Supplemental Table 1: Common and differential genomic abnormalities among the different cells
Common abnormalities:C (n=3); RLD (n=7); RPD (n=5) / C (n=2) / C (n=1)
Chr. / Gains / Losses / Gains / Losses / Gains / Losses
1 / q21.1-q23.1 / p22.1-p12//p32.3//p31.1-p22.3
2 / q36.3-q37.3
3 / q25.2-q29 / p26.1
4 / q22.3
5
6 / q24.1-q27
7 / q22.3-q36.3
8 / q21.13-q23.3
9 / p23-p21.2
10
11
12 / p11.23//q24.11-q24.33 / q23.3-q24.11 / q23.3-q24.11
13 / q11-q22.1//q31.1-q31.3
14 / q11.2-q32.33
15
16 / q22.2-q24.3
17 / q11.2-q24.3//p13.3-q25.3
18
19 / p13.3-p13.2
20
21 / q22.11-q22.3
22
X
Y
* In the second and third pattern, only the specific additional abnormalities are displayed.
Supplemental Table 2: Genes commonly deregulated by in vivo treatment with LD and PD and pathways in which they are involved.
Ingenuity Canonical Pathways / -log(p-value) / Ratio / MoleculesEIF2 Signaling / 1.71E01 / 3.09E-01 / RPL11,RPL27A,MAPK3,RPS23,EIF2A,RPL36AL,RPS24,RPS3A,EIF3B,EIF1AX,RPL12,RPL3,RRAS,EIF2B3,RPL23A,RPLP0,EIF3M,PIK3R3,EIF2AK4,RPS4X,RPL39,RPL26L1,EIF4A3,RPS25,RPL13A,EIF3K,EIF2S3,PPP1CC,RPS6,RPS8,RPS13,RPL14,RPS17/RPS17L,EIF2S1,RPL7,RPL6,RPS16,SOS1,RPLP2,EIF3A,RPS20,RPS3,MAP2K1,RPL18,RPL29,EIF3F,RPS2,EIF3J,RPL35A,RPS5,RPL5,UBA52,EIF4A1,EIF2B1,PIK3CB,EIF3L
Antigen Presentation Pathway / 1.32E01 / 5.25E-01 / B2M,PSMB9,PDIA3,HLA-A,HLA-DQA1,CIITA,NLRC5,HLA-DRB1,CD74,TAP1,MR1,HLA-G,HLA-C,HLA-E,HLA-DRB3,HLA-DRA,HLA-B,HLA-F,HLA-DPB1,TAP2,TAPBP
Regulation of eIF4 and p70S6K Signaling / 9.42E00 / 2.47E-01 / EIF2S3,MAPK3,PPP2R5B,RPS13,RPS8,RPS6,EIF2S1,RPS17/RPS17L,RPS23,EIF2A,RPS24,RPS3A,EIF3B,EIF1AX,SOS1,RPS16,EIF3A,RPS20,RPS3,MAP2K1,RRAS,EIF3F,RPS2,EIF2B3,EIF3J,MAPK12,EIF3M,PIK3R3,RPS4X,RPS5,EIF4A3,IRS1,EIF4A1,EIF2B1,PIK3CB,RPS25,PPP2R1B,EIF3L,EIF3K
Cytotoxic T Lymphocyte-mediated Apoptosis of Target Cells / 5.66E00 / 2.88E-01 / B2M,CASP3,CYCS,HLA-A,HLA-DQA1,HLA-DRB1,BCL2,HLA-G,HLA-E,HLA-C,HLA-DRB3,HLA-DRA,HLA-B,HLA-F,HLA-DPB1
