitD) or STAT1 or HIV
CECR1* = (VDR and VitD)
CERS2* = SP
CETP* = not SP
CFLAR* = (VDR and VitD)
CFP* = (VDR and VitD)
CFTR* = NFKB
CHCHD10* = (VDR and VitD)
CHEK1* = not TP53
CHEK2* = not TP53
CHGA* = EGR1
CHN2* = (VDR and VitD)
CHRNE* = ETS2
CHUK* = not TP53
CIITA* = IRF2
CISH* = STAT3
CITED4* = (VDR and VitD)
CKM* = TP53
CLDN2* = LEF1
CLDN3* = SP
CLDN7* = not CTBP1
CLEC5A* = (VDR and VitD)
CLIP4* = (VDR and VitD)
CLMN* = (VDR and VitD)
CLTA* = ASAP2
CLUHP3* = not (VDR and VitD)
CNR1* = not (VDR and VitD)
COL10A1* = not SIRT1
COL11A2* = SP
COL1A1* = not CIITA
COL1A2* = not NFKB
COL2A1* = not NFKB
COPS5* = NFKB
CORO1A* = (VDR and VitD)
CORO2B* = (VDR and VitD)
COX6B1* = HIV
COX6B2* = not (VDR and VitD)
CPT1A* = not PPARA
CPT1B* = PPARG
CPZ* = not (VDR and VitD)
CREB3* = JUN
CREBBP* = not YY1
CREM* = FOS
CRHR1* = NFKB
CRISPLD2* = (VDR and VitD)
CRP* = NFKB
CRYAB* = TFAP2A
CSF1* = not IL10
CSF3R* = not MYB
CSNK1A1* = (VDR and VitD)
CSRP1* = CEBP
CST5* = (VDR and VitD)
CST7* = not (VDR and VitD)
CSTB* = HIV
CTBP1* = HDAC1
CTCF* = not BCL3
CTGF* = not JUN
CTNNB1* = not TCF7L2
CTPS1* = TWIST
CTSB* = (VDR and VitD)
CTSD* = not BRCA1
CTSL* = JUN
CTSS* = SPI1
CTSZ* = (VDR and VitD)
CXADR* = not SNAI
CXCL1* = not BRCA1
CXCL10* = TLR4
CXCL12* = CXCR4
CXCL14* = SP
CXCL5* = SP
CXCL8* = not ERG
CXCL9* = JAK
CXCR1* = CXCR2
CXCR2* = NFKB
CXCR4* = CREB3 or not DNMT1
CXCR5* = not HIV
CXorf21* = not (VDR and VitD)
CYBB* = IRF8
CYCS* = BAD or BAK1
CYFIP2* = FOXD3
CYLD* = not LEF1
CYP17A1* = not NR2F1
CYP19A1* = not NFKB
CYP1B1* = not (VDR and VitD)
CYP24A1* = not PTH
CYP26B1* = (VDR and VitD)
CYP27A1* = SP
CYP27B1* = AKT1
CYP2C8* = HNF4A
CYP2E1* = NFATC1
CYP3A4* = (VDR and VitD)
CYP7A1* = not SMAD3
DAPK2* = KLF
DBF4* = SP
DBH* = YY1
DDB2* = BRCA1
DDIT4* = (VDR and VitD)
DDX26B* = (VDR and VitD)
DDX58* = TRIM25
DEFA1* = POU
DEFA3* = TLR4
DEFA4* = POU
DEFB1* = DEFB103B
DEFB103B* = (VDR and VitD)
DEFB4A* = (VDR and VitD)
DEFB4B* = (VDR and VitD)
DENND6B* = (VDR and VitD)
DEPTOR* = not (VDR and VitD)
DFNB31* = not (VDR and VitD)
DHFR* = not RB1
DICER1* = GATA1
DKK1* = TCF7L2
DLL1* = not (VDR and VitD)
DNAH10* = (VDR and VitD)
DNAJB4* = not (VDR and VitD)
DNASE2* = SP
DNM2* = STAT3
DNM3* = TWIST
DNMT1* = STAT3
DNMT3A* = not RB1
DOCK10* = not (VDR and VitD)
DPF3* = (VDR and VitD)
DR1* = not NR2F1
DRAM1* = E2F1
DROSHA* = E2F1
DST* = not IRF1
DTX4* = not (VDR and VitD)
DUSP1* = (VDR and VitD)
DVL1* = CSNK1A1
DVL2* = FZD6
E2F1* = not CCNA1 or not E2F6 or not E2F7 or NR4A1
E2F3* = not TP53
E2F6* = E2F1
E2F7* = not (VDR and VitD)
EAF2* = not PML
EAPP* = SP
EBI3* = not NFKBIA
EBNA1BP2* = RB1
EDN1* = STAT1
EDNRB* = SP
EEF2* = not HIV
EFCAB12* = (VDR and VitD)
EFNB1* = not HIV
EGF* = HGS or PTPN11 or not PTPRK
EGFR* = JUNB or not TSG101
EGLN1* = not SIRT1
EGLN3* = EPAS1
