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 E1B 19kDa AF060922 221479_s_at 0.87 0.80

--- CDNA FLJ41489 fis, clone BRTHA2004582 W05495 230710_at 0.86 0.70

RP1-93H18.5 hypothetical protein LOC441168 AV734646 229391_s_at 0.84 0.59 CCR4-NOT transcription complex, subunit 6- CNOT6L like NM_144571 1553267_a_at -0.97 -0.36 tumor necrosis factor (ligand) superfamily, TNFSF4 member 4 (tax-transcriptionally activated NM_003326 207426_s_at -0.93 -0.80

TWSG1 twisted gastrulation homolog 1 (Drosophila) NM_020648 219201_s_at -0.92 -0.01 proline-serine-threonine phosphatase PSTPIP2 interacting protein 2 NM_024430 219938_s_at -0.92 -0.66

--- CDNA FLJ34007 fis, clone FCBBF1000349 AF131798 233310_at -0.92 -0.31

BTBD10 BTB (POZ) domain containing 10 BC005071 223174_at -0.90 -0.50 Transcribed locus, moderately similar to --- NP_055301.1 neuronal thread protein AD7c- AV699953 240616_at -0.89 -0.36

RAB14 RAB14, member RAS oncogene family AA919115 200927_s_at -0.89 -0.41

ITFG1 Integrin alpha FG-GAP repeat containing 1 AI077660 1556151_at -0.89 -0.57 pleckstrin homology-like domain, family A, PHLDA3 member 3 NM_012396 218634_at -0.89 -0.28

C12orf5 chromosome 12 open reading frame 5 NM_020375 219099_at -0.88 -0.53 dystrophin (muscular dystrophy, Duchenne DMD and Becker types) NM_004010 203881_s_at -0.88 -0.58 splicing factor, arginine/serine-rich 2, SFRS2IP interacting protein NM_004719 206989_s_at -0.88 -0.47 ribonucleotide reductase M2 B (TP53 RRM2B inducible) AB036063 223342_at -0.88 -0.69

FAS Fas (TNF receptor superfamily, member 6) Z70519 216252_x_at -0.87 -0.66 Supplementary Table 2. (a) Treated Ratio alkylation sensitivity associated gene set (TRASA) sorted by correlation (page 2 of 2)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all)

WDFY1 WD repeat and FYVE domain containing 1 AK022888 224800_at -0.86 -0.59

MGC5370 hypothetical protein MGC5370 AA902480 229711_s_at -0.86 -0.79 adaptor-related protein complex 1, sigma 3 AP1S3 subunit AF393369 1555731_a_at -0.86 -0.38

FLJ13576 hypothetical protein FLJ13576 NM_022484 218962_s_at -0.85 -0.66

KIF21A kinesin family member 21A AB051495 226003_at -0.85 -0.03 complement component (3d/Epstein Barr CR2 virus) receptor 2 NM_001877 205544_s_at -0.84 -0.53

TOB1 transducer of ERBB2, 1 AA675892 202704_at -0.84 -0.56

FHL2 four and a half LIM domains 2 NM_001450 202949_s_at -0.84 -0.69 signal transducer and activator of AFFX- AFFX- STAT1 transcription 1, 91kDa HUMISGF3A/M97935_MB HUMISGF3A/M97 -0.83 -0.54 Supplementary Table 2. (a) Treated Ratio alkylation sensitivity associated gene set (TRASA) sorted by gene (page 1 of 2)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) adaptor-related protein complex 1, sigma 3 AP1S3 subunit AF393369 1555731_a_at -0.86 -0.38 BCL2/adenovirus E1B 19kDa interacting BNIP3 protein 3 U15174 201848_s_at 0.94 0.86 BCL2/adenovirus E1B 19kDa interacting BNIP3L protein 3-like /// BCL2/adenovirus E1B 19kDa AF060922 221479_s_at 0.87 0.80

BTBD10 BTB (POZ) domain containing 10 BC005071 223174_at -0.90 -0.50

C10orf75 Chromosome 10 open reading frame 75 AU151788 232230_at 0.88 0.68

C12orf5 chromosome 12 open reading frame 5 NM_020375 219099_at -0.88 -0.53 CCR4-NOT transcription complex, subunit 6- CNOT6L like NM_144571 1553267_a_at -0.97 -0.36 complement component (3d/Epstein Barr CR2 virus) receptor 2 NM_001877 205544_s_at -0.84 -0.53

CTA-126B4.3 CGI-96 protein AL022316 202937_x_at 0.92 0.48 dystrophin (muscular dystrophy, Duchenne DMD and Becker types) NM_004010 203881_s_at -0.88 -0.58

FAS Fas (TNF receptor superfamily, member 6) Z70519 216252_x_at -0.87 -0.66

FHL2 four and a half LIM domains 2 NM_001450 202949_s_at -0.84 -0.69

FLJ13576 hypothetical protein FLJ13576 NM_022484 218962_s_at -0.85 -0.66 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

ING2 inhibitor of growth family, member 2 NM_001564 205981_s_at 0.91 0.75

ITFG1 Integrin alpha FG-GAP repeat containing 1 AI077660 1556151_at -0.89 -0.57

KIF21A kinesin family member 21A AB051495 226003_at -0.85 -0.03 low density lipoprotein receptor (familial LDLR hypercholesterolemia) NM_000527 202068_s_at 0.98 0.85

LOC440731 hypothetical LOC440731 AI286239 237563_s_at 0.88 0.50

MGC5370 hypothetical protein MGC5370 AA902480 229711_s_at -0.86 -0.79 pleckstrin homology-like domain, family A, PHLDA3 member 3 NM_012396 218634_at -0.89 -0.28

PRO1843 hypothetical protein PRO1843 NM_018507 219599_at 0.90 0.38 proline-serine-threonine phosphatase PSTPIP2 interacting protein 2 NM_024430 219938_s_at -0.92 -0.66

RAB14 RAB14, member RAS oncogene family AA919115 200927_s_at -0.89 -0.41

RP1-93H18.5 hypothetical protein LOC441168 AV734646 229391_s_at 0.84 0.59 ribonucleotide reductase M2 B (TP53 RRM2B inducible) AB036063 223342_at -0.88 -0.69

SCD stearoyl-CoA desaturase (delta-9-desaturase) AB032261 200832_s_at 0.93 0.76 splicing factor, arginine/serine-rich 2, SFRS2IP interacting protein NM_004719 206989_s_at -0.88 -0.47 signal transducer and activator of AFFX- AFFX- STAT1 transcription 1, 91kDa HUMISGF3A/M97935_MB HUMISGF3A/M97 -0.83 -0.54 tumor necrosis factor (ligand) superfamily, TNFSF4 member 4 (tax-transcriptionally activated NM_003326 207426_s_at -0.93 -0.80 Supplementary Table 2. (a) Treated Ratio alkylation sensitivity associated gene set (TRASA) sorted by gene (page 2 of 2)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all)

TOB1 transducer of ERBB2, 1 AA675892 202704_at -0.84 -0.56

TWSG1 twisted gastrulation homolog 1 (Drosophila) NM_020648 219201_s_at -0.92 -0.01

WDFY1 WD repeat and FYVE domain containing 1 AK022888 224800_at -0.86 -0.59

ZNF395 zinc finger protein 395 /// F-box protein 16 BC001237 223216_x_at 0.93 0.82 Transcribed locus, moderately similar to --- NP_055301.1 neuronal thread protein AD7c- AV699953 240616_at -0.89 -0.36

--- CDNA FLJ34007 fis, clone FCBBF1000349 AF131798 233310_at -0.92 -0.31

--- CDNA FLJ41489 fis, clone BRTHA2004582 W05495 230710_at 0.86 0.70

------AK026764 226348_at 0.89 0.72

------AI375915 1555852_at 0.93 0.73 Supplementary Table 3. (a) Treated alkylation sensitivity associated gene set (TASA) sorted by correlation (page 1 of 5)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) Overlap lymphotoxin beta (TNF superfamily, member LTB 3) NM_002341 207339_s_at 0.81 0.61

AK3 adenylate kinase 3 AI653169 204347_at 0.80 0.55

FLJ21616 hypothetical protein FLJ21616 NM_024567 219269_at 0.79 0.53

------AL035604 234954_at 0.77 0.60 BCL2/adenovirus E1B 19kDa interacting BNIP3 protein 3 U15174 201848_s_at 0.77 0.61

------BG332462 213166_x_at 0.76 0.64

MGC14289 similar to RIKEN cDNA 1200014N16 gene AI188445 228280_at 0.76 0.58

------BF116254 213011_s_at 0.75 0.59

--- Full length insert cDNA clone ZA84A12 AV734646 229391_s_at 0.74 0.53

ARL2 ADP-ribosylation factor-like 2 NM_001667 202564_x_at 0.74 0.53 low density lipoprotein receptor (familial LDLR hypercholesterolemia) NM_000527 202068_s_at 0.74 0.59

------AB032261 200832_s_at 0.74 0.51

C20orf11 chromosome 20 open reading frame 11 BG480592 225376_at -0.70 -0.54

DTX4 deltex 4 homolog (Drosophila) AV728526 212611_at -0.71 -0.53

HSPH1 heat shock 105kDa/110kDa protein 1 NM_006644 206976_s_at -0.72 -0.50

ZC3HDC7 zinc finger CCCH type domain containing 7 NM_014153 218348_s_at -0.72 -0.56

NSFL1C NSFL1 (p97) cofactor (p47) AL109658 217830_s_at -0.72 -0.52

------AF333388 211456_x_at -0.72 -0.60

ATOH8 atonal homolog 8 (Drosophila) AL831857 1558705_at -0.72 -0.64

TM4SF12 transmembrane 4 superfamily member 12 NM_012338 219274_at -0.72 -0.64 BASA

MTMR6 myotubularin related protein 6 U47635 214429_at -0.72 -0.53

SLIC1 selectin ligand interactor cytoplasmic-1 AK055837 1563641_a_at -0.72 -0.56 tumor necrosis factor receptor superfamily, TNFRSF10B member 10b AF016266 209295_at -0.72 -0.56

SLC2A4RG SLC2A4 regulator BE898559 222650_s_at -0.72 -0.52

MT1X metallothionein 1X NM_005952 208581_x_at -0.72 -0.60

MGC34132 hypothetical protein MGC34132 AK023140 221935_s_at -0.73 -0.59

LOC146542 similar to hypothetical protein MGC13138 BE676210 235950_at -0.73 -0.50

SSH1 slingshot homolog 1 (Drosophila) AL041728 221752_at -0.74 -0.65 phospholipase D1, phophatidylcholine- PLD1 specific AI378587 226636_at -0.74 -0.53 ectodermal-neural cortex (with BTB-like ENC1 domain) NM_003633 201341_at -0.74 -0.71 Supplementary Table 3. (a) Treated alkylation sensitivity associated gene set (TASA) sorted by correlation (page 2 of 5)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) Overlap

CHKA choline kinase alpha AI991328 204233_s_at -0.74 -0.52 hypothetical protein FLJ22955 /// hypothetical FLJ22955 protein FLJ22955 BC006472 224522_s_at -0.74 -0.53 low density lipoprotein receptor-related LRP6 protein 6 AV725248 225745_at -0.75 -0.54

PHF16 PHD finger protein 16 NM_014735 204866_at -0.75 -0.59

INPP1 inositol polyphosphate-1-phosphatase NM_002194 202794_at -0.76 -0.64

MRPL4 mitochondrial ribosomal protein L4 BC000756 223743_s_at -0.76 -0.54

STIM2 stromal interaction molecule 2 T97323 225246_at -0.76 -0.61

BCAP29 B-cell receptor-associated protein 29 AW873330 225674_at -0.76 -0.56

ANKRD9 ankyrin repeat domain 9 AW194999 230972_at -0.76 -0.55 BASA nudix (nucleoside diphosphate linked moiety NUDT15 X)-type motif 15 NM_018283 219347_at -0.76 -0.52