mTOR Signaling / 5.41E00 / 1.96E-01 / MAPK3,PPP2R5B,RPS13,RPS8,FKBP1A,RPS6,RPS17/RPS17L,RPS23,PDGFC,RPS24,RPS3A,EIF3B,GPLD1,RPS16,EIF3A,RPS20,PRKCE,RPS3,PRKD1,EIF4B,DDIT4,RRAS,EIF3F,RPS2,EIF3J,EIF3M,PIK3R3,RPS4X,RPS5,EIF4A3,IRS1,EIF4A1,PIK3CB,RPS25,PPP2R1B,EIF3L,EIF3K
Protein Ubiquitination Pathway / 4.82E00 / 1.71E-01 / PSMB3,B2M,SACS,USP18,PSMA3,PSMD7,HLA-A,UBE2L3,UBE2N,PSMD9,UBR1,ANAPC10,DNAJC3,TAP1,USO1,USP3,USP53,HSP90AB1,USP42,HSPE1,USP16,PSMD10,HLA-B,UBE2E3,BIRC3,UBE2J1,UCHL3,PSMB9,PSME2,USP30,DNAJC2,UBE2S,HSPD1,PSMD8,PSMB7,ANAPC4,PSMC1,HLA-C,RBX1,UBE2G1,PSMA5,PSMB1,ANAPC5,TAP2,DNAJC7
OX40 Signaling Pathway / 4.28E00 / 2.3E-01 / B2M,HLA-A,HLA-DQA1,HLA-DRB1,MAPK12,BCL2,HLA-G,HLA-E,HLA-C,HLA-DRB3,HLA-DRA,HLA-B,HLA-F,HLA-DPB1
Allograft Rejection Signaling / 4.04E00 / 2.03E-01 / HLA-G,B2M,HLA-E,HLA-A,HLA-C,HLA-DRB3,HLA-DRA,HLA-DQA1,HLA-B,HLA-DRB1,HLA-F,HLA-DPB1
Mismatch Repair in Eukaryotes / 3.47E00 / 3.5E-01 / PCNA,MSH2,FEN1,RFC1,RFC5,MLH1,RFC3
RAN Signaling / 2.62E00 / 3.33E-01 / KPNA3,TNPO1,RANBP2,RAN,RANBP1,IPO5
Role of BRCA1 in DNA Damage Response / 2.04E00 / 1.9E-01 / RAD51,MSH2,ATF1,RBBP8,SMARCD2,RFC1,BRCC3,STAT1,RFC5,MLH1,CHEK1,RFC3
TGF-β Signaling / 2.00E00 / 1.69E-01 / RRAS,MAPK3,SMAD3,CREBBP,ACVR1,SMAD7,BMPR2,SMAD5,MAPK12,BCL2,TGFBR2,SOS1,MAP2K1,SMAD1,ACVR2A
α-Adrenergic Signaling / 1.91E00 / 1.63E-01 / PRKACB,RRAS,MAPK3,GNB2L1,PYGB,ITPR1,GNG7,GNG10,GNB4,GYS1,ADCY1,PRKCE,MAP2K1,ADCY7,PRKD1
TCA Cycle II (Eukaryotic) / 1.77E00 / 2.61E-01 / CS,DLD,MDH1,MDH2,OGDH,IDH3B
Cell Cycle: G1/S Checkpoint Regulation / 1.69E00 / 1.72E-01 / RPL11,CCND3,HDAC3,CCND2,RPL5,PA2G4,PAK1IP1,CDK4,SMAD3,GNL3,HDAC5
JAK/Stat Signaling / 1.67E00 / 1.71E-01 / PIK3R3,PTPN11,RRAS,MAPK3,SOS1,SOCS2,STAT2,PIK3CB,STAT3,STAT1,JAK3,MAP2K1
Interferon Signaling / 1.65E00 / 2.06E-01 / IFIT1,IFITM1,MX1,STAT2,STAT1,TAP1,BCL2
Role of JAK1 and JAK3 in γc Cytokine Signaling / 1.64E00 / 1.75E-01 / BLNK,PIK3R3,IL2RG,PTPN11,RRAS,IRS1,MAPK3,PIK3CB,STAT3,STAT1,JAK3
Supplemental Table 3: Genes exclusively deregulated by in vivo treatment with PD and pathways in which they are involved.