EGR1* = not EGFR or PLCG1
EGR3* = NFATC1
EIF2AK1* = not HDAC1
EIF2AK2* = IRF1
EIF2B5* = not HIV
EIF4G1* = not HIV
ELF* = SP or (VDR and VitD)
ELFN2* = not HIV
ELL* = (VDR and VitD)
EMID1* = not (VDR and VitD)
EN2* = (VDR and VitD)
EP300* = not TCF7L2
EPAS1* = not YY1
EPB41L1* = (VDR and VitD)
EPCAM* = not NFKB
EPO* = EP300
ERBB2* = SP
ERBB3* = not TWIST
ERCC1* = E2F1
ERCC5* = YY1
ERG* = ETS2
ERICD* = not E2F1
ESR* = not HDAC1
ESRRA* = (VDR and VitD)
ETF1* = not SP
ETS1* = WT1
ETS2* = not (VDR and VitD)
ETV1* = not (VDR and VitD)
ETV4* = E2F1
ETV6* = STAT3
EXT1* = (VDR and VitD)
EZH2* = E2F1
EZR* = RAC1
F11R* = not HIV
F13A1* = not (VDR and VitD)
F2R* = DNM2
F3* = not IL10
FABP1* = RXRA
FABP3* = (VDR and VitD)
FADS3* = not (VDR and VitD)
FAF1* = NFKB
FAIM3* = (VDR and VitD)
FAM116B* = (VDR and VitD)
FAM179A* = (VDR and VitD)
FAM200B* = not (VDR and VitD)
FANCE* = BRCA1
FANCM* = FOXC1
FAS* = FASLG or not NFKBIA
FASLG* = FOXO
FBP1* = (VDR and VitD)
FCER1A* = GATA2
FCER2* = not BCL6
FCN2* = HIV
FENDRR* = (VDR and VitD)
FFAR2* = (VDR and VitD)
FGF2* = not TP53
FGF7* = not FGFR1 or not FGFR3
FGF8* = NFKB
FGFR1* = (VDR and VitD)
FGFR3* = not (VDR and VitD)
FGR* = (VDR and VitD)
FLI1* = ETS2
FLJ34208* = not (VDR and VitD)
FLJ44511* = (VDR and VitD)
FLT1* = TP53
FLT3* = PML
FMNL2* = (VDR and VitD)
FMR1* = SP
FN1* = (VDR and VitD)
FOS* = CSF1 or MAPK9 or MITF or NF1 or not NKX3-1 or not PTEN or PTGS2
FOSL1* = JUN
FOSL2* = not (VDR and VitD)
FOXC1* = not EZH2
FOXD3* = E2F1
FOXF1* = (VDR and VitD)
FOXM1* = not FOXO
FOXO* = IKBKB or not SGK1
FOXP3* = CD83
FRIZZLED* = E2F1
FST* = SMAD3
FTH1P18* = not MYC
FUCA1* = (VDR and VitD)
FXR2* = SP
FXYD6* = (VDR and VitD)
FZD6* = not HIV
G6PD* = not CREM
GABARAP* = UVRAG
GABARAPL2* = BECN1
GAD1* = not HDAC1
GADD45A* = TP53
GADD45B* = IL6
GALT* = FOXO
GAPDH* = MYC
GAPVD1* = not HIV
GAST* = SP
GATA1* = BCL11A
GATA2* = not HDAC3
GATA3* = NFKB
GATA6* = CEBP
GCK* = INS
GDF15* = TP53
GEMIN2* = TPR
GFAP* = EP300
GFER* = not CEBP
GH2* = FOXF1
GJA1* = JUN
GJD3* = (VDR and VitD)
GLIPR1* = RXRA
GM2A* = (VDR and VitD)
GML* = TP53
GMPR* = (VDR and VitD)
GNAI1* = not (VDR and VitD)
GNLY* = (VDR and VitD)
GOLPH3* = (VDR and VitD)
GOT1* = (VDR and VitD)
GP1BB* = GATA1
GPA33* = not (VDR and VitD)
GPER* = (VDR and VitD)
GPLD1* = ARF
GPR114* = not (VDR and VitD)
GPR65* = (VDR and VitD)
GPR84* = (VDR and VitD)
GPT2* = (VDR and VitD)
GRIA2* = not GRIN2B or not TSPAN7
GRIN2B* = HDAC1
GRK5* = (VDR and VitD)
GSK3B* = not ADAR
GSN* = not (VDR and VitD)
GSTP1* = NFKB
GTF2B* = NFKB
H19* = E2F1
HAMP* = CEBP
HAP1* = not SSB
HAS2* = not YY1
HAVCR2* = CEACAM1 or HMGB1
HBEGF* = NFKB
HDAC1* = not EZH2
HDAC2* = MYC
HDAC3* = BTRC
HDAC4* = SP
HDAC7* = not BCL6
HES1* = FANCM or SOX9
HEXIM1* = HIV
HEY1* = JUN
HGF* = not CDH1 or FGF7 or KPNB1