C11orf17 chromosome 11 open reading frame 17 AI933861 242515_x_at -0.76 -0.55 neutrophil cytosolic factor 2 (65kDa, chronic NCF2 granulomatous disease, autosomal 2) BC001606 209949_at -0.76 -0.56 p21/Cdc42/Rac1-activated kinase 1 (STE20 PAK1 homolog, yeast) AU147145 230100_x_at -0.77 -0.52

MT1G metallothionein 1G NM_005950 204745_x_at -0.77 -0.58 ribonucleotide reductase M2 B (TP53 RRM2B inducible) AB036063 223342_at -0.77 -0.59

CCAR1 cell division cycle and apoptosis regulator 1 BG541830 224737_x_at -0.77 -0.61 mitogen-activated protein kinase associated MAPKAP1 protein 1 BG499947 222426_at -0.77 -0.53

ACP5 acid phosphatase 5, tartrate resistant NM_001611 204638_at -0.77 -0.51

MT2A metallothionein 2A NM_005953 212185_x_at -0.77 -0.61 Gardner-Rasheed feline sarcoma viral (v-fgr) FGR oncogene homolog NM_005248 208438_s_at -0.77 -0.55

GM2A GM2 ganglioside activator X61094 215891_s_at -0.77 -0.57

FKSG44 FKSG44 gene BF435621 227964_at -0.78 -0.56

LOC153346 hypothetical protein LOC153346 AU157049 232181_at -0.78 -0.55 solute carrier family 7 (cationic amino acid SLC7A6 transporter, y+ system), member 6 NM_003983 203580_s_at -0.78 -0.51

KIAA2024 similar to F10G7.10.p AI708334 230029_x_at -0.78 -0.50

TM7SF3 transmembrane 7 superfamily member 3 NM_016551 217974_at -0.78 -0.64

LMO7 LIM domain 7 AA100793 242722_at -0.78 -0.54 tumor necrosis factor (ligand) superfamily, TNFSF4 member 4 (tax-transcriptionally activated NM_003326 207426_s_at -0.79 -0.64

--- CDNA FLJ34764 fis, clone NT2NE2002311 BF540749 226478_at -0.79 -0.49 transducin-like enhancer of split 4 (E(sp1) TLE4 homolog, Drosophila) NM_007005 204872_at -0.79 -0.71 Supplementary Table 3. (a) Treated alkylation sensitivity associated gene set (TASA) sorted by correlation (page 3 of 5)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) Overlap

ANKRA2 ankyrin repeat, family A (RFXANK-like), 2 NM_023039 218769_s_at -0.79 -0.61

TMEM14A transmembrane protein 14A NM_014051 218477_at -0.79 -0.52 BASA

RAB38 RAB38, member RAS oncogene family NM_022337 219412_at -0.79 -0.65

------AI380089 236099_at -0.79 -0.60

MGC5370 hypothetical protein MGC5370 AA902480 229711_s_at -0.79 -0.64

------BC044305 1569338_at -0.79 -0.53

SRI sorcin L12387 208921_s_at -0.79 -0.53

LOC113386 similar to envelope protein AA635618 242140_at -0.80 -0.50

------BE326214 229287_at -0.80 -0.51

------AB018310 212856_at -0.80 -0.53 tumor necrosis factor receptor superfamily, TNFRSF10D member 10d, decoy with truncated death AI738556 227345_at -0.80 -0.69

LCMR1 lung cancer metastasis-related protein 1 BF109807 226300_at -0.80 -0.61

LOC283687 hypothetical protein LOC283687 AL109714 217104_at -0.80 -0.64

LOC117584 fring N66669 229861_at -0.80 -0.59 cofactor required for Sp1 transcriptional CRSP2 activation, subunit 2, 150kDa AI971089 202611_s_at -0.80 -0.56

MAN2C1 mannosidase, alpha, class 2C, member 1 NM_006715 203668_at -0.80 -0.54

CKLFSF6 chemokine-like factor super family 6 NM_017801 217947_at -0.81 -0.56 DMC1 dosage suppressor of mck1 homolog, DMC1 meiosis-specific homologous recombination NM_007068 208386_x_at -0.81 -0.60 tumor necrosis factor receptor superfamily, TNFRSF6 member 6 Z70519 216252_x_at -0.81 -0.54 xeroderma pigmentosum, complementation XPC group C D21089 209375_at -0.81 -0.49 pseudogene MGC10997 /// pseudogene MGC10997 MGC10997 BC004405 224429_x_at -0.81 -0.56 pleckstrin homology-like domain, family A, PHLDA3 member 3 NM_012396 218634_at -0.81 -0.52

IL27RA interleukin 27 receptor, alpha NM_004843 205926_at -0.82 -0.51

TOP1 topoisomerase (DNA) I J03250 208901_s_at -0.82 -0.51

RAD18 RAD18 homolog (S. cerevisiae) AF169796 223417_at -0.83 -0.53

--- Clone IMAGE:5311129, mRNA AA114166 212993_at -0.83 -0.59

TIF1 transcriptional intermediary factor 1 AL538264 213301_x_at -0.83 -0.59

RAB23 RAB23, member RAS oncogene family AF161486 223463_at -0.83 -0.53

FKBP5 FK506 binding protein 5 W86302 224856_at -0.84 -0.73 cAMP responsive element binding protein-like CREBL2 2 AL529409 201989_s_at -0.84 -0.62 Supplementary Table 3. (a) Treated alkylation sensitivity associated gene set (TASA) sorted by correlation (page 4 of 5)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) Overlap

--- CDNA FLJ43676 fis, clone SYNOV4009129 BE464337 229512_at -0.84 -0.60 ubiquinol-cytochrome c reductase complex HSPC051 (7.2 kD) BE208777 228142_at -0.84 -0.51

HUMGT198A GT198, complete ORF BE964655 213951_s_at -0.84 -0.54

DPYSL2 dihydropyrimidinase-like 2 NM_001386 200762_at -0.84 -0.61 F-box and WD-40 domain protein 7 FBXW7 (archipelago homolog, Drosophila) BE551877 222729_at -0.85 -0.56

EHF ets homologous factor AI763378 225645_at -0.85 -0.55

C14orf46 chromosome 14 open reading frame 46 BG028765 228583_at -0.85 -0.60

------N30132 238929_at -0.85 -0.51

------AW452674 243374_x_at -0.85 -0.62 NADH dehydrogenase (ubiquinone) NDUFV3 flavoprotein 3, 10kDa NM_021075 226616_s_at -0.86 -0.56 Notch homolog 1, translocation-associated NOTCH1 (Drosophila) NM_017617 218902_at -0.86 -0.71 transcription termination factor, RNA TTF2 polymerase II AF080255 204407_at -0.86 -0.57

LAMP1 lysosomal-associated membrane protein 1 NM_005561 201552_at -0.87 -0.69 SMAD, mothers against DPP homolog 5 SMAD5 (Drosophila) AI439752 235451_at -0.88 -0.65

HSPA1B heat shock 70kDa protein 1B NM_005346 202581_at -0.88 -0.73

------AA827805 241364_at -0.88 -0.59

CDA08 T-cell immunomodulatory protein AI077660 1556151_at -0.88 -0.60

DKFZp451J0118 taxilin AL049795 212300_at -0.89 -0.59

CP110 CP110 protein NM_014711 204662_at -0.89 -0.57

SRP46 Splicing factor, arginine/serine-rich, 46kD AI343248 213152_s_at -0.90 -0.72

RAB14 RAB14, member RAS oncogene family AA919115 200927_s_at -0.90 -0.54

SLC35E3 solute carrier family 35, member E3 NM_018656 218988_at -0.90 -0.54

FLJ90709 hypothetical protein FLJ90709 BF696757 235241_at -0.90 -0.58

FLJ13576 hypothetical protein FLJ13576 NM_022484 218962_s_at -0.91 -0.64 proteasome (prosome, macropain) 26S PSMC2 subunit, ATPase, 2 BF215487 201067_at -0.91 -0.57

SSBP3 single stranded DNA binding protein 3 AA102468 222482_at -0.91 -0.57

GMRP-1 K+ channel tetramerization protein BC005071 223174_at -0.92 -0.64

LOC286434 hypothetical protein LOC286434 N32185 59433_at -0.92 -0.57

------AV699953 240616_at -0.93 -0.56 dystonia 1, torsion (autosomal dominant; DYT1 torsin A) NM_000113 202349_at -0.95 -0.69 Supplementary Table 3. (a) Treated alkylation sensitivity associated gene set (TASA) sorted by correlation (page 5 of 5)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) Overlap likely ortholog of mouse hypoxia induced HIG1 gene 1 BE739519 221896_s_at -0.98 -0.53 Supplementary Table 3. (b) Treated alkylation sensitivity associated gene set (TASA) sorted by gene (page 1 of 5)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) Overlap

ACP5 acid phosphatase 5, tartrate resistant NM_001611 204638_at -0.77 -0.51

AK3 adenylate kinase 3 AI653169 204347_at 0.80 0.55

ANKRA2 ankyrin repeat, family A (RFXANK-like), 2 NM_023039 218769_s_at -0.79 -0.61

ANKRD9 ankyrin repeat domain 9 AW194999 230972_at -0.76 -0.55 BASA

ARL2 ADP-ribosylation factor-like 2 NM_001667 202564_x_at 0.74 0.53

ATOH8 atonal homolog 8 (Drosophila) AL831857 1558705_at -0.72 -0.64

BCAP29 B-cell receptor-associated protein 29 AW873330 225674_at -0.76 -0.56 BCL2/adenovirus E1B 19kDa interacting BNIP3 protein 3 U15174 201848_s_at 0.77 0.61

C11orf17 chromosome 11 open reading frame 17 AI933861 242515_x_at -0.76 -0.55

C14orf46 chromosome 14 open reading frame 46 BG028765 228583_at -0.85 -0.60

C20orf11 chromosome 20 open reading frame 11 BG480592 225376_at -0.70 -0.54

CCAR1 cell division cycle and apoptosis regulator 1 BG541830 224737_x_at -0.77 -0.61

CDA08 T-cell immunomodulatory protein AI077660 1556151_at -0.88 -0.60

CHKA choline kinase alpha AI991328 204233_s_at -0.74 -0.52

CKLFSF6 chemokine-like factor super family 6 NM_017801 217947_at -0.81 -0.56

CP110 CP110 protein NM_014711 204662_at -0.89 -0.57 cAMP responsive element binding protein-like CREBL2 2 AL529409 201989_s_at -0.84 -0.62 cofactor required for Sp1 transcriptional CRSP2 activation, subunit 2, 150kDa AI971089 202611_s_at -0.80 -0.56

DKFZp451J0118 taxilin AL049795 212300_at -0.89 -0.59 DMC1 dosage suppressor of mck1 homolog, DMC1 meiosis-specific homologous recombination NM_007068 208386_x_at -0.81 -0.60

DPYSL2 dihydropyrimidinase-like 2 NM_001386 200762_at -0.84 -0.61

DTX4 deltex 4 homolog (Drosophila) AV728526 212611_at -0.71 -0.53 dystonia 1, torsion (autosomal dominant; DYT1 torsin A) NM_000113 202349_at -0.95 -0.69

EHF ets homologous factor AI763378 225645_at -0.85 -0.55 ectodermal-neural cortex (with BTB-like ENC1 domain) NM_003633 201341_at -0.74 -0.71 F-box and WD-40 domain protein 7 FBXW7 (archipelago homolog, Drosophila) BE551877 222729_at -0.85 -0.56 Gardner-Rasheed feline sarcoma viral (v-fgr) FGR oncogene homolog NM_005248 208438_s_at -0.77 -0.55

FKBP5 FK506 binding protein 5 W86302 224856_at -0.84 -0.73

FKSG44 FKSG44 gene BF435621 227964_at -0.78 -0.56

FLJ13576 hypothetical protein FLJ13576 NM_022484 218962_s_at -0.91 -0.64 Supplementary Table 3. (b) Treated alkylation sensitivity associated gene set (TASA) sorted by gene (page 2 of 5)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) Overlap