EIF2 Signaling / 6.68E00 / 4.53E-01 / EIF2S2,RAF1,MAPK1,PIK3R1,KRAS,EIF3C/EIF3CL,RPS11,RPS7,RPL7A,EIF4G2,EIF3D,PAIP1,RPL19,RPL8,EIF2C1,PPP1CA,ATM,EIF2AK1,PABPC1,AKT2,RPL27,RPL37,RPL7L1,EIF3E,RPL15,FAU,RPL10,RPS15,PIK3CD,RPS15A,RPL41,RPL13A,RPS27A,RPSA,RPL24,RPL31,PIK3CA,EIF2B4,RPS18,PPP1CB,RPL26,RPS21,EIF4G1,RPL37A,EIF2B2,RPL10A,RPS27,AKT1,RPL18A,RPS9,RPL35,AKT3,PIK3R2,RPL13,EIF3H,GRB2,RPL34,RPL17,RPS2,RPS28,RPS19,RPL30,EIF2C2,RPL21,RPL23,RPL39L,RPL36,RPS27L,RPL9,RPS12,EIF3G,RRAS2,RPS10,RPS26,RPL28,RPL36A,EIF4A1,RPL32,EIF3I,RPL3L,EIF2AK2,RPS14
Protein Ubiquitination Pathway / 6.51E00 / 4.26E-01 / USP45,PSMA7,USP20,PSMB8,PAN2,BAG1,UBE2D4,USP10,PSMA2,PSMC2,DNAJC16,DNAJB12,UBE2Q1,DNAJC27,USP19,THOP1,SKP2,UBD,USP31,HSPA8,PSMB2,ZBTB12,PSMD12,PSMA4,HSPB11,DNAJC14,PSMD1,UBE2C,ANAPC2,USP18,HLA-A,CUL1,CDC23,DNAJA1,USP39,UCHL1,PSMC6,PSMD14,AMFR,CRYAA,PSMD13,MDM2,PSMD5,FZR1,PSME1,DNAJC24,CUL2,USP37,HSPA14,USP5,DNAJC6,UBE2D2,TCEB2,UBE2V2,FBXW7,DNAJB2,TCEB1,PSMC5,USP7,HSPA4,DNAJC8,UCHL5,SUGT1,USP40,NEDD4L,BRCA1,PSMA6,PSMB5,DNAJC19,HSPA9,PSMC4,PSMD6,PSMD3,DNAJB14,PSMD11,HSPA13,HSP90AA1,PSMD4,UBE2E1,VHL,USP51,USP21,USP14,ANAPC1/ANAPC1P1,CDC20,DNAJC12,USP54,DNAJC10,PSMB6,UBE2F,USP13,UBE2V1,DNAJC1,DNAJB1,HSPA4L,PSMB4,HSPH1,PSMA1,USP1,DNAJB9,UBE2D1,UBE3A,UBE2L6,SKP1/SKP1P2,DNAJC21,HSCB,PSMD2,DNAJB11,CDC34,PSMC3,DNAJB5,UBE2D3
Cell Cycle: G2/M DNA Damage Checkpoint Regulation / 6.43E00 / 6.04E-01 / YWHAH,CUL1,PTPMT1,CCNB2,EP300,YWHAQ,TOP2A,BRCA1,CHEK2,ATM,TP53,PRKDC,CDC25C,YWHAG,CKS2,YWHAE,YWHAB,CDK7,WEE1,PLK1,MDM2,SKP1/SKP1P2,CDK1,SKP2,CCNB1,MDM4,TOP2B,PKMYT1,ATR
DNA damage-induced 14-3-3σ Signaling / 5.86E00 / 7.62E-01 / TP53,CCNE2,AKT2,CCNB2,RAD9A,CDK1,CCNB1,RAD1,CCNE1,AKT1,HUS1,AKT3,BRCA1,ATR,CDK2,ATM
Role of CHK Proteins in Cell Cycle Checkpoint Control / 4.96E00 / 5.61E-01 / PPP2CA,RAD9A,RAD50,HUS1,RFC2,E2F5,SLC19A1,PPP2R5C,BRCA1,E2F2,CHEK2,ATM,CDC25A,TP53,CDC25C,PPP2R5D,PLK1,RPA1,PPP2R5A,CDK1,NBN,RAD1,PPP2CB,RFC4,PPP2R4,PPP2R3A,E2F1,TLK1,CLSPN,TLK2,ATR,CDK2