HGS* = SRC
HHLA2* = not (VDR and VitD)
HIC1* = E2F1
HIF1A* = not HIPK2
HIPK2* = (VDR and VitD)
HIST1H2AC* = UBE2C
HLA-A* = IRF1
HLA-B* = not HIV
HLA-C* = not HIV
HLA-DOA* = CIITA
HLA-DRA* = not HDAC1
HLA-DRB1* = HIV
HMGA1* = E2F1
HMGA2* = not BRCA1
HMGB1* = TLR4
HMGCS1* = not (VDR and VitD)
HMOX1* = not HIV
HMSD* = (VDR and VitD)
HNF4A* = not TP53
HNRNPA2B1* = not BRCA1
HOXA10* = (VDR and VitD)
HOXA9* = KAT6A
HOXB13* = not EZH2
HP* = (VDR and VitD)
HPSE* = NFKB
HSD11B1* = not PPARG
HSD17B1* = not TFAP2A
HSD17B11* = CEBP
HSD17B2* = SP
HSF1* = SIRT1
HSP90AA1* = not STAT1
HSPA4* = not HIV
HSPA5* = not BRCA1
HSPD1* = not RUNX
HTR1A* = not PARP1
HTT* = (VDR and VitD)
HYAL1* = not SP
ICAM1* = NFATC1
ICAM2* = not HIV
ID* = HOXA9 or not (VDR and VitD)
IDO1* = PTMA
IFI16* = TP53
IFI27* = (VDR and VitD)
IFI44* = not (VDR and VitD)
IFI44L* = not (VDR and VitD)
IFIT1* = not (VDR and VitD)
IFIT3* = not (VDR and VitD)
IFITM* = not KLF or not (VDR and VitD)
IFNA* = IRF5 or not SIGLEC1 or IRF7
IFNAR1* = STAT3
IFNB1* = not PTPN6
IFNG* = IL18R1 or IL27RA or IL6ST
IFNGR1* = not IRF2
IGF1* = CAV1
IGF1R* = (VDR and VitD)
IGF2* = not WT1
IGFBP3* = not (VDR and VitD)
IGFBP7* = JUN
IGK* = MYC
IGLV6-57* = (VDR and VitD)
IGSF9* = not (VDR and VitD)
IKBKB* = SLPI
IKBKE* = STAT3
IL10* = FLI1 or not HDAC4 or MSC or not PGR
IL12* = not STAT5B
IL12A* = NFKB
IL12B* = IL18
IL13* = IL33 or not TBX21
IL15* = MYB
IL17* = not (VDR and VitD)
IL17A* = CD44
IL17C* = NFKB
IL18* = CASP1
IL18R1* = STAT4
IL1A* = EGF or not PI3
IL1B* = not CASP3 or HAVCR2 or IL8
IL1RL1* = HIV
IL1RN* = not PI3
IL2* = CD27 or not CXCL10 or SPN
IL21* = STAT3
IL22* = not (VDR and VitD)
IL22RA1* = not IL22
IL23A* = NFKB
IL23R* = not (VDR and VitD)
IL27* = IRF1
IL27RA* = (VDR and VitD)
IL2RA* = FOXP3
IL2RB* = RXRA
IL2RG* = HLA-A
IL3* = JUN
IL33* = HIV
IL4* = not CXCL9 or not FOXP3 or not ICAM1
IL5* = YY1
IL6* = AHR or CCL5 or IL1A or not TNFRSF1B or not ZFP36
IL6ST* = IL10
IL7* = MYB
IL7R* = not (VDR and VitD)
IL8* = ADRBK1
ILK* = XPO1
INS* = (VDR and VitD)
INSR* = (VDR and VitD)
IPO7* = MYC
IRF1* = IRF7 or STAT2
IRF2* = IRF1
IRF3* = DDX58
IRF4* = not BCL6
IRF5* = (VDR and VitD)
IRF7* = not TNFAIP3
IRF8* = not WT1
IRF9* = BRCA1
IRS1* = FN1 or PIK3C or not SOCS
ITGA2B* = not NRAS
ITGA4* = not (VDR and VitD)
ITGA5* = SP
ITGAD* = SP
ITGAV* = not SP
ITGAX* = CEBP
ITGB2* = (VDR and VitD)
ITGB7* = HIV
JAG1* = NOTCH1
JAK* = INSR or PDGFA
JUN* = not TNFAIP3
JUNB* = SMAD3
KALRN* = (VDR and VitD)
KAT2A* = TP53
KAT6A* = not AKT1
KCNA3* = not (VDR and VitD)
KCNF1* = (VDR and VitD)
KCNK5* = (VDR and VitD)
KCNQ2* = SP
KCNQ3* = not (VDR and VitD)
KCTD12* = (VDR and VitD)
KCTD17* = (VDR and VitD)
KDM6B* = JUN
KHDRBS3* = (VDR and VitD)
KIAA0040* = (VDR and VitD)
KIAA1211L* = (VDR and VitD)
KIAA1324L* = (VDR and VitD)