FLJ21616 hypothetical protein FLJ21616 NM_024567 219269_at 0.79 0.53 hypothetical protein FLJ22955 /// hypothetical FLJ22955 protein FLJ22955 BC006472 224522_s_at -0.74 -0.53

FLJ90709 hypothetical protein FLJ90709 BF696757 235241_at -0.90 -0.58

GM2A GM2 ganglioside activator X61094 215891_s_at -0.77 -0.57

GMRP-1 K+ channel tetramerization protein BC005071 223174_at -0.92 -0.64 likely ortholog of mouse hypoxia induced HIG1 gene 1 BE739519 221896_s_at -0.98 -0.53

HSPA1B heat shock 70kDa protein 1B NM_005346 202581_at -0.88 -0.73 ubiquinol-cytochrome c reductase complex HSPC051 (7.2 kD) BE208777 228142_at -0.84 -0.51

HSPH1 heat shock 105kDa/110kDa protein 1 NM_006644 206976_s_at -0.72 -0.50

HUMGT198A GT198, complete ORF BE964655 213951_s_at -0.84 -0.54

IL27RA interleukin 27 receptor, alpha NM_004843 205926_at -0.82 -0.51

INPP1 inositol polyphosphate-1-phosphatase NM_002194 202794_at -0.76 -0.64

KIAA2024 similar to F10G7.10.p AI708334 230029_x_at -0.78 -0.50

LAMP1 lysosomal-associated membrane protein 1 NM_005561 201552_at -0.87 -0.69

LCMR1 lung cancer metastasis-related protein 1 BF109807 226300_at -0.80 -0.61 low density lipoprotein receptor (familial LDLR hypercholesterolemia) NM_000527 202068_s_at 0.74 0.59

LMO7 LIM domain 7 AA100793 242722_at -0.78 -0.54

LOC113386 similar to envelope protein AA635618 242140_at -0.80 -0.50

LOC117584 fring N66669 229861_at -0.80 -0.59

LOC146542 similar to hypothetical protein MGC13138 BE676210 235950_at -0.73 -0.50

LOC153346 hypothetical protein LOC153346 AU157049 232181_at -0.78 -0.55

LOC283687 hypothetical protein LOC283687 AL109714 217104_at -0.80 -0.64

LOC286434 hypothetical protein LOC286434 N32185 59433_at -0.92 -0.57 low density lipoprotein receptor-related LRP6 protein 6 AV725248 225745_at -0.75 -0.54 lymphotoxin beta (TNF superfamily, member LTB 3) NM_002341 207339_s_at 0.81 0.61

MAN2C1 mannosidase, alpha, class 2C, member 1 NM_006715 203668_at -0.80 -0.54 mitogen-activated protein kinase associated MAPKAP1 protein 1 BG499947 222426_at -0.77 -0.53 pseudogene MGC10997 /// pseudogene MGC10997 MGC10997 BC004405 224429_x_at -0.81 -0.56

MGC14289 similar to RIKEN cDNA 1200014N16 gene AI188445 228280_at 0.76 0.58

MGC34132 hypothetical protein MGC34132 AK023140 221935_s_at -0.73 -0.59 Supplementary Table 3. (b) Treated alkylation sensitivity associated gene set (TASA) sorted by gene (page 3 of 5)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) Overlap

MGC5370 hypothetical protein MGC5370 AA902480 229711_s_at -0.79 -0.64

MRPL4 mitochondrial ribosomal protein L4 BC000756 223743_s_at -0.76 -0.54

MT1G metallothionein 1G NM_005950 204745_x_at -0.77 -0.58

MT1X metallothionein 1X NM_005952 208581_x_at -0.72 -0.60

MT2A metallothionein 2A NM_005953 212185_x_at -0.77 -0.61

MTMR6 myotubularin related protein 6 U47635 214429_at -0.72 -0.53 neutrophil cytosolic factor 2 (65kDa, chronic NCF2 granulomatous disease, autosomal 2) BC001606 209949_at -0.76 -0.56 NADH dehydrogenase (ubiquinone) NDUFV3 flavoprotein 3, 10kDa NM_021075 226616_s_at -0.86 -0.56 Notch homolog 1, translocation-associated NOTCH1 (Drosophila) NM_017617 218902_at -0.86 -0.71

NSFL1C NSFL1 (p97) cofactor (p47) AL109658 217830_s_at -0.72 -0.52 nudix (nucleoside diphosphate linked moiety NUDT15 X)-type motif 15 NM_018283 219347_at -0.76 -0.52 p21/Cdc42/Rac1-activated kinase 1 (STE20 PAK1 homolog, yeast) AU147145 230100_x_at -0.77 -0.52

PHF16 PHD finger protein 16 NM_014735 204866_at -0.75 -0.59 pleckstrin homology-like domain, family A, PHLDA3 member 3 NM_012396 218634_at -0.81 -0.52 phospholipase D1, phophatidylcholine- PLD1 specific AI378587 226636_at -0.74 -0.53 proteasome (prosome, macropain) 26S PSMC2 subunit, ATPase, 2 BF215487 201067_at -0.91 -0.57

RAB14 RAB14, member RAS oncogene family AA919115 200927_s_at -0.90 -0.54

RAB23 RAB23, member RAS oncogene family AF161486 223463_at -0.83 -0.53

RAB38 RAB38, member RAS oncogene family NM_022337 219412_at -0.79 -0.65

RAD18 RAD18 homolog (S. cerevisiae) AF169796 223417_at -0.83 -0.53 ribonucleotide reductase M2 B (TP53 RRM2B inducible) AB036063 223342_at -0.77 -0.59

SLC2A4RG SLC2A4 regulator BE898559 222650_s_at -0.72 -0.52

SLC35E3 solute carrier family 35, member E3 NM_018656 218988_at -0.90 -0.54 solute carrier family 7 (cationic amino acid SLC7A6 transporter, y+ system), member 6 NM_003983 203580_s_at -0.78 -0.51

SLIC1 selectin ligand interactor cytoplasmic-1 AK055837 1563641_a_at -0.72 -0.56 SMAD, mothers against DPP homolog 5 SMAD5 (Drosophila) AI439752 235451_at -0.88 -0.65

SRI sorcin L12387 208921_s_at -0.79 -0.53

SRP46 Splicing factor, arginine/serine-rich, 46kD AI343248 213152_s_at -0.90 -0.72

SSBP3 single stranded DNA binding protein 3 AA102468 222482_at -0.91 -0.57

SSH1 slingshot homolog 1 (Drosophila) AL041728 221752_at -0.74 -0.65 Supplementary Table 3. (b) Treated alkylation sensitivity associated gene set (TASA) sorted by gene (page 4 of 5)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) Overlap

STIM2 stromal interaction molecule 2 T97323 225246_at -0.76 -0.61

TIF1 transcriptional intermediary factor 1 AL538264 213301_x_at -0.83 -0.59 transducin-like enhancer of split 4 (E(sp1) TLE4 homolog, Drosophila) NM_007005 204872_at -0.79 -0.71

TM4SF12 transmembrane 4 superfamily member 12 NM_012338 219274_at -0.72 -0.64 BASA

TM7SF3 transmembrane 7 superfamily member 3 NM_016551 217974_at -0.78 -0.64

TMEM14A transmembrane protein 14A NM_014051 218477_at -0.79 -0.52 BASA tumor necrosis factor receptor superfamily, TNFRSF10B member 10b AF016266 209295_at -0.72 -0.56 tumor necrosis factor receptor superfamily, TNFRSF10D member 10d, decoy with truncated death AI738556 227345_at -0.80 -0.69 tumor necrosis factor receptor superfamily, TNFRSF6 member 6 Z70519 216252_x_at -0.81 -0.54 tumor necrosis factor (ligand) superfamily, TNFSF4 member 4 (tax-transcriptionally activated NM_003326 207426_s_at -0.79 -0.64

TOP1 topoisomerase (DNA) I J03250 208901_s_at -0.82 -0.51 transcription termination factor, RNA TTF2 polymerase II AF080255 204407_at -0.86 -0.57 xeroderma pigmentosum, complementation XPC group C D21089 209375_at -0.81 -0.49

ZC3HDC7 zinc finger CCCH type domain containing 7 NM_014153 218348_s_at -0.72 -0.56

------AW452674 243374_x_at -0.85 -0.62

------AA827805 241364_at -0.88 -0.59

------AV699953 240616_at -0.93 -0.56

------N30132 238929_at -0.85 -0.51

------AI380089 236099_at -0.79 -0.60

------AL035604 234954_at 0.77 0.60

--- CDNA FLJ43676 fis, clone SYNOV4009129 BE464337 229512_at -0.84 -0.60

--- Full length insert cDNA clone ZA84A12 AV734646 229391_s_at 0.74 0.53

------BE326214 229287_at -0.80 -0.51

--- CDNA FLJ34764 fis, clone NT2NE2002311 BF540749 226478_at -0.79 -0.49

------BG332462 213166_x_at 0.76 0.64

------BF116254 213011_s_at 0.75 0.59

--- Clone IMAGE:5311129, mRNA AA114166 212993_at -0.83 -0.59

------AB018310 212856_at -0.80 -0.53

------AF333388 211456_x_at -0.72 -0.60

------AB032261 200832_s_at 0.74 0.51 Supplementary Table 3. (b) Treated alkylation sensitivity associated gene set (TASA) sorted by gene (page 5 of 5)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) Overlap

------BC044305 1569338_at -0.79 -0.53 Supplementary Table 4. (a) 240 Genes differentially expressed between extreme responding cell lines. Sorted by correlation (page 1 of 8)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all)

MGMT O-6-methylguanine-DNA methyltransferase NM_002412 204880_at 0.95 0.74 phosphatidylinositol transfer protein, PITPNC1 cytoplasmic 1 NM_012417 219155_at 0.86 0.09

C21orf56 chromosome 21 open reading frame 56 AL136871 223360_at 0.86 0.54

C10orf58 chromosome 10 open reading frame 58 BF512388 228155_at 0.83 0.25 adaptor-related protein complex 1, sigma 3 AP1S3 subunit AF393369 1555733_s_at 0.83 0.36 v-rel reticuloendotheliosis viral oncogene REL homolog (avian) NM_002908 206036_s_at 0.82 0.30

WDFY1 WD repeat and FYVE domain containing 1 AK022888 224800_at 0.80 0.50

--- CDNA FLJ41375 fis, clone BRCAN2007700 BE739287 235242_at 0.78 0.33

PXN paxillin NM_002859 201087_at 0.78 0.36 immunoglobulin kappa constant /// Clone P2- IGKC 32 anti-oxidized LDL immunoglobulin light L14458 211644_x_at 0.78 0.26

TncRNA trophoblast-derived noncoding RNA AV699657 234989_at 0.75 0.28

IMP-3 IGF-II mRNA-binding protein 3 NM_006547 203820_s_at 0.75 0.48

AK3 adenylate kinase 3 NM_013410 204348_s_at 0.74 0.33 UDP-N-acetyl-alpha-D- GALNTL4 galactosamine:polypeptide N- BC037341 1554079_at 0.74 0.41

JAK1 Janus kinase 1 (a protein tyrosine kinase) AL039831 201648_at 0.74 0.31

BZW2 basic leucine zipper and W2 domains 2 NM_014038 217809_at 0.74 0.36

SLC35D2 solute carrier family 35, member D2 AJ005866 213083_at 0.73 0.26

BTLA B and T lymphocyte associated AW294080 236226_at 0.73 0.23

EVI2A ecotropic viral integration site 2A NM_014210 204774_at 0.73 0.51

TRIP6 thyroid hormone receptor interactor 6 AF000974 209129_at 0.72 0.48

CD226 CD226 antigen NM_006566 207315_at 0.71 0.36

--- CDNA FLJ26120 fis, clone SYN00419 AI355441 225239_at 0.71 0.34 lymphotoxin beta (TNF superfamily, member LTB 3) NM_002341 207339_s_at 0.71 0.50