ATM Signaling / 4.6E00 / 5.41E-01 / MAP2K4,GADD45B,RAD9A,CCNB2,CBX5,RAD50,EP300,SMC1A,JUN,NFKBIA,BID,BRCA1,BLM,CHEK2,CDC25A,ATM,TP53,SMC3,CDC25C,TRIM28,MAPK9,MDM2,CREB3L4,CDK1,CCNB1,NBN,MDM4,MAPK14,SMC2,H2AFX,TLK1,TLK2,CDK2
Mitotic Roles of Polo-Like Kinase / 4.48E00 / 5.31E-01 / ANAPC2,KIF23,CDC20,ANAPC1/ANAPC1P1,PPP2CA,PLK3,CDC7,CCNB2,CDC23,SMC1A,PLK4,CDC26,PPP2R5C,RAD21,CHEK2,CDC25A,SMC3,CDC25C,ESPL1,WEE1,PPP2R5D,PRC1,PLK1,CDK1,FZR1,PPP2R5A,CCNB1,PPP2CB,PPP2R4,PPP2R3A,PKMYT1,HSP90AA1,KIF11,CDC27
Regulation of eIF4 and p70S6K Signaling / 4.21E00 / 4.05E-01 / EIF2S2,RAF1,MAPK1,PPP2CA,PIK3R1,KRAS,PAIP2,EIF3C/EIF3CL,RPS11,RPS7,EIF4G2,EIF3D,PAIP1,EIF2C1,ATM,ITGA4,PABPC1,RPS6KB1,AKT2,ITGA5,EIF3E,PPP2CB,FAU,PPP2R3A,PPP2R4,RPS15,PIK3CD,RPS15A,RPSA,RPS27A,PIK3CA,EIF2B4,RPS18,RPS21,EIF4G1,EIF2B2,EIF4EBP1,RPS27,AKT1,RPS9,MKNK1,AKT3,PPP2R5C,PIK3R2,ITGB1,EIF3H,GRB2,RPS2,PPP2R5D,RPS28,RPS19,EIF2C2,ITGA3,RPS27L,PPP2R5A,RPS12,EIF3G,RRAS2,MAPK14,RPS10,RPS26,EIF4A1,EIF3I,RPS14
Cell Cycle Control of Chromosomal Replication / 3.44E00 / 5.67E-01 / MCM5,CDC45,ORC2,CDK7,CDC6,CDC7,ORC6,RPA1,RPA2,MCM3,RPA3,CDK5,ORC3,ORC5,CHEK2,CDK2,MCM7
Cyclins and Cell Cycle Regulation / 3.26E00 / 4.25E-01 / RAF1,PPP2CA,SUV39H1,CUL1,HDAC10,CCNB2,CCNA2,HDAC7,E2F5,TGFB2,PPP2R5C,E2F2,CDC25A,ATM,TP53,HDAC9,CCNE2,HDAC4,HDAC8,TFDP1,HDAC2,CDK7,WEE1,PPP2R5D,HDAC1,SKP1/SKP1P2,CDK1,PPP2R5A,SKP2,CCNB1,PPP2CB,CCNE1,PPP2R4,PPP2R3A,E2F1,ATR,CDK2
IGF-1 Signaling / 3.2E00 / 4.31E-01 / RAF1,SOCS1,SOCS3,PIK3CA,CTGF,MAPK1,YWHAH,PIK3R1,SOCS6,SRF,KRAS,JAK2,IGFBP7,PRKAG1,YWHAQ,CASP9,JUN,AKT1,IGF1,FOXO3,PRKAR1B,CSNK2A1,RPS6KB2,AKT3,PIK3R2,IGFBP1,RASA1,ATM,RPS6KB1,AKT2,YWHAG,YWHAE,GRB2,YWHAB,PRKAR2A,SOCS4,CSNK2A2,FOS,PRKAR2B,RRAS2,FOXO1,IGFBP3,PIK3CD,SOCS5
