Supplementary Table 1. (a) Basal alkylation sensitivity associated gene set (BASA) sorted by correlation (page 1 of 2) Present in Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) % accuracy Network MGMT O-6-methylguanine-DNA methyltransferase NM_002412 204880_at 0.95 0.74 69 Yes C21orf56 chromosome 21 open reading frame 56 AL136871 223360_at 0.86 0.54 56 No NQO2 NAD(P)H dehydrogenase, quinone 2 NM_000904 203814_s_at -0.71 -0.53 69 No glycerol-3-phosphate dehydrogenase 2 GPD2 (mitochondrial) U36310 210007_s_at -0.72 -0.59 63 Yes RAD54B RAD54 homolog B (S. cerevisiae) NM_012415 219494_at -0.72 -0.66 63 Yes PIAS2 protein inhibitor of activated STAT, 2 AF361054 1555514_a_at -0.73 -0.58 69 No FLJ12442 hypothetical protein FLJ12442 NM_022908 218051_s_at -0.73 -0.53 69 No TM4SF12 transmembrane 4 superfamily member 12 NM_012338 219274_at -0.76 -0.58 63 No LRRK1 leucine-rich repeat kinase 1 AW792857 1565627_a_at -0.76 -0.53 81 No ARSB arylsulfatase B AW168942 232197_x_at -0.77 -0.52 75 No PPP2R1B protein phosphatase 2 (formerly 2A) T79584 202883_s_at -0.78 -0.58 56 Yes MSC musculin (activated B-cell factor-1) AF060154 209928_s_at -0.78 -0.55 69 Yes LOC283130 hypothetical protein LOC283130 AI336233 236436_at -0.79 -0.58 69 No LAMC1 laminin, gamma 1 (formerly LAMB2) NM_002293 200771_at -0.79 -0.69 75 Yes FLJ12886 hypothetical protein FLJ12886 NM_019108 221335_x_at -0.81 -0.59 75 No discoidin, CUB and LCCL domain containing DCBLD1 1 NM_173674 1553768_a_at -0.81 -0.53 75 No CMIP c-Maf-inducing protein AI363061 224992_s_at -0.81 -0.54 63 Yes --- --- AI825302 238700_at -0.82 -0.64 63 No platelet/endothelial cell adhesion molecule PECAM1 (CD31 antigen) M37780 208983_s_at -0.82 -0.62 63 Yes FLJ32942 hypothetical protein FLJ32942 BG150433 227711_at -0.82 -0.61 75 No LOC284801 hypothetical protein LOC284801 AL531683 225762_x_at -0.83 -0.62 63 No guanine nucleotide binding protein (G GNB5 protein), beta 5 NM_006578 207124_s_at -0.83 -0.71 81 Yes sarcoglycan, beta (43kDa dystrophin- SGCB associated glycoprotein) U29586 205120_s_at -0.83 -0.68 63 Yes SFXN2 sideroflexin 2 AL530504 227560_at -0.83 -0.54 56 No SYPL synaptophysin-like protein AI768845 201259_s_at -0.84 -0.58 69 No DTNBP1 dystrobrevin binding protein 1 AF061734 223446_s_at -0.84 -0.68 75 Yes LOC203069 hypothetical protein LOC203069 AI081543 212866_at -0.84 -0.74 75 No MESDC2 mesoderm development candidate 2 AK026606 224675_at -0.85 -0.65 63 No FIGNL1 fidgetin-like 1 NM_022116 1552921_a_at -0.85 -0.71 69 Yes PHYH phytanoyl-CoA hydroxylase (Refsum disease) NM_006214 203335_at -0.85 -0.61 75 Yes Supplementary Table 1. (a) Basal alkylation sensitivity associated gene set (BASA) sorted by correlation (page 2 of 2) Present in Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) % accuracy Network TM4SF7 transmembrane 4 superfamily member 7 BC000389 209263_x_at -0.85 -0.68 75 No echinoderm microtubule associated protein EML4 like 4 NM_019063 220386_s_at -0.85 -0.60 81 No CKLFSF3 chemokine-like factor super family 3 AY166714 1555705_a_at -0.86 -0.58 69 No MGC45731 hypothetical protein MGC45731 AW003092 227080_at -0.86 -0.58 63 No phosphoinositide-3-kinase, regulatory