------AI652899 228812_at 0.70 0.30 fasciculation and elongation protein zeta 1 FEZ1 (zygin I) NM_005103 203562_at 0.69 0.36

CHI3L2 chitinase 3-like 2 U58515 213060_s_at 0.68 0.52

LOC285628 hypothetical protein LOC285628 AL389942 232504_at 0.68 0.31

STC2 stanniocalcin 2 BC000658 203439_s_at 0.67 0.18 guanine nucleotide binding protein (G GNG2 protein), gamma 2 AK026424 224964_s_at 0.66 0.36

CRY1 cryptochrome 1 (photolyase-like) D83702 209674_at 0.66 0.02 Supplementary Table 4. (a) 240 Genes differentially expressed between extreme responding cell lines. Sorted by correlation (page 2 of 8)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all)

LAMP3 lysosomal-associated membrane protein 3 NM_014398 205569_at 0.64 0.21 phospholipase A2, group IVA (cytosolic, PLA2G4A calcium-dependent) M68874 210145_at 0.64 0.43

FUCA1 fucosidase, alpha-L- 1, tissue NM_000147 202838_at 0.63 0.23

CAPN2 calpain 2, (m/II) large subunit M23254 208683_at 0.63 0.49

IMAP1 immunity associated protein 1 NM_130759 1552316_a_at 0.62 0.48 COBW domain containing 2 /// COBW-like CBWD2 protein AW169333 229804_x_at 0.61 0.37

RAB34 RAB34, member RAS oncogene family AF322067 224710_at 0.60 0.01 prion protein (p27-30) (Creutzfeld-Jakob PRNP disease, Gerstmann-Strausler-Scheinker NM_000311 201300_s_at 0.57 0.22 DnaJ (Hsp40) homolog, subfamily C, member DNAJC12 12 NM_021800 218976_at 0.56 0.20

ARRDC3 arrestin domain containing 3 AB037797 224797_at -0.48 -0.31 solute carrier family 2 (facilitated SLC2A5 glucose/fructose transporter), member 5 BE560461 204429_s_at -0.49 -0.22 heat shock 70kDa protein 5 (glucose- HSPA5 regulated protein, 78kDa) AF216292 211936_at -0.52 -0.23

PIR pirin (iron-binding nuclear protein) NM_003662 207469_s_at -0.52 -0.08 protein disulfide isomerase related protein ERP70 (calcium-binding protein, intestinal-related) BC000425 208658_at -0.54 -0.34

ARMET arginine-rich, mutated in early stage tumors NM_006010 202655_at -0.54 -0.15

ZNF564 zinc finger protein 564 AK092760 1553957_at -0.55 -0.48

--- Hypothetical gene supported by BC040060 AI138766 1560818_at -0.57 -0.35

AQP3 aquaporin 3 N74607 39248_at -0.58 -0.19

TCF4 transcription factor 4 BF433429 212382_at -0.58 -0.31

TCEAL3 transcription elongation factor A (SII)-like 3 AA847654 227279_at -0.58 -0.44

GMPPA GDP-mannose pyrophosphorylase A NM_013335 218070_s_at -0.58 -0.47 ELK3, ETS-domain protein (SRF accessory ELK3 protein 2) AW575374 221773_at -0.59 -0.45

LOXL4 lysyl oxidase-like 4 AW190565 227145_at -0.59 -0.31

OGFR opioid growth factor receptor AF172449 211513_s_at -0.59 -0.28

MKL2 MKL/myocardin-like 2 NM_014048 218259_at -0.59 -0.44

GPR2 G protein-coupled receptor 2 NM_016602 220565_at -0.60 -0.16

JM11 JM11 protein AI668708 239403_at -0.60 -0.33 O-acyltransferase (membrane bound) domain OACT2 containing 2 AI761250 213288_at -0.60 -0.16 Fc fragment of IgG, low affinity IIb, receptor FCGR2B for (CD32) M31933 210889_s_at -0.60 -0.07 tumor necrosis factor (ligand) superfamily, TNFSF12-TNFSF13 member 12-member 13 /// tumor necrosis AF114013 210314_x_at -0.60 -0.55 Supplementary Table 4. (a) 240 Genes differentially expressed between extreme responding cell lines. Sorted by correlation (page 3 of 8)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all)

IFNAR2 interferon (alpha, beta and omega) receptor 2 L41944 204786_s_at -0.60 -0.37

--- CDNA FLJ10196 fis, clone HEMBA1004776 W74476 226997_at -0.61 -0.07

CNR1 cannabinoid receptor 1 (brain) U73304 213436_at -0.61 -0.42

PPT2 palmitoyl-protein thioesterase 2 AF020543 209490_s_at -0.61 -0.25

C22orf14 chromosome 22 open reading frame 14 AI655697 229721_x_at -0.61 -0.31 synovial sarcoma, X breakpoint 2 interacting SSX2IP protein AW136988 203015_s_at -0.62 -0.45

ARG99 ARG99 protein BF109231 226322_at -0.62 -0.29

--- Clone IMAGE:3606519, mRNA, partial cds BC009463 1559822_s_at -0.62 -0.37

TIF1 transcriptional intermediary factor 1 AL538264 213301_x_at -0.62 -0.56

------AI140519 244367_at -0.62 -0.30

NRG1 neuregulin 1 NM_013959 206343_s_at -0.62 -0.26

FLJ39441 hypothetical protein FLJ39441 BE780878 235440_at -0.63 -0.53 multiple C2-domains with two transmembrane MCTP2 regions 2 AK026984 229021_at -0.63 -0.43

KIAA1856 KIAA1856 protein AI936523 226691_at -0.63 -0.39

------AA053713 237669_at -0.63 -0.34

FLJ21924 hypothetical protein FLJ21924 NM_024774 219705_at -0.63 -0.49

MAN1A1 mannosidase, alpha, class 1A, member 1 NM_005907 208116_s_at -0.63 -0.31 similar to carbonic anhydrase VB, LOC340591 mitochondrial precursor; carbonic AA521288 238435_at -0.64 -0.44

NID nidogen (enactin) NM_002508 202008_s_at -0.64 -0.16 spectrin repeat containing, nuclear envelope SYNE1 1 AF043290 209447_at -0.64 -0.43

------AI869296 243121_x_at -0.64 -0.33

FLJ14050 hypothetical protein FLJ14050 NM_024869 220430_at -0.65 -0.31

AMACR alpha-methylacyl-CoA racemase AF047020 209426_s_at -0.65 -0.50

------AA404996 244633_at -0.65 -0.45

FLJ13154 hypothetical protein FLJ13154 BC006291 1554016_a_at -0.65 -0.40

CTSC cathepsin C NM_001814 201487_at -0.66 -0.36

RHEB Ras homolog enriched in brain AA678073 241795_at -0.66 -0.36 transmembrane gamma-carboxyglutamic acid TMG4 protein 4 BF905445 238513_at -0.66 -0.23

LOC144871 hypothetical protein LOC144871 BG913589 1558080_s_at -0.67 -0.35 CDK5 regulatory subunit associated protein 1- CDKAL1 like 1 NM_017774 220039_s_at -0.67 -0.38 Supplementary Table 4. (a) 240 Genes differentially expressed between extreme responding cell lines. Sorted by correlation (page 4 of 8)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all)

DUSP16 dual specificity phosphatase 16 AB051487 224832_at -0.67 -0.51

NS3TP2 HCV NS3-transactivated protein 2 AW575493 218706_s_at -0.67 -0.41

------BG432887 243699_at -0.67 -0.44 DnaJ (Hsp40) homolog, subfamily B, member DNAJB11 11 BC001144 223054_at -0.67 -0.16

ACP2 acid phosphatase 2, lysosomal NM_001610 202767_at -0.67 -0.31

DSG2 desmoglein 2 BF031829 217901_at -0.67 -0.34 ectodermal-neural cortex (with BTB-like ENC1 domain) AF010314 201340_s_at -0.67 -0.45

KIAA0830 KIAA0830 protein AF131747 212573_at -0.68 -0.29

------AA243143 214182_at -0.68 -0.47

KIAA1324 maba1 AI565067 226248_s_at -0.68 -0.40

ARHGAP5 Rho GTPase activating protein 5 AK023014 233849_s_at -0.68 -0.42

MT1F metallothionein 1F (functional) BF246115 213629_x_at -0.68 -0.52

RAB38 RAB38, member RAS oncogene family NM_022337 219412_at -0.68 -0.39

------BC029166 1566156_at -0.68 -0.31

------AA205444 228415_at -0.69 -0.20

------AA922496 244891_x_at -0.69 -0.36 transcription factor AP-2 beta (activating TFAP2B enhancer binding protein 2 beta) NM_003221 1553394_a_at -0.69 -0.43

APG4C APG4 autophagy 4 homolog C (S. cerevisiae) BF197009 228190_at -0.69 -0.54

MGC4170 MGC4170 protein AK001821 212959_s_at -0.69 -0.35

------AI439886 227344_at -0.69 -0.47 ASF1 anti-silencing function 1 homolog B (S. ASF1B cerevisiae) NM_018154 218115_at -0.69 -0.55

ATP8B2 ATPase, Class I, type 8B, member 2 AB032963 226771_at -0.69 -0.33

C21orf4 chromosome 21 open reading frame 4 NM_006134 219600_s_at -0.69 -0.33 Fc fragment of IgG, low affinity IIa, receptor FCGR2A for (CD32) /// Fc fragment of IgG, low affinity U90939 210992_x_at -0.69 -0.14

SCARF1 scavenger receptor class F, member 1 AB052950 1555021_a_at -0.70 -0.27

LOC157570 hypothetical protein LOC157570 AA740849 235588_at -0.70 -0.49

--- Similar to LOC93426 protein BC035731 1559960_x_at -0.70 -0.55

------T81422 236191_at -0.70 -0.01

--- CDNA: FLJ22146 fis, clone HEP22153 AK025799 232236_at -0.70 -0.35 glycerol-3-phosphate dehydrogenase 2 GPD2 (mitochondrial) U36310 210007_s_at -0.70 -0.59 Supplementary Table 4. (a) 240 Genes differentially expressed between extreme responding cell lines. Sorted by correlation (page 5 of 8)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all)

--- CDNA FLJ36327 fis, clone THYMU2005748 AW974657 240877_x_at -0.71 -0.57

SELS selenoprotein S AF328864 223209_s_at -0.71 -0.39

------AI345813 231422_x_at -0.71 -0.39 aldehyde dehydrogenase 7 family, member ALDH7A1 A1 BC002515 208951_at -0.71 -0.33

SPTBN1 spectrin, beta, non-erythrocytic 1 NM_003128 200672_x_at -0.71 -0.61

ZNF592 zinc finger protein 592 NM_014630 204473_s_at -0.72 -0.49

NQO2 NAD(P)H dehydrogenase, quinone 2 NM_000904 203814_s_at -0.72 -0.53

CALR calreticulin NM_004343 200935_at -0.72 -0.10

C17orf27 chromosome 17 open reading frame 27 AA233374 225929_s_at -0.72 -0.17

MGC12197 BM-011 protein BC010357 1555501_s_at -0.72 -0.62

FLJ10979 hypothetical protein FLJ10979 AA564740 235710_at -0.72 -0.39

ATP10D ATPase, Class V, type 10D AI478147 213238_at -0.72 -0.51

EDN1 endothelin 1 BC036851 1564630_at -0.72 -0.50

GOLPH2 golgi phosphoprotein 2 NM_016548 217771_at -0.72 -0.50

DKFZp313A2432 hypothetical protein DKFZp313A2432 AI742358 230006_s_at -0.72 -0.62 5,10-methenyltetrahydrofolate synthetase (5- MTHFS formyltetrahydrofolate cyclo-ligase) NM_006441 203433_at -0.72 -0.60

ILF3 interleukin enhancer binding factor 3, 90kDa AF147209 208931_s_at -0.72 -0.53 Full-length cDNA clone CS0DB002YN21 of --- Neuroblastoma Cot 10-normalized of Homo AA833830 230896_at -0.72 -0.42