KIF17* = XPO1
KIF2B* = AHCTF1 or PLK1 or RPS27
KIR3DL1* = E2F1
KIR3DS1* = IL15 or IL2 or TLR3
KIT* = not (VDR and VitD)
KLF* = NANOG or NR1I2 or not (VDR and VitD)
KLK3* = not BTG2 or not CCND3 or HIST1H2AC
KPNB1* = RANBP1
KRAS* = MYC
KRT16* = EP300
KRT17* = STAT3
KRT4* = not ELF
KRT7* = (VDR and VitD)
LAG3* = (VDR and VitD)
LAMA1* = KLF
LAMA3* = not EP300
LC3* = BECN1
LCK* = MYB
LCP2* = (VDR and VitD)
LDHA* = MYC
LDLR* = not ATF
LDLRAD3* = not (VDR and VitD)
LEF1* = AES
LEFTY1* = POU
LEP* = CEBP
LFNG* = (VDR and VitD)
LGALS3* = MUC1
LGALS3BP* = not STAT3
LGALS9* = (VDR and VitD)
LILRA1* = (VDR and VitD)
LILRB4* = (VDR and VitD)
LIMK2* = ROCK1
LINC00086* = not (VDR and VitD)
LIPE* = NFKB
LMO2* = not PRDM1
LMP1* = not IRF5
LNX1* = (VDR and VitD)
LOR* = not JUNB
LPAR* = not SNAI
LPGAT1* = (VDR and VitD)
LPL* = NRIP1
LPO* = (VDR and VitD)
LRP1* = THBS1
LRP4* = not HIV
LRP5* = not DKK1
LRP6* = AXIN or not LRP5
LRRC3B* = (VDR and VitD)
LRRC8A* = (VDR and VitD)
LRRC8D* = not HIV
LSP1* = not (VDR and VitD)
LTBP1* = not STAT3
LTC4S* = not NFKB
LTF* = CEBP
LTK* = not (VDR and VitD)
LY96* = STAT1
MAD2L1* = BRCA1
MAP2K1* = not CDC42 or MAP3K7 or RAF1
MAP3K2* = SRC
MAP3K7* = TRIM5
MAP4* = not TP53
MAPK1* = CCL11 or DUSP1 or not PEBP1 or PTPRF or not RAP1B or SDC1
MAPK13* = not RALB
MAPK14* = BLK or CD36 or RALB
MAPK3* = F11R
MAPK3_2* = MAP2K1
MAPK7* = MEF2C
MAPK8* = ANGPT
MAPK9* = JAK
MARCKS* = (VDR and VitD)
MAT2A* = MYB
MAT2B* = SP
MBP* = not (VDR and VitD)
MCHR1* = (VDR and VitD)
MCL1* = (VDR and VitD)
MDM2* = not TFAP4
MECOM* = RUNX
MEF2C* = not HIPK2
MEF2D* = not HDAC7 or MAPK7
MET* = not TP53
MICA* = not STAT3
MICA_SP1* = SP
MKI67* = SATB1
MLC* = not (VDR and VitD)
MLC1* = MYLK
MLPH* = not (VDR and VitD)
MMP1* = not TP53
MMP13* = not STAT1
MMP14* = NFKB
MMP2* = not ATF
MMP3* = JUN
MMP7* = CTNNB1
MMP9* = CXCL12
MPEG1* = not (VDR and VitD)
MPO* = IL12B or IL23R
MPP3* = not (VDR and VitD)
MPZL1* = not HIV
MRC1* = (VDR and VitD)
MRS2* = (VDR and VitD)
MS4A14* = not (VDR and VitD)
MS4A7* = not (VDR and VitD)
MSC* = EPAS1
MSN* = ROCK1
MSR1* = JUN
MST1* = not MYC
MT2A* = not (VDR and VitD)
MTA1* = SP
MTOR* = not DDIT4
MUC1* = not PIAS3
MUC2* = NFKB
MUC4* = not YY1
MX1* = TLR8
MX2* = IFNB1
MXI1* = not MYCN
MYB* = FOSL2
MYBL2* = E2F1
MYBPH* = (VDR and VitD)
MYC* = not MXI1
MYCN* = YBX1
MYLK* = not (VDR and VitD)
MYOZ1* = not (VDR and VitD)
NAB2* = EGR3
NACC2* = not (VDR and VitD)
NAMPT* = NFKB
NANOG* = STAT3
NAPSB* = (VDR and VitD)
NBEAL2* = not (VDR and VitD)
NCAM1* = not (VDR and VitD)
NCF1* = (VDR and VitD)
NCF1B* = (VDR and VitD)
NCF1C* = (VDR and VitD)
NCOR1* = (VDR and VitD)
NCOR2* = (VDR and VitD)
NCR3LG1* = not HIV
NDST3* = (VDR and VitD)
NDUFA10* = (VDR and VitD)
NDUFA6* = (VDR and VitD)
NDUFAF4* = (VDR and VitD)
NDUFB7* = (VDR and VitD)