PIK3R1 subunit, polypeptide 1 (p85 alpha) AI680192 212239_at -0.87 -0.76 63 No MAGEF1 melanoma antigen, family F, 1 NM_022149 218176_at -0.88 -0.72 81 Yes TMEM14A transmembrane protein 14A NM_014051 218477_at -0.88 -0.70 63 No ANKRD9 ankyrin repeat domain 9 AW194999 230972_at -0.90 -0.67 75 No MGC11266 hypothetical protein MGC11266 BE326728 226118_at -0.91 -0.70 63 Yes DTYMK deoxythymidylate kinase (thymidylate kinase) NM_012145 203270_at -0.91 -0.58 56 No CANP cancer-associated nucleoprotein AA960844 1557128_at -0.91 -0.50 63 No --- --- BE467688 231259_s_at -0.92 -0.52 56 No H2AFV H2A histone family, member V BF343852 212206_s_at -0.92 -0.70 69 No NET1 neuroepithelial cell transforming gene 1 NM_005863 201830_s_at -0.92 -0.58 56 Yes TSAP6 dudulin 2 NM_018234 218424_s_at -0.92 -0.70 75 Yes --- --- AA227879 235919_at -0.93 -0.58 56 No CKLF chemokine-like factor NM_016951 219161_s_at -0.94 -0.62 75 No MUTYH mutY homolog (E. coli) NM_012222 207727_s_at -0.97 -0.76 69 Yes ALL 94 Supplementary Table 1. (b) Basal alkylation sensitivity associated gene set (BASA) sorted by gene (page 1 of 2) Present in Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) % accuracy Network ANKRD9 ankyrin repeat domain 9 AW194999 230972_at -0.90 -0.67 75 No ARSB arylsulfatase B AW168942 232197_x_at -0.77 -0.52 75 No C21orf56 chromosome 21 open reading frame 56 AL136871 223360_at 0.86 0.54 56 No CANP cancer-associated nucleoprotein AA960844 1557128_at -0.91 -0.50 63 No CKLF chemokine-like factor NM_016951 219161_s_at -0.94 -0.62 75 No CKLFSF3 chemokine-like factor super family 3 AY166714 1555705_a_at -0.86 -0.58 69 No CMIP c-Maf-inducing protein AI363061 224992_s_at -0.81 -0.54 63 Yes discoidin, CUB and LCCL domain containing DCBLD1 1 NM_173674 1553768_a_at -0.81 -0.53 75 No DTNBP1 dystrobrevin binding protein 1 AF061734 223446_s_at -0.84 -0.68 75 Yes DTYMK deoxythymidylate kinase (thymidylate kinase) NM_012145 203270_at -0.91 -0.58 56 No echinoderm microtubule associated protein EML4 like 4 NM_019063 220386_s_at -0.85 -0.60 81 No FIGNL1 fidgetin-like 1 NM_022116 1552921_a_at -0.85 -0.71 69 Yes FLJ12442 hypothetical protein FLJ12442 NM_022908 218051_s_at -0.73 -0.53 69 No FLJ12886 hypothetical protein FLJ12886 NM_019108 221335_x_at -0.81 -0.59 75 No FLJ32942 hypothetical protein FLJ32942 BG150433 227711_at -0.82 -0.61 75 No guanine nucleotide binding protein (G GNB5 protein), beta 5 NM_006578 207124_s_at -0.83 -0.71 81 Yes glycerol-3-phosphate dehydrogenase 2 GPD2 (mitochondrial) U36310 210007_s_at -0.72 -0.59 63 Yes H2AFV H2A histone family, member V BF343852 212206_s_at -0.92 -0.70 69 No LAMC1 laminin, gamma 1 (formerly LAMB2) NM_002293 200771_at -0.79 -0.69 75 Yes LOC203069 hypothetical protein LOC203069 AI081543 212866_at -0.84 -0.74 75 No LOC283130 hypothetical protein LOC283130 AI336233 236436_at -0.79 -0.58 69 No LOC284801 hypothetical protein LOC284801 AL531683 225762_x_at -0.83 -0.62 63 No LRRK1 leucine-rich repeat kinase 1 AW792857 1565627_a_at -0.76 -0.53 81 No MAGEF1 melanoma antigen, family F, 1 NM_022149 218176_at -0.88 -0.72 81 Yes MESDC2 mesoderm development candidate 2 AK026606 224675_at -0.85 -0.65 63 No MGC11266 