RAD54B RAD54 homolog B (S. cerevisiae) NM_012415 219494_at -0.73 -0.66

FAD158 factor for adipocyte differentiation 158 AL136919 223533_at -0.73 -0.72

------AW510657 228904_at -0.73 -0.33 lymphocyte antigen 64 homolog, LY64 radioprotective 105kDa (mouse) NM_005582 206206_at -0.73 -0.07

FLJ12442 hypothetical protein FLJ12442 NM_022908 218051_s_at -0.73 -0.53 Partial mRNA for immunoglobulin heavy chain --- variable region (IGHV gene), isolate B-CLL M24670 211635_x_at -0.73 0.04

LXN latexin NM_020169 218729_at -0.74 -0.33

KIAA0152 KIAA0152 gene product BC000371 200616_s_at -0.74 -0.44

------NM_001943 1553105_s_at -0.74 -0.43

------AI827550 229606_at -0.74 -0.40 MRNA full length insert cDNA clone --- EUROIMAGE 2344436 AF086401 1559361_at -0.74 -0.56

------BF508702 227184_at -0.74 -0.63 Supplementary Table 4. (a) 240 Genes differentially expressed between extreme responding cell lines. Sorted by correlation (page 6 of 8)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all)

------AF130104 210596_at -0.74 -0.39

CGI-111 CGI-111 protein NM_016048 218170_at -0.75 -0.64

NRN1 neuritin 1 NM_016588 218625_at -0.75 -0.13

KIAA0186 KIAA0186 gene product NM_021067 206102_at -0.75 -0.55 phospholipase D1, phophatidylcholine- PLD1 specific AI378587 226636_at -0.75 -0.56

--- Clone IMAGE:4794726, mRNA BF513121 226189_at -0.75 -0.43

DPYSL2 dihydropyrimidinase-like 2 NM_022044 218681_s_at -0.75 -0.27

--- Hypothetical protein LOC125150 BG108034 229119_s_at -0.75 -0.45

------AI458297 236244_at -0.75 -0.44

FLJ10901 hypothetical protein FLJ10901 NM_018265 219010_at -0.75 -0.56 hypothetical protein from EUROIMAGE LOC58489 588495 AI339710 225436_at -0.75 -0.60 leucine zipper-EF-hand containing LETM2 transmembrane protein 2 BE467261 226705_at -0.75 -0.44 protein phosphatase 3 (formerly 2B), catalytic PPP3CA subunit, alpha isoform (calcineurin A alpha) AL353950 202429_s_at -0.76 -0.40

--- Clone IMAGE:4814008, mRNA BI547087 1568983_a_at -0.76 -0.24 protein tyrosine phosphatase, receptor type, PTPRK K NM_002844 203038_at -0.76 -0.33

PDCD6 programmed cell death 6 AI435073 244139_s_at -0.76 -0.55

LRRK1 leucine-rich repeat kinase 1 AW792857 1565627_a_at -0.76 -0.53

------BF115793 236346_at -0.76 -0.25

GAMT guanidinoacetate N-methyltransferase NM_000156 205354_at -0.76 -0.48

ARSB arylsulfatase B AW168942 232197_x_at -0.77 -0.52

KIAA1608 KIAA1608 AB046828 226849_at -0.77 -0.66

ZNF124 zinc finger protein 124 (HZF-16) NM_003431 206928_at -0.77 -0.45

FLJ13912 hypothetical protein FLJ13912 NM_022770 218719_s_at -0.77 -0.54

IL27RA interleukin 27 receptor, alpha AI983115 222062_at -0.78 -0.44

PIAS2 protein inhibitor of activated STAT, 2 AF077953 214442_s_at -0.78 -0.59

MGC13057 hypothetical protein MGC13057 BE645119 228195_at -0.78 -0.47

MGST3 microsomal glutathione S-transferase 3 NM_004528 201403_s_at -0.78 -0.58

PTAFR platelet-activating factor receptor D10202 206278_at -0.78 -0.73 protein phosphatase 2 (formerly 2A), PPP2R1B regulatory subunit A (PR 65), beta isoform T79584 202883_s_at -0.78 -0.58

HOXB4 homeo box B4 AL137449 231767_at -0.78 -0.48 Supplementary Table 4. (a) 240 Genes differentially expressed between extreme responding cell lines. Sorted by correlation (page 7 of 8)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all)

C1orf19 chromosome 1 open reading frame 19 BF111780 225400_at -0.78 -0.68

MSC musculin (activated B-cell factor-1) AF060154 209928_s_at -0.78 -0.55 cytochrome P450, family 4, subfamily V, CYP4V2 polypeptide 2 AU146978 226745_at -0.79 -0.52

LOC283130 hypothetical protein LOC283130 AI336233 236436_at -0.79 -0.58

HOXB2 homeo box B2 NM_002145 205453_at -0.79 -0.38

MSI2 musashi homolog 2 (Drosophila) BF029215 243579_at -0.79 -0.37

------BF511695 236424_at -0.79 -0.46

LAMC1 laminin, gamma 1 (formerly LAMB2) NM_002293 200771_at -0.79 -0.69

E2F2 E2F transcription factor 2 AL561296 228361_at -0.79 -0.65

FKBP5 FK506 binding protein 5 NM_004117 204560_at -0.79 -0.74

SLD5 SLD5 homolog /// SLD5 homolog BC005995 211767_at -0.80 -0.38

SEPHS2 selenophosphate synthetase 2 NM_012248 200961_at -0.81 -0.70

TM4SF12 transmembrane 4 superfamily member 12 AI056699 230625_s_at -0.81 -0.65 discoidin, CUB and LCCL domain containing DCBLD1 1 NM_173674 1553768_a_at -0.81 -0.53

ETV5 ets variant gene 5 (ets-related molecule) BF060791 203348_s_at -0.81 -0.46

CMIP c-Maf-inducing protein AI363061 224992_s_at -0.81 -0.54

FLJ12886 hypothetical protein FLJ12886 NM_019108 221335_x_at -0.81 -0.59

CCND2 cyclin D2 NM_001759 200953_s_at -0.82 -0.37

MGC29816 hypothetical protein MGC29816 BC004344 212313_at -0.82 -0.73 membrane-bound transcription factor MBTPS1 protease, site 1 NM_003791 201620_at -0.82 -0.47 solute carrier family 35 (UDP-glucuronic SLC35D1 acid/UDP-N-acetylgalactosamine dual AI769637 209712_at -0.82 -0.50

------AI825302 238700_at -0.82 -0.64 platelet/endothelial cell adhesion molecule PECAM1 (CD31 antigen) M37780 208983_s_at -0.82 -0.62

FLJ32942 hypothetical protein FLJ32942 BG150433 227711_at -0.82 -0.61

FLNB filamin B, beta (actin binding protein 278) AV712733 208613_s_at -0.82 -0.44

SLC35B1 solute carrier family 35, member B1 NM_005827 202433_at -0.83 -0.35 guanine nucleotide binding protein (G GNB5 protein), beta 5 NM_006578 207124_s_at -0.83 -0.71 sarcoglycan, beta (43kDa dystrophin- SGCB associated glycoprotein) U29586 205120_s_at -0.83 -0.68

------AI870547 242406_at -0.83 -0.49

SFXN2 sideroflexin 2 AL530504 227560_at -0.83 -0.54 Supplementary Table 4. (a) 240 Genes differentially expressed between extreme responding cell lines. Sorted by correlation (page 8 of 8)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all)

LOC284801 hypothetical protein LOC284801 AL531683 225762_x_at -0.83 -0.62

DTNBP1 dystrobrevin binding protein 1 AF061734 223446_s_at -0.83 -0.68

SYPL synaptophysin-like protein AI768845 201259_s_at -0.84 -0.58

CDW92 CDW92 antigen AK022549 224595_at -0.84 -0.27

LOC203069 hypothetical protein LOC203069 AI081543 212866_at -0.84 -0.74

FIGNL1 fidgetin-like 1 NM_022116 1552921_a_at -0.85 -0.71

MESDC2 mesoderm development candidate 2 AK026606 224675_at -0.85 -0.65

TM4SF7 transmembrane 4 superfamily member 7 BC000389 209263_x_at -0.85 -0.68

PHYH phytanoyl-CoA hydroxylase (Refsum disease) NM_006214 203335_at -0.85 -0.61

CPNE3 copine III AA541758 202118_s_at -0.86 -0.46 NADH dehydrogenase (ubiquinone) NDUFV3 flavoprotein 3, 10kDa NM_021075 226616_s_at -0.86 -0.46

MGC45731 hypothetical protein MGC45731 AW003092 227080_at -0.86 -0.58 phosphoinositide-3-kinase, regulatory PIK3R1 subunit, polypeptide 1 (p85 alpha) AI680192 212239_at -0.87 -0.76

MAGEF1 melanoma antigen, family F, 1 NM_022149 218176_at -0.87 -0.72

TMEM14A transmembrane protein 14A NM_014051 218477_at -0.87 -0.70 echinoderm microtubule associated protein EML4 like 4 AV707345 223068_at -0.88 -0.60

CRTAP cartilage associated protein BQ876971 1555889_a_at -0.89 -0.29

ANKRD9 ankyrin repeat domain 9 AW194999 230972_at -0.90 -0.67

------AW517716 222281_s_at -0.90 -0.30

MGC11266 hypothetical protein MGC11266 BE326728 226118_at -0.91 -0.70

CANP cancer-associated nucleoprotein AA960844 1557128_at -0.91 -0.50

DTYMK deoxythymidylate kinase (thymidylate kinase) NM_012145 203270_at -0.91 -0.58

H2AFV H2A histone family, member V BF343852 212206_s_at -0.92 -0.70

------BE467688 231259_s_at -0.92 -0.52

NET1 neuroepithelial cell transforming gene 1 NM_005863 201830_s_at -0.92 -0.58

TSAP6 dudulin 2 NM_018234 218424_s_at -0.92 -0.70

CKLFSF3 chemokine-like factor super family 3 AL574900 224733_at -0.93 -0.58

------AA227879 235919_at -0.93 -0.58

CKLF chemokine-like factor NM_016951 219161_s_at -0.94 -0.62

MUTYH mutY homolog (E. coli) NM_012222 207727_s_at -0.97 -0.76 Supplementary Table 4. (b) 240 Genes differentially expressed between extreme responding cell lines. Sorted by gene (page 1 of 8)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all)

ACP2 acid phosphatase 2, lysosomal NM_001610 202767_at -0.67 -0.31

AK3 adenylate kinase 3 NM_013410 204348_s_at 0.74 0.33 aldehyde dehydrogenase 7 family, member ALDH7A1 A1 BC002515 208951_at -0.71 -0.33

AMACR alpha-methylacyl-CoA racemase AF047020 209426_s_at -0.65 -0.50

ANKRD9 ankyrin repeat domain 9 AW194999 230972_at -0.90 -0.67 adaptor-related protein complex 1, sigma 3 AP1S3 subunit AF393369 1555733_s_at 0.83 0.36

APG4C APG4 autophagy 4 homolog C (S. cerevisiae) BF197009 228190_at -0.69 -0.54

AQP3 aquaporin 3 N74607 39248_at -0.58 -0.19

ARG99 ARG99 protein BF109231 226322_at -0.62 -0.29

ARHGAP5 Rho GTPase activating protein 5 AK023014 233849_s_at -0.68 -0.42

ARMET arginine-rich, mutated in early stage tumors NM_006010 202655_at -0.54 -0.15

ARRDC3 arrestin domain containing 3 AB037797 224797_at -0.48 -0.31

ARSB arylsulfatase B AW168942 232197_x_at -0.77 -0.52 ASF1 anti-silencing function 1 homolog B (S. ASF1B cerevisiae) NM_018154 218115_at -0.69 -0.55