NDUFS6* = (VDR and VitD)
NDUFS7* = (VDR and VitD)
NDUFV1* = SP
NDUFV2* = SP
NECTIN1* = not HIV
NEFL* = JUN
NEGR1* = (VDR and VitD)
NEO1* = (VDR and VitD)
NEUROG3* = E2F3
NF1* = not TWIST
NFAT* = not AKT1
NFATC1* = MAPK8 or not PPIA
NFE2* = not MYC
NFKB* = (not ETV3 or SQSTM1 or not (VDR and VitD)) and not NFKBIA
NFKBIA* = NR0B2  or not RIPK2  or TRAF1
NGEF* = FGR
NIM1* = not (VDR and VitD)
NINJ1* = (VDR and VitD)
NKX3-1* = not TP53
NLRP12* = (VDR and VitD)
NME1* = STAT3
NMNAT2* = (VDR and VitD)
NOD2* = not NR1I2
NOG* = BMP2
NOL7* = MYC
NOS2* = not NFKBIA
NOS3* = NFKB
NOTCH1* = EZH2
NOX4* = NFKB
NOX5* = NFKB
NPAS4* = not (VDR and VitD)
NPTX1* = not (VDR and VitD)
NPTX2* = not (VDR and VitD)
NR0B2* = EP300
NR1H4* = not STAT1
NR1I2* = DR1 or NR1H4
NR2F1* = not ESRRA
NR4A1* = not PML
NR4A2* = not (VDR and VitD)
NRAS* = SOS1
NREP* = not (VDR and VitD)
NRF1* = ESR
NRIP1* = TFDP1
NRXN1* = TCF4
NTN1* = NEO1
NTNG2* = (VDR and VitD)
NUP* = KIF2B or TAOK1
NXF1* = TPR
OCEL1* = (VDR and VitD)
OCLN* = HEY1
ODC1* = not APC
OGDHL* = (VDR and VitD)
OLFML3* = not (VDR and VitD)
OPRM1* = SP
OPTN* = not (VDR and VitD)
ORM1* = (VDR and VitD)
OSM* = STAT5B
OTOF* = (VDR and VitD)
OTUD1* = not (VDR and VitD)
OXTR* = NFKB
PARD6A* = ROCK1
PARP1* = ETS1
PAX* = not WT1
PCDH9* = not HIV
PCK1* = not SREBF1
PCK2* = not NFKB
PCNA* = not EP300
PCSK6* = not ASCL1
PCTP* = (VDR and VitD)
PDCD1LG2* = (VDR and VitD)
PDE5A* = not POU
PDGFA* = (VDR and VitD)
PDGFRL* = (VDR and VitD)
PDIA2* = SP
PDIA6* = not YY1
PDK2* = not PPARG
PDK4* = not INS
PDLIM4* = (VDR and VitD)
PDPN* = not PTPN11
PDZD2* = (VDR and VitD)
PEBP1* = not EZH2
PER1* = SIRT1
PERP* = not TP53
PEX5L* = (VDR and VitD)
PF4* = GATA1
PFKFB4* = (VDR and VitD)
PFKL* = AKT1
PFKM* = MYC
PGAM2* = (VDR and VitD)
PGR* = SP
PHACTR1* = not (VDR and VitD)
PHGDH* = SP
PI3* = (VDR and VitD)
PI3K* = (VDR and VitD)
PIAS3* = STAT3
PIK3C* = KIT  or RAS  or ZYX
PINX1* = (VDR and VitD)
PIP5K1C* = ROCK1
PKIB* = not (VDR and VitD)
PLAU* = NFKB
PLAUR* = NFKB
PLCG1* = BCR
PLD1* = not (VDR and VitD)
PLIN2* = not PPARA
PLK1* = XPO1
PLOD157812* = RPS6KB1
PLOD162749* = IL2
PMAIP1* = TP53
PMEPA1* = SP
PML* = STAT1
PMP22* = (VDR and VitD)
PNOC* = (VDR and VitD)
PNPLA1* = (VDR and VitD)
POLB* = ATF
POLR2C* = ELL
POLR2H* = GSK3B
POLR2I* = ELL
POLR2L* = GSK3B
POU* = HMGA2
PPARA* = STAT3
PPARD* = JUN
PPARG* = not NCOR1
PPFIBP1* = not (VDR and VitD)
PPP1R13B* = E2F1
PPP1R16B* = (VDR and VitD)
PPP2R* = XPO1
PPP2R2B* = not TFAP4
PRDM1* = not PAX
PRDM2* = YY1
PRDX3* = NRF1
PRDX5* = NRF1
PRF1* = CD28
PRICKLE1* = (VDR and VitD)
PRKACA* = ITGA4
PRKC* = TFAP2A
PRKCE* = not SP
PRKCH* = (VDR and VitD)
PRKD1* = SOS1
PRNP* = (VDR and VitD)
PRODH* = not MYC
PROX1* = not HEY1
PRSS50* = CEBP
PRUNE2* = not (VDR and VitD)
PSMC5* = CREBBP
PTAFR* = NFKB
PTEN* = TFAP2A