DNA Double-Strand Break Repair by Homologous Recombination / 2.8E00 / 6.25E-01 / LIG1,GEN1,POLA1,RAD52,BRCA2,RPA1,BRCA1,RAD50,ATM,NBN
Role of BRCA1 in DNA Damage Response / 2.72E00 / 4.6E-01 / BARD1,FANCF,RBL1,RAD50,FANCE,FANCB,RFC2,E2F5,SLC19A1,BRCA1,BLM,BRIP1,CHEK2,E2F2,ATM,TP53,FANCG,PLK1,RPA1,FANCC,NBN,POU2F1,RFC4,E2F1,MSH6,BRCA2,ATR,HLTF,FANCA
Hypoxia Signaling in the Cardiovascular System / 2.67E00 / 4.69E-01 / UBE2D2,UBE2V2,EP300,UBE2F,JUN,AKT1,NFKBIA,SUMO1,UBE2V1,UBE2D4,NFKBIB,ATM,TP53,P4HB,UBE2Q1,COPS5,NQO1,CSNK1D,MDM2,CREB3L4,UBE2D1,UBE2L6,HIF1AN,HSP90AA1,CDC34,UBE2D3,VHL,LDHA,UBE2E1,UBE2C
NRF2-mediated Oxidative Stress Response / 2.62E00 / 3.74E-01 / MAP2K4,RAF1,FTL,MAPK1,PIK3R1,DNAJC6,GCLC,KRAS,DNAJB2,CLPP,DNAJC8,KEAP1,ABCC1,DNAJA3,JUND,DNAJA2,FOSL1,TXN,DNAJC16,PRKD3,CBR1,ATM,MGST1,DNAJB12,DNAJC19,DNAJB14,STIP1,DNAJC14,PIK3CD,MAP2K3,PTPLAD1,ABCC4,GSTP1,MAP2K5,EPHX1,PIK3CA,USP14,PRDX1,DNAJC10,DNAJA1,EP300,CUL3,AKR1A1,AKT1,JUN,MAP3K7,VCP,PMF1,DNAJC1,UBE2K,PIK3R2,DNAJB1,PRKCA,SOD1,GSTA4,NQO1,MAPK9,HERPUD1,DNAJB9,GSTO1,DNAJC21,FOS,MAPK14,RRAS2,MGST2,DNAJB11,CAT,CCT7,CDC34,DNAJB5
Molecular Mechanisms of Cancer / 2.5E00 / 3.4E-01 / RAP2B,RAC2,RAF1,SHH,TGFBR1,AXIN1,PIK3R1,SUV39H1,KRAS,ARHGEF1,RBL1,PTCH2,ZBTB17,PAK1,BMP8A,NFKBIB,PRKD3,BMP8B,ATM,TP53,SMAD2,CCNE2,AKT2,STK36,TFDP1,PTCH1,RALB,RAP1A,DAXX,GAB1,APH1A,E2F1,MAP2K3,PIK3CD,NOTCH1,CAMK2G,RAP2A,FYN,PIK3CA,PSENEN,JAK2,CDC42,EP300,CASP6,ARHGEF19,HHAT,AKT1,JUN,BBC3,E2F5,BID,ARHGEF3,PIK3R2,PRKDC,PAK2,GRB2,GNAQ,ADCY6,MDM2,BAK1,GNAI3,FOS,CCNE1,RASGRP1,BMP6,ATR,CTNND1,PSEN1,MAP2K4,MAPK1,MYC,CASP9,SUFU,ARHGEF11,BRCA1,RASA1,FZD2,E2F2,RALGDS,CDC25A,ARHGEF15,TYK2,RAC1,RAPGEF3,FZD9,AURKA,RALBP1,RHOQ,RND3,RHOA,FZD3,PLCB3,LEF1,CDK2,BMP2,RHOH,PRKAG1,FAS,BRAF,LAMTOR3,NFKBIA,MAP3K7,BMPR1A,PRKAR1B,TGFB2,AKT3,CHEK2,PRKCA,PAK4,CDC25C,LRP5,ADCY3,PRKAR2A,GNAI1,MAPK9,NBN,RRAS2,PRKAR2B,MAPK14,FZD4,NF1,FOXO1,BCL2L11