ATP10D ATPase, Class V, type 10D AI478147 213238_at -0.72 -0.51

ATP8B2 ATPase, Class I, type 8B, member 2 AB032963 226771_at -0.69 -0.33

BTLA B and T lymphocyte associated AW294080 236226_at 0.73 0.23

BZW2 basic leucine zipper and W2 domains 2 NM_014038 217809_at 0.74 0.36

C10orf58 chromosome 10 open reading frame 58 BF512388 228155_at 0.83 0.25

C17orf27 chromosome 17 open reading frame 27 AA233374 225929_s_at -0.72 -0.17

C1orf19 chromosome 1 open reading frame 19 BF111780 225400_at -0.78 -0.68

C21orf4 chromosome 21 open reading frame 4 NM_006134 219600_s_at -0.69 -0.33

C21orf56 chromosome 21 open reading frame 56 AL136871 223360_at 0.86 0.54

C22orf14 chromosome 22 open reading frame 14 AI655697 229721_x_at -0.61 -0.31

CALR calreticulin NM_004343 200935_at -0.72 -0.10

CANP cancer-associated nucleoprotein AA960844 1557128_at -0.91 -0.50

CAPN2 calpain 2, (m/II) large subunit M23254 208683_at 0.63 0.49 COBW domain containing 2 /// COBW-like CBWD2 protein AW169333 229804_x_at 0.61 0.37

CCND2 cyclin D2 NM_001759 200953_s_at -0.82 -0.37

CD226 CD226 antigen NM_006566 207315_at 0.71 0.36 Supplementary Table 4. (b) 240 Genes differentially expressed between extreme responding cell lines. Sorted by gene (page 2 of 8)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) CDK5 regulatory subunit associated protein 1- CDKAL1 like 1 NM_017774 220039_s_at -0.67 -0.38

CDW92 CDW92 antigen AK022549 224595_at -0.84 -0.27

CGI-111 CGI-111 protein NM_016048 218170_at -0.75 -0.64

CHI3L2 chitinase 3-like 2 U58515 213060_s_at 0.68 0.52

CKLF chemokine-like factor NM_016951 219161_s_at -0.94 -0.62

CKLFSF3 chemokine-like factor super family 3 AL574900 224733_at -0.93 -0.58

CMIP c-Maf-inducing protein AI363061 224992_s_at -0.81 -0.54

CNR1 cannabinoid receptor 1 (brain) U73304 213436_at -0.61 -0.42

CPNE3 copine III AA541758 202118_s_at -0.86 -0.46

CRTAP cartilage associated protein BQ876971 1555889_a_at -0.89 -0.29

CRY1 cryptochrome 1 (photolyase-like) D83702 209674_at 0.66 0.02

CTSC cathepsin C NM_001814 201487_at -0.66 -0.36 cytochrome P450, family 4, subfamily V, CYP4V2 polypeptide 2 AU146978 226745_at -0.79 -0.52 discoidin, CUB and LCCL domain containing DCBLD1 1 NM_173674 1553768_a_at -0.81 -0.53

DKFZp313A2432 hypothetical protein DKFZp313A2432 AI742358 230006_s_at -0.72 -0.62 DnaJ (Hsp40) homolog, subfamily B, member DNAJB11 11 BC001144 223054_at -0.67 -0.16 DnaJ (Hsp40) homolog, subfamily C, member DNAJC12 12 NM_021800 218976_at 0.56 0.20

DPYSL2 dihydropyrimidinase-like 2 NM_022044 218681_s_at -0.75 -0.27

DSG2 desmoglein 2 BF031829 217901_at -0.67 -0.34

DTNBP1 dystrobrevin binding protein 1 AF061734 223446_s_at -0.83 -0.68

DTYMK deoxythymidylate kinase (thymidylate kinase) NM_012145 203270_at -0.91 -0.58

DUSP16 dual specificity phosphatase 16 AB051487 224832_at -0.67 -0.51

E2F2 E2F transcription factor 2 AL561296 228361_at -0.79 -0.65

EDN1 endothelin 1 BC036851 1564630_at -0.72 -0.50 ELK3, ETS-domain protein (SRF accessory ELK3 protein 2) AW575374 221773_at -0.59 -0.45 echinoderm microtubule associated protein EML4 like 4 AV707345 223068_at -0.88 -0.60 ectodermal-neural cortex (with BTB-like ENC1 domain) AF010314 201340_s_at -0.67 -0.45 protein disulfide isomerase related protein ERP70 (calcium-binding protein, intestinal-related) BC000425 208658_at -0.54 -0.34

ETV5 ets variant gene 5 (ets-related molecule) BF060791 203348_s_at -0.81 -0.46

EVI2A ecotropic viral integration site 2A NM_014210 204774_at 0.73 0.51 Supplementary Table 4. (b) 240 Genes differentially expressed between extreme responding cell lines. Sorted by gene (page 3 of 8)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all)

FAD158 factor for adipocyte differentiation 158 AL136919 223533_at -0.73 -0.72 Fc fragment of IgG, low affinity IIa, receptor FCGR2A for (CD32) /// Fc fragment of IgG, low affinity U90939 210992_x_at -0.69 -0.14 Fc fragment of IgG, low affinity IIb, receptor FCGR2B for (CD32) M31933 210889_s_at -0.60 -0.07 fasciculation and elongation protein zeta 1 FEZ1 (zygin I) NM_005103 203562_at 0.69 0.36

FIGNL1 fidgetin-like 1 NM_022116 1552921_a_at -0.85 -0.71

FKBP5 FK506 binding protein 5 NM_004117 204560_at -0.79 -0.74

FLJ10901 hypothetical protein FLJ10901 NM_018265 219010_at -0.75 -0.56

FLJ10979 hypothetical protein FLJ10979 AA564740 235710_at -0.72 -0.39

FLJ12442 hypothetical protein FLJ12442 NM_022908 218051_s_at -0.73 -0.53

FLJ12886 hypothetical protein FLJ12886 NM_019108 221335_x_at -0.81 -0.59

FLJ13154 hypothetical protein FLJ13154 BC006291 1554016_a_at -0.65 -0.40

FLJ13912 hypothetical protein FLJ13912 NM_022770 218719_s_at -0.77 -0.54

FLJ14050 hypothetical protein FLJ14050 NM_024869 220430_at -0.65 -0.31

FLJ21924 hypothetical protein FLJ21924 NM_024774 219705_at -0.63 -0.49

FLJ32942 hypothetical protein FLJ32942 BG150433 227711_at -0.82 -0.61

FLJ39441 hypothetical protein FLJ39441 BE780878 235440_at -0.63 -0.53

FLNB filamin B, beta (actin binding protein 278) AV712733 208613_s_at -0.82 -0.44

FUCA1 fucosidase, alpha-L- 1, tissue NM_000147 202838_at 0.63 0.23 UDP-N-acetyl-alpha-D- GALNTL4 galactosamine:polypeptide N- BC037341 1554079_at 0.74 0.41

GAMT guanidinoacetate N-methyltransferase NM_000156 205354_at -0.76 -0.48

GMPPA GDP-mannose pyrophosphorylase A NM_013335 218070_s_at -0.58 -0.47 guanine nucleotide binding protein (G GNB5 protein), beta 5 NM_006578 207124_s_at -0.83 -0.71 guanine nucleotide binding protein (G GNG2 protein), gamma 2 AK026424 224964_s_at 0.66 0.36

GOLPH2 golgi phosphoprotein 2 NM_016548 217771_at -0.72 -0.50 glycerol-3-phosphate dehydrogenase 2 GPD2 (mitochondrial) U36310 210007_s_at -0.70 -0.59

GPR2 G protein-coupled receptor 2 NM_016602 220565_at -0.60 -0.16

H2AFV H2A histone family, member V BF343852 212206_s_at -0.92 -0.70

HOXB2 homeo box B2 NM_002145 205453_at -0.79 -0.38

HOXB4 homeo box B4 AL137449 231767_at -0.78 -0.48 heat shock 70kDa protein 5 (glucose- HSPA5 regulated protein, 78kDa) AF216292 211936_at -0.52 -0.23 Supplementary Table 4. (b) 240 Genes differentially expressed between extreme responding cell lines. Sorted by gene (page 4 of 8)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all)

IFNAR2 interferon (alpha, beta and omega) receptor 2 L41944 204786_s_at -0.60 -0.37 immunoglobulin kappa constant /// Clone P2- IGKC 32 anti-oxidized LDL immunoglobulin light L14458 211644_x_at 0.78 0.26

IL27RA interleukin 27 receptor, alpha AI983115 222062_at -0.78 -0.44

ILF3 interleukin enhancer binding factor 3, 90kDa AF147209 208931_s_at -0.72 -0.53

IMAP1 immunity associated protein 1 NM_130759 1552316_a_at 0.62 0.48

IMP-3 IGF-II mRNA-binding protein 3 NM_006547 203820_s_at 0.75 0.48

JAK1 Janus kinase 1 (a protein tyrosine kinase) AL039831 201648_at 0.74 0.31

JM11 JM11 protein AI668708 239403_at -0.60 -0.33

KIAA0152 KIAA0152 gene product BC000371 200616_s_at -0.74 -0.44

KIAA0186 KIAA0186 gene product NM_021067 206102_at -0.75 -0.55

KIAA0830 KIAA0830 protein AF131747 212573_at -0.68 -0.29

KIAA1324 maba1 AI565067 226248_s_at -0.68 -0.40

KIAA1608 KIAA1608 AB046828 226849_at -0.77 -0.66

KIAA1856 KIAA1856 protein AI936523 226691_at -0.63 -0.39

LAMC1 laminin, gamma 1 (formerly LAMB2) NM_002293 200771_at -0.79 -0.69

LAMP3 lysosomal-associated membrane protein 3 NM_014398 205569_at 0.64 0.21 leucine zipper-EF-hand containing LETM2 transmembrane protein 2 BE467261 226705_at -0.75 -0.44

LOC144871 hypothetical protein LOC144871 BG913589 1558080_s_at -0.67 -0.35

LOC157570 hypothetical protein LOC157570 AA740849 235588_at -0.70 -0.49

LOC203069 hypothetical protein LOC203069 AI081543 212866_at -0.84 -0.74

LOC283130 hypothetical protein LOC283130 AI336233 236436_at -0.79 -0.58

LOC284801 hypothetical protein LOC284801 AL531683 225762_x_at -0.83 -0.62

LOC285628 hypothetical protein LOC285628 AL389942 232504_at 0.68 0.31 similar to carbonic anhydrase VB, LOC340591 mitochondrial precursor; carbonic AA521288 238435_at -0.64 -0.44 hypothetical protein from EUROIMAGE LOC58489 588495 AI339710 225436_at -0.75 -0.60

LOXL4 lysyl oxidase-like 4 AW190565 227145_at -0.59 -0.31

LRRK1 leucine-rich repeat kinase 1 AW792857 1565627_a_at -0.76 -0.53 lymphotoxin beta (TNF superfamily, member LTB 3) NM_002341 207339_s_at 0.71 0.50

LXN latexin NM_020169 218729_at -0.74 -0.33 lymphocyte antigen 64 homolog, LY64 radioprotective 105kDa (mouse) NM_005582 206206_at -0.73 -0.07 Supplementary Table 4. (b) 240 Genes differentially expressed between extreme responding cell lines. Sorted by gene (page 5 of 8)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all)

MAGEF1 melanoma antigen, family F, 1 NM_022149 218176_at -0.87 -0.72

MAN1A1 mannosidase, alpha, class 1A, member 1 NM_005907 208116_s_at -0.63 -0.31 membrane-bound transcription factor MBTPS1 protease, site 1 NM_003791 201620_at -0.82 -0.47 multiple C2-domains with two transmembrane MCTP2 regions 2 AK026984 229021_at -0.63 -0.43