PTGDS* = not HES1
PTGES* = NFKB
PTGIR* = SP
PTGS2* = not (VDR and VitD)
PTH* = not APEX1
PTHLH* = NFKB
PTK2B* = IL2RG or SPP1
PTMA* = not ESR
PTPN11* = HLA-DRB1
PTPN14* = not (VDR and VitD)
PTPN6* = (VDR and VitD)
PTPRE* = not (VDR and VitD)
PTPRF* = not (VDR and VitD)
PTPRK* = not HIV
PTPRN2* = not (VDR and VitD)
PTPRS* = not HIV
PTTG1* = not KLF
PTX3* = not (VDR and VitD)
PURA* = not IRF3
QPCT* = (VDR and VitD)
RAB11FIP1* = (VDR and VitD)
RAB27A* = not (VDR and VitD)
RAB37* = (VDR and VitD)
RAB3A* = NR1I2
RAC1* = ARHGEF2 or ROR2
RAF1* = not FCER1A or not RRAS2
RALB* = CXCR4
RANBP1* = XPO1
RANBP2* = XPO1
RAP1A* = not TWIST
RAP1B* = ITGB2 or RAPGEF1
RAPGEF1* = BCAR1 or VLDLR
RARA_B* = RARA_B or not HDAC1
RARG* = not (VDR and VitD)
RAS* = TCF7L2
RASA4CP* = (VDR and VitD)
RASGEF1A* = not (VDR and VitD)
RASGRP1* = E2F1
RASSF1* = not TP53
RB1* = UHRF1
RBL1* = not RB1
RBL2* = NAB2
RECQL4* = not HDAC1
RELT* = not HIV
REPIN1* = (VDR and VitD)
RETN* = SP
RFC3* = AHR
RGS16* = not (VDR and VitD)
RGS4* = not PROX1
RHOB* = not HDAC1
RHOH* = (VDR and VitD)
RIPK2* = FAS
RNASE1* = LMO2
RNASE2* = HNF4A
RNASE4* = ANG
RNASE7* = IFNG or TLR2
RNASEL* = BRCA1
RND3* = AES
RNPS1* = TPR
ROCK1* = not HIV
ROR2* = (VDR and VitD)
RORC* = not (VDR and VitD)
RPRD2* = (VDR and VitD)
RPS27* = XPO1
RPS6KA3* = NR3C1
RPS6KB1* = IRS1
RRAGB* = TSC1
RREB1* = not (VDR and VitD)
RUNX* = not TWIST
RXRA* = not (VDR and VitD)
S100A10* = not (VDR and VitD)
S100A6* = not NFKBIA
S100A9* = not HIV
SAA2* = NFKB
SALL4* = STAT3
SAMHD1* = not IL7 or TLR9
SARDH* = (VDR and VitD)
SARNP* = TPR
SAT1* = PPARG
SATB1* = not EZH2
SATB2* = not HIV
SCARB1* = not HIV
SCD* = not (VDR and VitD)
SCPEP1* = (VDR and VitD)
SDC1* = MMP9 or PRKACA
SDHD* = (VDR and VitD)
SDS* = (VDR and VitD)
SELE* = not ATF
SELPLG* = not HIV
SEMA4D* = not HIV
SEMA6A* = not (VDR and VitD)
SERINC3* = not HIV
SERINC5* = not HIV
SERPINA1* = IL1B or IL6
SERPINA3* = not NFKB
SERPINB1* = NFKB
SERPINB5* = SP
SERPINB6* = (VDR and VitD)
SERPINC1* = not NR2F1
SERPINE1* = not E2F1
SFT2D1* = (VDR and VitD)
SFTPD* = not (VDR and VitD)
SFXN3* = (VDR and VitD)
SFXN4* = (VDR and VitD)
SGK1* = not APC
SHANK1* = not (VDR and VitD)
SHE* = (VDR and VitD)
SHH* = STAT3
SIGIRR* = SP
SIGLEC1* = TLR7
SIGLEC6* = (VDR and VitD)
SIK1* = not YWHAB
SIM1* = not (VDR and VitD)
SIRPG* = (VDR and VitD)
SIRT1* = FOXO
SIRT4* = (VDR and VitD)
SIVA* = TP53 or E2F1
SKP2* = not (VDR and VitD)
SLC17A7* = (VDR and VitD)
SLC19A1* = not HIV
SLC20A1* = not HIV
SLC22A23* = (VDR and VitD)
SLC25A20* = (VDR and VitD)
SLC25A27* = NFKB
SLC25A4* = (VDR and VitD)
SLC29A1* = not HIV
SLC2A1* = not (VDR and VitD)
SLC2A3* = HMGA1
SLC31A1* = (VDR and VitD)
SLC37A2* = (VDR and VitD)
SLC46A1* = NRF1
SLC4A7* = not HIV
SLC51A* = not (VDR and VitD)
SLC5A5* = APEX1
SLC5A8* = CEBP