hypothetical protein MGC11266 BE326728 226118_at -0.91 -0.70 63 Yes MGC45731 hypothetical protein MGC45731 AW003092 227080_at -0.86 -0.58 63 No MGMT O-6-methylguanine-DNA methyltransferase NM_002412 204880_at 0.95 0.74 69 Yes MSC musculin (activated B-cell factor-1) AF060154 209928_s_at -0.78 -0.55 69 Yes MUTYH mutY homolog (E. coli) NM_012222 207727_s_at -0.97 -0.76 69 Yes Supplementary Table 1. (b) Basal alkylation sensitivity associated gene set (BASA) sorted by gene (page 2 of 2) Present in Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) % accuracy Network NET1 neuroepithelial cell transforming gene 1 NM_005863 201830_s_at -0.92 -0.58 56 Yes NQO2 NAD(P)H dehydrogenase, quinone 2 NM_000904 203814_s_at -0.71 -0.53 69 No platelet/endothelial cell adhesion molecule PECAM1 (CD31 antigen) M37780 208983_s_at -0.82 -0.62 63 Yes PHYH phytanoyl-CoA hydroxylase (Refsum disease) NM_006214 203335_at -0.85 -0.61 75 Yes PIAS2 protein inhibitor of activated STAT, 2 AF361054 1555514_a_at -0.73 -0.58 69 No phosphoinositide-3-kinase, regulatory PIK3R1 subunit, polypeptide 1 (p85 alpha) AI680192 212239_at -0.87 -0.76 63 No protein phosphatase 2 (formerly 2A), PPP2R1B regulatory subunit A (PR 65), beta isoform T79584 202883_s_at -0.78 -0.58 56 Yes RAD54B RAD54 homolog B (S. cerevisiae) NM_012415 219494_at -0.72 -0.66 63 Yes SFXN2 sideroflexin 2 AL530504 227560_at -0.83 -0.54 56 No sarcoglycan, beta (43kDa dystrophin- SGCB associated glycoprotein) U29586 205120_s_at -0.83 -0.68 63 Yes SYPL synaptophysin-like protein AI768845 201259_s_at -0.84 -0.58 69 No TM4SF12 transmembrane 4 superfamily member 12 NM_012338 219274_at -0.76 -0.58 63 No TM4SF7 transmembrane 4 superfamily member 7 BC000389 209263_x_at -0.85 -0.68 75 No TMEM14A transmembrane protein 14A NM_014051 218477_at -0.88 -0.70 63 No TSAP6 dudulin 2 NM_018234 218424_s_at -0.92 -0.70 75 Yes --- --- AI825302 238700_at -0.82 -0.64 63 No --- --- AA227879 235919_at -0.93 -0.58 56 No --- --- BE467688 231259_s_at -0.92 -0.52 56 No ALL 94 Supplementary Table 2. (a) Treated Ratio alkylation sensitivity associated gene set (TRASA) sorted by correlation (page 1 of 2) Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) low density lipoprotein receptor (familial LDLR hypercholesterolemia) NM_000527 202068_s_at 0.98 0.85 BCL2/adenovirus E1B 19kDa interacting BNIP3 protein 3 U15174 201848_s_at 0.94 0.86 --- --- AI375915 1555852_at 0.93 0.73 ZNF395 zinc finger protein 395 /// F-box protein 16 BC001237 223216_x_at 0.93 0.82 SCD stearoyl-CoA desaturase (delta-9-desaturase) AB032261 200832_s_at 0.93 0.76 histone 2, H2aa /// similar to Histone H2A.o HIST2H2AA (H2A/o) (H2A.2) (H2a-615) /// histone H2A/r NM_003516 218280_x_at 0.92 0.67 CTA-126B4.3 CGI-96 protein AL022316 202937_x_at 0.92 0.48 ING2 inhibitor of growth family, member 2 NM_001564 205981_s_at 0.91 0.75 PRO1843 hypothetical protein PRO1843 NM_018507 219599_at 0.90 0.38 --- --- AK026764 226348_at 0.89 0.72 C10orf75 Chromosome 10 open reading frame 75 AU151788 232230_at 0.88 0.68 LOC440731 hypothetical LOC440731 AI286239 237563_s_at 0.88 0.50 BCL2/adenovirus E1B 19kDa interacting BNIP3L protein 3-like /// BCL2/adenovirus