MESDC2 mesoderm development candidate 2 AK026606 224675_at -0.85 -0.65

MGC11266 hypothetical protein MGC11266 BE326728 226118_at -0.91 -0.70

MGC12197 BM-011 protein BC010357 1555501_s_at -0.72 -0.62

MGC13057 hypothetical protein MGC13057 BE645119 228195_at -0.78 -0.47

MGC29816 hypothetical protein MGC29816 BC004344 212313_at -0.82 -0.73

MGC4170 MGC4170 protein AK001821 212959_s_at -0.69 -0.35

MGC45731 hypothetical protein MGC45731 AW003092 227080_at -0.86 -0.58

MGMT O-6-methylguanine-DNA methyltransferase NM_002412 204880_at 0.95 0.74

MGST3 microsomal glutathione S-transferase 3 NM_004528 201403_s_at -0.78 -0.58

MKL2 MKL/myocardin-like 2 NM_014048 218259_at -0.59 -0.44

MSC musculin (activated B-cell factor-1) AF060154 209928_s_at -0.78 -0.55

MSI2 musashi homolog 2 (Drosophila) BF029215 243579_at -0.79 -0.37

MT1F metallothionein 1F (functional) BF246115 213629_x_at -0.68 -0.52 5,10-methenyltetrahydrofolate synthetase (5- MTHFS formyltetrahydrofolate cyclo-ligase) NM_006441 203433_at -0.72 -0.60

MUTYH mutY homolog (E. coli) NM_012222 207727_s_at -0.97 -0.76 NADH dehydrogenase (ubiquinone) NDUFV3 flavoprotein 3, 10kDa NM_021075 226616_s_at -0.86 -0.46

NET1 neuroepithelial cell transforming gene 1 NM_005863 201830_s_at -0.92 -0.58

NID nidogen (enactin) NM_002508 202008_s_at -0.64 -0.16

NQO2 NAD(P)H dehydrogenase, quinone 2 NM_000904 203814_s_at -0.72 -0.53

NRG1 neuregulin 1 NM_013959 206343_s_at -0.62 -0.26

NRN1 neuritin 1 NM_016588 218625_at -0.75 -0.13

NS3TP2 HCV NS3-transactivated protein 2 AW575493 218706_s_at -0.67 -0.41 O-acyltransferase (membrane bound) domain OACT2 containing 2 AI761250 213288_at -0.60 -0.16

OGFR opioid growth factor receptor AF172449 211513_s_at -0.59 -0.28

PDCD6 programmed cell death 6 AI435073 244139_s_at -0.76 -0.55 platelet/endothelial cell adhesion molecule PECAM1 (CD31 antigen) M37780 208983_s_at -0.82 -0.62 Supplementary Table 4. (b) 240 Genes differentially expressed between extreme responding cell lines. Sorted by gene (page 6 of 8)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all)

PHYH phytanoyl-CoA hydroxylase (Refsum disease) NM_006214 203335_at -0.85 -0.61

PIAS2 protein inhibitor of activated STAT, 2 AF077953 214442_s_at -0.78 -0.59 phosphoinositide-3-kinase, regulatory PIK3R1 subunit, polypeptide 1 (p85 alpha) AI680192 212239_at -0.87 -0.76

PIR pirin (iron-binding nuclear protein) NM_003662 207469_s_at -0.52 -0.08 phosphatidylinositol transfer protein, PITPNC1 cytoplasmic 1 NM_012417 219155_at 0.86 0.09 phospholipase A2, group IVA (cytosolic, PLA2G4A calcium-dependent) M68874 210145_at 0.64 0.43 phospholipase D1, phophatidylcholine- PLD1 specific AI378587 226636_at -0.75 -0.56 protein phosphatase 2 (formerly 2A), PPP2R1B regulatory subunit A (PR 65), beta isoform T79584 202883_s_at -0.78 -0.58 protein phosphatase 3 (formerly 2B), catalytic PPP3CA subunit, alpha isoform (calcineurin A alpha) AL353950 202429_s_at -0.76 -0.40

PPT2 palmitoyl-protein thioesterase 2 AF020543 209490_s_at -0.61 -0.25 prion protein (p27-30) (Creutzfeld-Jakob PRNP disease, Gerstmann-Strausler-Scheinker NM_000311 201300_s_at 0.57 0.22

PTAFR platelet-activating factor receptor D10202 206278_at -0.78 -0.73 protein tyrosine phosphatase, receptor type, PTPRK K NM_002844 203038_at -0.76 -0.33

PXN paxillin NM_002859 201087_at 0.78 0.36

RAB34 RAB34, member RAS oncogene family AF322067 224710_at 0.60 0.01

RAB38 RAB38, member RAS oncogene family NM_022337 219412_at -0.68 -0.39

RAD54B RAD54 homolog B (S. cerevisiae) NM_012415 219494_at -0.73 -0.66 v-rel reticuloendotheliosis viral oncogene REL homolog (avian) NM_002908 206036_s_at 0.82 0.30

RHEB Ras homolog enriched in brain AA678073 241795_at -0.66 -0.36

SCARF1 scavenger receptor class F, member 1 AB052950 1555021_a_at -0.70 -0.27

SELS selenoprotein S AF328864 223209_s_at -0.71 -0.39

SEPHS2 selenophosphate synthetase 2 NM_012248 200961_at -0.81 -0.70

SFXN2 sideroflexin 2 AL530504 227560_at -0.83 -0.54 sarcoglycan, beta (43kDa dystrophin- SGCB associated glycoprotein) U29586 205120_s_at -0.83 -0.68 solute carrier family 2 (facilitated SLC2A5 glucose/fructose transporter), member 5 BE560461 204429_s_at -0.49 -0.22

SLC35B1 solute carrier family 35, member B1 NM_005827 202433_at -0.83 -0.35 solute carrier family 35 (UDP-glucuronic SLC35D1 acid/UDP-N-acetylgalactosamine dual AI769637 209712_at -0.82 -0.50

SLC35D2 solute carrier family 35, member D2 AJ005866 213083_at 0.73 0.26

SLD5 SLD5 homolog /// SLD5 homolog BC005995 211767_at -0.80 -0.38

SPTBN1 spectrin, beta, non-erythrocytic 1 NM_003128 200672_x_at -0.71 -0.61 Supplementary Table 4. (b) 240 Genes differentially expressed between extreme responding cell lines. Sorted by gene (page 7 of 8)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) synovial sarcoma, X breakpoint 2 interacting SSX2IP protein AW136988 203015_s_at -0.62 -0.45

STC2 stanniocalcin 2 BC000658 203439_s_at 0.67 0.18 spectrin repeat containing, nuclear envelope SYNE1 1 AF043290 209447_at -0.64 -0.43

SYPL synaptophysin-like protein AI768845 201259_s_at -0.84 -0.58

TCEAL3 transcription elongation factor A (SII)-like 3 AA847654 227279_at -0.58 -0.44

TCF4 transcription factor 4 BF433429 212382_at -0.58 -0.31 transcription factor AP-2 beta (activating TFAP2B enhancer binding protein 2 beta) NM_003221 1553394_a_at -0.69 -0.43

TIF1 transcriptional intermediary factor 1 AL538264 213301_x_at -0.62 -0.56

TM4SF12 transmembrane 4 superfamily member 12 AI056699 230625_s_at -0.81 -0.65

TM4SF7 transmembrane 4 superfamily member 7 BC000389 209263_x_at -0.85 -0.68

TMEM14A transmembrane protein 14A NM_014051 218477_at -0.87 -0.70 transmembrane gamma-carboxyglutamic acid TMG4 protein 4 BF905445 238513_at -0.66 -0.23 tumor necrosis factor (ligand) superfamily, TNFSF12-TNFSF13 //member 12-member 13 /// tumor necrosis AF114013 210314_x_at -0.60 -0.55

TRIP6 thyroid hormone receptor interactor 6 AF000974 209129_at 0.72 0.48

TSAP6 dudulin 2 NM_018234 218424_s_at -0.92 -0.70

TncRNA trophoblast-derived noncoding RNA AV699657 234989_at 0.75 0.28

WDFY1 WD repeat and FYVE domain containing 1 AK022888 224800_at 0.80 0.50

ZNF124 zinc finger protein 124 (HZF-16) NM_003431 206928_at -0.77 -0.45

ZNF564 zinc finger protein 564 AK092760 1553957_at -0.55 -0.48

ZNF592 zinc finger protein 592 NM_014630 204473_s_at -0.72 -0.49

--- Clone IMAGE:4794726, mRNA BF513121 226189_at -0.75 -0.43 MRNA full length insert cDNA clone --- EUROIMAGE 2344436 AF086401 1559361_at -0.74 -0.56

--- Similar to LOC93426 protein BC035731 1559960_x_at -0.70 -0.55

------AA053713 237669_at -0.63 -0.34 Partial mRNA for immunoglobulin heavy chain --- variable region (IGHV gene), isolate B-CLL M24670 211635_x_at -0.73 0.04 Full-length cDNA clone CS0DB002YN21 of --- Neuroblastoma Cot 10-normalized of Homo AA833830 230896_at -0.72 -0.42

------AI140519 244367_at -0.62 -0.30

------BF508702 227184_at -0.74 -0.63

------AA404996 244633_at -0.65 -0.45

--- Hypothetical gene supported by BC040060 AI138766 1560818_at -0.57 -0.35 Supplementary Table 4. (b) 240 Genes differentially expressed between extreme responding cell lines. Sorted by gene (page 8 of 8)

Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all)

--- CDNA FLJ26120 fis, clone SYN00419 AI355441 225239_at 0.71 0.34

------AA922496 244891_x_at -0.69 -0.36

------AI869296 243121_x_at -0.64 -0.33

------NM_001943 1553105_s_at -0.74 -0.43

--- Clone IMAGE:3606519, mRNA, partial cds BC009463 1559822_s_at -0.62 -0.37

------AI345813 231422_x_at -0.71 -0.39

--- CDNA: FLJ22146 fis, clone HEP22153 AK025799 232236_at -0.70 -0.35

--- Hypothetical protein LOC125150 BG108034 229119_s_at -0.75 -0.45

------AW510657 228904_at -0.73 -0.33

--- CDNA FLJ10196 fis, clone HEMBA1004776 W74476 226997_at -0.61 -0.07

------AI439886 227344_at -0.69 -0.47

------BG432887 243699_at -0.67 -0.44

------AA205444 228415_at -0.69 -0.20

------AA243143 214182_at -0.68 -0.47

------AI458297 236244_at -0.75 -0.44

------T81422 236191_at -0.70 -0.01

--- CDNA FLJ36327 fis, clone THYMU2005748 AW974657 240877_x_at -0.71 -0.57

--- Clone IMAGE:4814008, mRNA BI547087 1568983_a_at -0.76 -0.24

------BC029166 1566156_at -0.68 -0.31

------AI652899 228812_at 0.70 0.30

------BF511695 236424_at -0.79 -0.46

------AI825302 238700_at -0.82 -0.64

------AF130104 210596_at -0.74 -0.39

------AI827550 229606_at -0.74 -0.40

--- CDNA FLJ41375 fis, clone BRCAN2007700 BE739287 235242_at 0.78 0.33

------BF115793 236346_at -0.76 -0.25

------AI870547 242406_at -0.83 -0.49

------AA227879 235919_at -0.93 -0.58

------AW517716 222281_s_at -0.90 -0.30

------BE467688 231259_s_at -0.92 -0.52 Supplementary Table 5. Proteins identified in basally activated network (page 1 of 11) High relative Modulated or Entrez Gene Name Description Affymetrix Probeset ID expression Associated Family ID amiloride binding protein 1 (amine oxidase ABP1 (copper-containing)) 241795_at Highest sensitivity Modulated enzyme 26

ACP2 acid phosphatase 2, lysosomal 202767_at Highest sensitivity Modulated phosphatase 53

Actin NA NA Associated group

ADAM10 ADAM metallopeptidase domain 10 NA NA Associated peptidase 102 ADAM metallopeptidase domain 19 (meltrin ADAM19 beta) NA NA Associated peptidase 8728

Adenylate Cyclase NA NA Associated group apoptosis-inducing factor, mitochondrion- AIFM2 associated, 2 231422_x_at Highest sensitivity Modulated enzyme 84883