SLC6A12* = (VDR and VitD)
SLC6A6* = not HIV
SLC7A1* = not HIV
SLC7A2* = (VDR and VitD)
SLC9A1* = not HIV
SLC9A3* = not (VDR and VitD)
SLC9A9* = (VDR and VitD)
SLC9C2* = not (VDR and VitD)
SLCO4C1* = not (VDR and VitD)
SLPI* = DEFA1 or DEFA4
SLU7* = TPR
SMAD2* = not CTBP1
SMAD3* = MAPK3_2
SMAD4* = not PMEPA1
SMAD7* = not SMAD3
SMO* = not (VDR and VitD)
SNAI* = not NCOR1 or not PER2
SNRPA* = SRSF2
SNRPC* = SRSF2
SNRPD3* = TPR
SOCS* = not STAT4 or not (VDR and VitD) or IRF1
SOD1* = CEBP
SOD2* = not SP
SOS1* = IGF1R
SOX7* = JUN
SOX9* = SP
SP* = not ATM or IRF9
SPARC* = SATB1
SPAST* = NRF1
SPI1* = not FOS
SPN* = SP
SPP1* = (VDR and VitD)
SPRR1B* = JUN
SPRY4* = (VDR and VitD)
SQSTM1* = not HIV
SRC* = (VDR and VitD)
SREBF1* = SP
SRR* = FOS
SRRM3* = (VDR and VitD)
SRSF1* = MYC
SRSF2* = TPR
SRSF6* = TPR
SSB* = TBP
SSTR1* = not EZH2
SSTR2* = not TP53
ST3GAL1* = (VDR and VitD)
ST3GAL3* = MYC
ST3GAL4* = not (VDR and VitD)
ST3GAL5* = ATF
STAR* = CEBP
STARD7* = CTNNB1
STAT1* = not (VDR and VitD)
STAT2* = STAT1
STAT3* = IL22RA1 or MTOR or RAC1
STAT4* = not GATA3
STAT5B* = PTK2B
STAT6* = IL4
STEAP3* = (VDR and VitD)
STIM1* = not WT1
STMN1* = JUN
STS* = STAT3
SUB1* = not HIV
SULF2* = (VDR and VitD)
SULT1C2* = (VDR and VitD)
SUMO1* = not YBX1
SUMO2* = MTA1
SURF1* = MYC
SURF2* = MYC
SUZ12* = E2F1
SYCP2* = (VDR and VitD)
SYN1* = EGR1
SYT3* = (VDR and VitD)
TAB2* = not CYLD
TAF7* = SP
TAOK1* = XPO1
TAP1* = IRF1
TBC1D2* = (VDR and VitD)
TBL1X* = not (VDR and VitD)
TBP* = NFKB
TBX15* = (VDR and VitD)
TBX21* = NFKB
TBX3* = not SIRT1
TBXA2R* = not WT1
TBXAS1* = not TP53
TCF4* = EGR1
TCF7L2* = WNT
TCF7L2_LEF* = CTNNB1
TCFL5* = POU
TCN1* = not (VDR and VitD)
TDRD10* = (VDR and VitD)
TERF2* = SP
TERT* = not TP53
TESPA1* = (VDR and VitD)
TFAP2A* = YY1
TFAP4* = MYC
TFDP1* = not RB1
TFE3* = (VDR and VitD)
TFEB* = HIV
TFF1* = not BRCA1
TGFB1* = not FST  or not HGF  or IGF1  or RPS6KB1  or not SMAD2  or SMAD7
TGFB3* = FOS
TGM2* = (VDR and VitD)
TGM5* = not (VDR and VitD)
THBD* = not EP300
THBS1* = WT1
THEM4* = (VDR and VitD)
THEMIS2* = (VDR and VitD)
THOC2* = TPR
THOC6* = TPR
TIAM2* = RXRA
TICAM1* = not SP
TIMP1* = not NFKB
TIMP3* = SP
TJP1* = not HDAC1
TK1* = SP
TLE6* = (VDR and VitD)
TLR1* = FOXO
TLR2* = CD14 or TLR1
TLR3* = not IRF8
TLR4* = not STAT6
TLR7* = NFKB
TLR8* = TNF
TLR9* = not PTMA
TMEM136* = (VDR and VitD)
TMEM255A* = not (VDR and VitD)
TMEM37* = (VDR and VitD)
TMEM86A* = (VDR and VitD)
TMPO* = SP
TNC* = SMAD4
TNF* = not (VDR and VitD)
TNFA* = not SERPINA1
TNFAIP3* = not (VDR and VitD)
TNFAIP6* = CEBP
TNFRSF10A* = not CFLAR
TNFRSF10B* = not SIRT1
TNFRSF10D* = not CFLAR
TNFRSF12A* = NR1I2
TNFRSF13C* = NFKB
TNFRSF1A* = not HIV
TNFRSF1B* = IL10
TNFRSF21* = not HIV
TNFSF10* = not SP
TNFSF11* = IL17A
TNFSF14* = SP
TOMM40* = HIV
TOP2A* = E2F1