PI3K/AKT Signaling / 2.44E00 / 3.7E-01 / RAF1,MAPK1,YWHAH,PPP2CA,PIK3R1,KRAS,YWHAQ,IKBKB,NFKBIB,ITGA4,MCL1,TP53,RPS6KB1,AKT2,RHEB,YWHAG,YWHAE,YWHAB,TYK2,ITGA5,SYNJ2,PPP2CB,GAB1,PPP2R4,PPP2R3A,HSP90AA1,PIK3CD,INPP5K,TSC1,PIK3CA,INPPL1,JAK2,EIF4EBP1,AKT1,NFKBIA,FOXO3,RPS6KB2,AKT3,PPP2R5C,PIK3R2,ITGB1,GRB2,PPP2R5D,MDM2,IKBKE,ITGA3,PPP2R5A,RRAS2,FOXO1,SYNJ1
DNA Double-Strand Break Repair by Non-Homologous End Joining / 2.1E00 / 5.62E-01 / PRKDC,DCLRE1C,XRCC6,XRCC4,XRCC5,RAD50,PARP1,ATM,NBN
mTOR Signaling / 1.89E00 / 3.6E-01 / PLD2,MAPK1,PPP2CA,PIK3R1,KRAS,EIF3C/EIF3CL,RPS11,RPS7,EIF4G2,EIF3D,PRKD3,ATM,RPS6KB1,AKT2,RHEB,STK11,RAC1,VEGFC,EIF3E,ATG13,PPP2CB,FAU,RPS6KA6,RHOQ,RND3,PPP2R3A,PPP2R4,RHOA,RPS15,PIK3CD,RPS15A,PLD6,RPSA,RPS27A,TSC1,PIK3CA,RPS18,RPS21,EIF4G1,RHOH,PRKAG1,EIF4EBP1,PGF,RPS27,AKT1,RPS9,RPS6KB2,AKT3,PPP2R5C,PIK3R2,PRKCA,MAPKAP1,EIF3H,RPS2,PPP2R5D,RPS28,RPS19,RPS27L,PPP2R5A,RPS12,PLD4,EIF3G,RRAS2,RPS10,RPS26,EIF4A1,EIF3I,RPS14
Cell Cycle: G1/S Checkpoint Regulation / 1.85E00 / 4.06E-01 / SUV39H1,CUL1,HDAC10,RBL1,MYC,HDAC7,TGFB2,E2F5,E2F2,CDC25A,ATM,TP53,HDAC9,CCNE2,HDAC4,HDAC2,TFDP1,HDAC8,HDAC1,MDM2,SKP1/SKP1P2,SKP2,CCNE1,E2F1,ATR,CDK2
ERK/MAPK Signaling / 1.78E00 / 3.42E-01 / RAF1,RAC2,YWHAH,MAPK1,PPP2CA,PIK3R1,SRF,KRAS,PPP1R14B,MYC,YWHAQ,PAK1,ELF3,PPP1CA,ATM,ITGA4,YWHAG,YWHAB,CRKL,VRK2,RAC1,ITGA5,PPP1R11,RAPGEF3,CREB3L4,RAP1A,PPP2CB,PLA2G6,PLA2G2D,PPP2R3A,PPP2R4,DUSP1,PPP1R12A,PIK3CD,DUSP4,FYN,PIK3CA,H3F3A/H3F3B,PTK2B,PPP1CB,RAPGEF4,PRKAG1,EIF4EBP1,EP300,BRAF,LAMTOR3,PPP1R10,MKNK1,PRKAR1B,PPP2R5C,PIK3R2,PRKCA,ITGB1,PAK4,PAK2,PLA2G12A,GRB2,PPP2R5D,PLA2G4C,PRKAR2A,NFATC1,ITGA3,PPP2R5A,FOS,PPP1R3D,ELF2,PRKAR2B,RRAS2
NF-κB Activation by Viruses / 1.68E00 / 3.8E-01 / RAF1,PIK3CA,MAPK1,PIK3R1,KRAS,IKBKB,AKT1,NFKBIA,ITGAV,AKT3,PIK3R2,NFKBIB,PRKD3,ITGB5,PRKCA,ITGA4,ATM,CR2,ITGB1,AKT2,ITGA5,IKBKE,ITGA3,ITGAL,TNFRSF14,TRAF2,RRAS2,IKBKAP,PIK3CD,EIF2AK2
Antiproliferative Role of TOB in T Cell Signaling / 1.62E00 / 5E-01 / PABPC1,CCNA2,SMAD2,CCNE1,CCNE2,TGFBR1,MAPK1,CUL1,TGFB2,CDC34,SKP1/SKP1P2,CDK2,SKP2
Myc Mediated Apoptosis Signaling / 1.4E00 / 4E-01 / TP53,MAP2K4,PIK3CA,AKT2,YWHAG,YWHAH,YWHAE,YWHAB,GRB2,PIK3R1,MAPK9,KRAS,FAS,YWHAQ,MYC,AKT1,RRAS2,CASP9,IGF1,AKT3,BID,PIK3CD,PIK3R2,ATM
ERK5 Signaling / 1.39E00 / 3.91E-01 / IL6ST,SH2D2A,RPS6KB1,YWHAG,YWHAE,YWHAH,YWHAB,SGK1,GNAQ,MEF2A,KRAS,CREB3L4,EP300,CTF1,YWHAQ,MYC,FOS,RPS6KA6,RRAS2,AKT1,GAB1,FOXO3,RPS6KB2,FOSL1,MAP2K5
JAK/Stat Signaling / 1.37E00 / 3.86E-01 / SOCS3,RAF1,SOCS1,PIK3CA,PIAS2,MAPK1,PIK3R1,SOCS6,KRAS,JAK2,AKT1,AKT3,PIK3R2,STAT5B,ATM,STAT6,AKT2,GRB2,TYK2,GNAQ,SOCS4,PIAS3,FOS,RRAS2,PIAS4,PIK3CD,SOCS5
Supplemental Table 4: Canonical Pathways significantly deregulated in tumors resistant to LD
Glycoaminoglycan-protein Linkage Region Biosynthesis / 2.76E00 / 2.86E-01 / XYLT2,B3GAT3
B Cell Development / 2.51E00 / 1.03E-01 / CD79B,CD40,CD79A
Vitamin-C Transport / 1.89E00 / 1.43E-01 / SLC2A1,SLC2A3
Altered T Cell and B Cell Signaling in Rheumatoid Arthritis / 1.73E00 / 4.65E-02 / CD79B,CD40,IL10,CD79A
Mismatch Repair in Eukaryotes / 1.72E00 / 1E-01 / SLC19A1,POLD1
Chondroitin Sulfate Biosynthesis / 1.57E00 / 5.77E-02 / XYLT2,B3GAT3,CHPF2
Thyroid Hormone Biosynthesis / 1.57E00 / 3.33E-01 / CTSD
Heparan Sulfate Biosynthesis / 1.53E00 / 5.45E-02 / XYLT2,EXTL3,B3GAT3
Dermatan Sulfate Biosynthesis / 1.53E00 / 5.56E-02 / XYLT2,B3GAT3,CHPF2
Antioxidant Action of Vitamin C / 1.48E00 / 4.08E-02 / SLC2A5,SLC2A1,IKBKE,SLC2A3
Activation of IRF by Cytosolic Pattern Recognition Receptors / 1.4E00 / 4.76E-02 / CD40,IL10,IKBKE
1,25-dihydroxyvitamin D3 Biosynthesis / 1.4E00 / 3.33E-01 / POR
Tetrahydrobiopterin Biosynthesis I / 1.4E00 / 3.33E-01 / SPR
Hypusine Biosynthesis / 1.4E00 / 3.33E-01 / DHPS
Tetrahydrobiopterin Biosynthesis II / 1.4E00 / 3.33E-01 / SPR