TP53* = BAX  or not BRCA2  or not HTT  or SIK1
TP53I3* = TP53
TP53INP1* = not MYCN
TP63* = not SATB2
TP73* = YY1
TPR* = NUP
TPT1* = (VDR and VitD)
TRAF1* = not NFKBIA
TRAF2* = NFKB
TRAF3IP3* = (VDR and VitD)
TREM1* = (VDR and VitD)
TRIM2* = (VDR and VitD)
TRIM22* = not (VDR and VitD)
TRIM25* = not (VDR and VitD)
TRIM28* = CEBP
TRIM35* = (VDR and VitD)
TRIM5* = TLR4
TRPV6* = (VDR and VitD)
TSC1* = (VDR and VitD)
TSC2* = not MYC
TSHB* = POU
TSPAN5* = GATA6
TSPAN7* = not HIV
TTC39A* = (VDR and VitD)
TUBB3* = not (VDR and VitD)
TUBB4A* = (VDR and VitD)
TWIST* = not HDAC2 or not SUZ12
TXLNB* = not (VDR and VitD)
TXNIP* = not HDAC1
TYK2* = not STAT3
TYMS* = not TP53
UBA7* = not PML
UBE2C* = MYC
UBE2D3* = not SNAI
UBE2I* = not WT1
UBE2S* = EGR1
UBXN11* = (VDR and VitD)
UCP2* = not STAT3
UGT1A1* = AHR
UGT2B15* = JUN
UGT3A2* = not (VDR and VitD)
UHRF1* = E2F1
UMPS* = not CAD
UPF3B* = RANBP2
UPK3A* = (VDR and VitD)
UPP1* = NFKB
UQCRC1* = (VDR and VitD)
UQCRFS1* = (VDR and VitD)
UVRAG* = HIV
VAMP2* = SP
VAT1L* = not (VDR and VitD)
VCAM1* = not POU
VDR* = MAPK14 or not MDM2  or PRKC  or PTH  or not SUMO1  or not SUMO2  or TP63  or VitD
VEGFA* = not JUN
VIM* = not AKT1
VitD* = not CYP24A1 or CYP27B1
VLDLR* = not HIC1 or PPARG
VMP1* = ZEB1
VWF* = ERG
WASF2* = not HIV
WDR91* = not (VDR and VitD)
WLS* = (VDR and VitD)
WNK2* = (VDR and VitD)
WNT* = AP2M1 or not NOG
WRN* = not TP53
WT1* = IFI16
XBP1* = not BCL6
XIAP* = not AR
XKR8* = (VDR and VitD)
XPO1* = MYC
YBX1* = TWIST
YWHAB* = PPP2R
YY1* = SP
ZAP70* = not PTPN6
ZCCHC24* = (VDR and VitD)
ZDHHC18* = (VDR and VitD)
ZEB1* = PARP1 or SALL4
ZFP36* = MAPK3
ZNF* = not ID
ZNRD1* = PAX
ZYX* = CTNNB1
"""

off=["CD59","CSTB","NEDD4L","POLR2A","POLR2K","PPIA","AP2A1"] #Set these genes to False

coll  = util.Collector()
for i in range(50):
    model = boolean2.Model( text, mode='async')
    model.initialize()
    model.iterate( steps=40)
    nodes = model.nodes
    coll.collect( states=model.states, nodes=nodes )    # this collects states for each run
    avgs = coll.get_averages( normalize=True )  # this step averages the values for each node
                                                # returns a dictionary keyed by nodes and a list of values
                                                # with the average state for in each timestep

print(type(avgs), len(avgs), list(avgs.keys())[:5])  # Type, number of nodes, sample keys

# Write averages to a file (Python 2.7 compatible, no brackets)
with open("VitD_ON_HIV_ON_40steps_1k_nodes_averages.txt", "w") as f:
    for node, avg_values in avgs.items():
        avg_values_str = ", ".join(map(str, avg_values))  # Convert list to a comma-separated string
        f.write("{}: {}\n".format(node, avg_values_str))
print("Averages written to 'VitD_ON_HIV_ON_40steps_1k_nodes_averages.txt'.")