T Helper Cell Differentiation / 1.31E00 / 4.35E-02 / CD40,IL10,BCL6
Mitotic Roles of Polo-Like Kinase / 1.31E00 / 4.69E-02 / CDC20,PKMYT1,ANAPC11
Supplemental Table 5: Canonical Pathways significantly deregulated in tumors resistant to PD
FcγRIIB Signaling in B Lymphocytes / 2.45E00 / 1.02E-01 / PIK3C2A,PIK3C3,MAPK8,LYN,CD79A
Endoplasmic Reticulum Stress Pathway / 2.01E00 / 1.67E-01 / MAPK8,EIF2AK3,TAOK3
Role of IL-17A in Arthritis / 1.94E00 / 8.33E-02 / PIK3C2A,PIK3C3,NFKBIE,MAPK8,MAPKAPK2
CD40 Signaling / 1.7E00 / 7.35E-02 / PIK3C2A,PIK3C3,NFKBIE,MAPK8,MAPKAPK2
IL-17A Signaling in Airway Cells / 1.7E00 / 7.14E-02 / JAK1,PIK3C2A,PIK3C3,NFKBIE,MAPK8
SAPK/JNK Signaling / 1.67E00 / 6E-02 / MAP4K3,PIK3C2A,PIK3C3,ZAK,MAPK8,GNG5
14-3-3-mediated Signaling / 1.62E00 / 5.93E-02 / TUBA8,PIK3C2A,TP73,PIK3C3,MAPK8,TUBA4A,PLCB1
UDP-N-acetyl-D-galactosamine Biosynthesis I / 1.6E00 / 1E00 / GALE
Role of Pattern Recognition Receptors in Recognition of Bacteria and Viruses / 1.56E00 / 6.32E-02 / OAS2,PIK3C2A,IL10,TICAM1,PIK3C3,MAPK8
p53 Signaling / 1.54E00 / 6.32E-02 / PIK3C2A,TP73,PIK3C3,MAPK8,TP53BP2,DRAM1
IL-17 Signaling / 1.48E00 / 6.76E-02 / JAK1,PIK3C2A,PIK3C3,MAPK8,MAPKAPK2
Paxillin Signaling / 1.45E00 / 5.45E-02 / ARF1,PIK3C2A,PIK3C3,MAPK8,ACTN4,GIT2
4-1BB Signaling in T Lymphocytes / 1.37E00 / 8.57E-02 / NFKBIE,TNFSF9,MAPK8
PDGF Signaling / 1.37E00 / 6.33E-02 / JAK1,ABL2,PIK3C2A,PIK3C3,MAPK8
IL-2 Signaling / 1.36E00 / 7.14E-02 / JAK1,PIK3C2A,PIK3C3,MAPK8
Leukocyte Extravasation Signaling / 1.34E00 / 4.59E-02 / TEC,F11R,ARHGAP6,PIK3C2A,PIK3C3,CYBA,MAPK8,ARHGAP12,ACTN4
Role of NFAT in Regulation of the Immune Response / 1.32E00 / 4.3E-02 / PIK3C2A,PIK3C3,NFKBIE,MEF2D,LYN,PLCB1,GNG5,CD79A
EGF Signaling / 1.31E00 / 6.9E-02 / JAK1,PIK3C2A,PIK3C3,MAPK8
IL-9 Signaling / 1.3E00 / 7.89E-02 / JAK1,PIK3C2A,PIK3C3
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