AK3L1 adenylate kinase 3-like 1 225342_at Lowest sensitivity Modulated kinase 205

Akt NA NA Associated group aldehyde dehydrogenase 7 family, member ALDH7A1 A1 208950_s_at Highest sensitivity Modulated enzyme 501

AMACR alpha-methylacyl-CoA racemase 209426_s_at Highest sensitivity Modulated enzyme 23600 adaptor-related protein complex 1, beta 1 AP1B1 subunit NA NA Associated transporter 162 adaptor-related protein complex 1, gamma 1 AP1G1 subunit NA NA Associated transporter 164 adaptor-related protein complex 1, gamma 2 AP1G2 subunit NA NA Associated transporter 8906 adaptor-related protein complex 1, mu 1 AP1M1 subunit NA NA Associated transporter 8907 adaptor-related protein complex 1, mu 2 AP1M2 subunit NA NA Associated transporter 10053 adaptor-related protein complex 1, sigma 1 AP1S1 subunit NA NA Associated transporter 1174 adaptor-related protein complex 1, sigma 2 AP1S2 subunit NA NA Associated transporter 8905 adaptor-related protein complex 1, sigma 3 AP1S3 subunit 1555734_x_at Lowest sensitivity Modulated transporter 130340 APEX nuclease (multifunctional DNA repair APEX1 enzyme) 1 NA NA Associated enzyme 328 amyloid beta (A4) precursor protein APP (peptidase nexin-II, Alzheimer disease) NA NA Associated other 351

AQP3 aquaporin 3 (Gill blood group) 39248_at Highest sensitivity Modulated transporter 360

ARF6 ADP-ribosylation factor 6 214182_at Highest sensitivity Modulated transporter 382

ARHGAP5 Rho GTPase activating protein 5 233849_s_at Highest sensitivity Modulated enzyme 394

ARHGDIA Rho GDP dissociation inhibitor (GDI) alpha NA NA Associated other 396

ARMET arginine-rich, mutated in early stage tumors 202655_at Highest sensitivity Modulated other 7873

ARRDC3 arrestin domain containing 3 224797_at Highest sensitivity Modulated other 57561 ASF1 anti-silencing function 1 homolog B (S. ASF1B cerevisiae) 218115_at Highest sensitivity Modulated other 55723 transcription BCL3 B-cell CLL/lymphoma 3 NA NA Associated regulator 602 biogenesis of lysosome-related organelles BLOC1S1 complex-1, subunit 1 NA NA Associated other 2647 Supplementary Table 5. Proteins identified in basally activated network (page 2 of 11) High relative Modulated or Entrez Gene Name Description Affymetrix Probeset ID expression Associated Family ID biogenesis of lysosome-related organelles BLOC1S2 complex-1, subunit 2 NA NA Associated other 282991 BCL2/adenovirus E1B 19kDa interacting BNIP3 protein 3 NA NA Associated other 664 BCL2/adenovirus E1B 19kDa interacting BNIP3L protein 3-like NA NA Associated other 665 translation BZW2 basic leucine zipper and W2 domains 2 217809_at Lowest sensitivity Modulated regulator 28969

C10ORF58 chromosome 10 open reading frame 58 228155_at Lowest sensitivity Modulated other 84293

Calcineurin protein(s) NA NA Associated complex

Calpain NA NA Associated complex transcription CALR calreticulin 200935_at Highest sensitivity Modulated regulator 811

CAPN2 calpain 2, (m/II) large subunit 208683_at Lowest sensitivity Modulated peptidase 824

Caspase NA NA Associated group

Cbp/p300 NA NA Associated group

CCL27 chemokine (C-C motif) ligand 27 NA NA Associated cytokine 10850

CCND2 cyclin D2 200953_s_at Highest sensitivity Modulated other 894 G-protein CCR10 chemokine (C-C motif) receptor 10 220565_at Highest sensitivity Modulated coupled 2826

CD226 CD226 molecule 207315_at Lowest sensitivity Modulated other 10666 transmembran CD247 CD247 molecule NA NA Associated e receptor 919

CD38 CD38 molecule 236191_at Highest sensitivity Modulated enzyme 952 CCAAT/enhancer binding protein (C/EBP), transcription CEBPE epsilon NA NA Associated regulator 1053

CENPO centromere protein O 226118_at Highest sensitivity Modulated other 79172

CHI3L2 chitinase 3-like 2 213060_s_at Lowest sensitivity Modulated enzyme 1117

CISH cytokine inducible SH2-containing protein NA NA Associated other 1154 Cbp/p300-interacting transactivator, with transcription CITED1 Glu/Asp-rich carboxy-terminal domain, 1 NA NA Associated regulator 4435 Cbp/p300-interacting transactivator, with transcription CITED2 Glu/Asp-rich carboxy-terminal domain, 2 NA NA Associated regulator 10370 Cbp/p300-interacting transactivator, with transcription CITED4 Glu/Asp-rich carboxy-terminal domain, 4 NA NA Associated regulator 163732

Ck2 NA NA Associated complex

CKM creatine kinase, muscle NA NA Associated kinase 1158

CKS2 CDC28 protein kinase regulatory subunit 2 NA NA Associated kinase 1164

CMIP c-Maf-inducing protein 224992_s_at Highest sensitivity Modulated other 80790 CKLF-like MARVEL transmembrane domain CMTM3 containing 3 224733_at Highest sensitivity Modulated cytokine 123920 G-protein CNR1 cannabinoid receptor 1 (brain) 213436_at Highest sensitivity Modulated coupled 1268 Supplementary Table 5. Proteins identified in basally activated network (page 3 of 11) High relative Modulated or Entrez Gene Name Description Affymetrix Probeset ID expression Associated Family ID

COL4A1 collagen, type IV, alpha 1 NA NA Associated other 1282

CPNE3 copine III 202118_s_at Highest sensitivity Modulated kinase 8895 CREB binding protein (Rubinstein-Taybi transcription CREBBP syndrome) NA NA Associated regulator 1387

CRTAP cartilage associated protein 1555889_a_at Highest sensitivity Modulated other 10491

CRY1 cryptochrome 1 (photolyase-like) 209674_at Lowest sensitivity Modulated enzyme 1407

CTLA4 cytotoxic T-lymphocyte-associated protein 4 NA NA Associated other 1493 catenin (cadherin-associated protein), beta 1, transcription CTNNB1 88kDa NA NA Associated regulator 1499

CTSC cathepsin C 201487_at Highest sensitivity Modulated peptidase 1075 translation CUGBP1 CUG triplet repeat, RNA binding protein 1 NA NA Associated regulator 10658 chemokine (C-X-C motif) ligand 13 (B-cell CXCL13 chemoattractant) NA NA Associated cytokine 10563 chemokine (C-X-C motif) ligand 6 CXCL6 (granulocyte chemotactic protein 2) NA NA Associated cytokine 6372 dystroglycan 1 (dystrophin-associated transmembran DAG1 glycoprotein 1) NA NA Associated e receptor 1605

DDX17 DEAD (Asp-Glu-Ala-Asp) box polypeptide 17 NA NA Associated enzyme 10521

DDX5 DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 NA NA Associated enzyme 1655

DERL1 Der1-like domain family, member 1 NA NA Associated other 79139

DKFZP564K142 implantation-associated protein 210596_at Highest sensitivity Modulated enzyme 84061 DnaJ (Hsp40) homolog, subfamily B, member DNAJB11 11 223054_at Highest sensitivity Modulated other 51726

DNTT deoxynucleotidyltransferase, terminal NA NA Associated enzyme 1791

DSG2 desmoglein 2 1553105_s_at Highest sensitivity Modulated other 1829

DTNBP1 dystrobrevin binding protein 1 223446_s_at Highest sensitivity Modulated other 84062

DUSP16 dual specificity phosphatase 16 224832_at Highest sensitivity Modulated phosphatase 80824

DUSP6 dual specificity phosphatase 6 NA NA Associated phosphatase 1848

E2f NA NA Associated group transcription E2F2 E2F transcription factor 2 228361_at Highest sensitivity Modulated regulator 1870 transcription E2F4 E2F transcription factor 4, p107/p130-binding NA NA Associated regulator 1874 transcription E2F7 E2F transcription factor 7 NA NA Associated regulator 144455

EBI3 Epstein-Barr virus induced gene 3 NA NA Associated cytokine 10148

EDN1 endothelin 1 1564630_at Highest sensitivity Modulated other 1906

EGF epidermal growth factor (beta-urogastrone) NA NA Associated growth factor 1950 E74-like factor 3 (ets domain transcription transcription ELF3 factor, epithelial-specific ) NA NA Associated regulator 1999 Supplementary Table 5. Proteins identified in basally activated network (page 4 of 11) High relative Modulated or Entrez Gene Name Description Affymetrix Probeset ID expression Associated Family ID ELK3, ETS-domain protein (SRF accessory transcription ELK3 protein 2) 221773_at Highest sensitivity Modulated regulator 2004 ectodermal-neural cortex (with BTB-like ENC1 domain) 201340_s_at Highest sensitivity Modulated peptidase 8507

ENG endoglin (Osler-Rendu-Weber syndrome 1) NA NA Associated other 2022

EPB41L1 erythrocyte membrane protein band 4.1-like 1 NA NA Associated other 2036 v-erb-b2 erythroblastic leukemia viral ERBB2 oncogene homolog 2 NA NA Associated kinase 2064

EREG epiregulin NA NA Associated growth factor 2069

ERRFI1 ERBB receptor feedback inhibitor 1 NA NA Associated other 54206 ligand- ESR1 estrogen receptor 1 NA NA Associated dependent 2099

Ets NA NA Associated group transcription ETV5 ets variant gene 5 (ets-related molecule) 203348_s_at Highest sensitivity Modulated regulator 2119

F2 coagulation factor II (thrombin) NA NA Associated peptidase 2147 coagulation factor VIII, procoagulant F8 component (hemophilia A) NA NA Associated other 2157 Fc fragment of IgG, low affinity IIa, receptor transmembran FCGR2A (CD32) NA NA Associated e receptor 2212 Fc fragment of IgG, low affinity IIb, receptor transmembran FCGR2B (CD32) 210889_s_at Highest sensitivity Modulated e receptor 2213 Fc fragment of IgG, low affinity IIc, receptor transmembran FCGR2C for (CD32) 210992_x_at Highest sensitivity Modulated e receptor 9103 fer (fps/fes related) tyrosine kinase FER (phosphoprotein NCP94) NA NA Associated kinase 2241 fasciculation and elongation protein zeta 1 FEZ1 (zygin I) 203562_at Lowest sensitivity Modulated other 9638

FGF18 fibroblast growth factor 18 NA NA Associated growth factor 8817 fibroblast growth factor receptor 1 (fms- FGFR1 related tyrosine kinase 2, Pfeiffer syndrome) 226705_at Highest sensitivity Modulated kinase 2260

FHL2 four and a half LIM domains 2 NA NA Associated other 2274

FIGNL1 fidgetin-like 1 1552921_a_at Highest sensitivity Modulated other 63979

FKBP4 FK506 binding protein 4, 59kDa NA NA Associated enzyme 2288

FKBP5 FK506 binding protein 5 204560_at Highest sensitivity Modulated enzyme 2289

FLNB filamin B, beta (actin binding protein 278) 208613_s_at Highest sensitivity Modulated other 2317

FN1 fibronectin 1 NA NA Associated enzyme 2335

FSTL1 follistatin-like 1 NA NA Associated other 11167

FUCA1 fucosidase, alpha-L- 1, tissue 202838_at Lowest sensitivity Modulated enzyme 2517

GAS6 growth arrest-specific 6 NA NA Associated growth factor 2621

GIMAP1 GTPase, IMAP family member 1 1552316_a_at Lowest sensitivity Modulated other 170575

GINS1 GINS complex subunit 1 (Psf1 homolog) 206102_at Highest sensitivity Modulated other 9837 Supplementary Table 5. Proteins identified in basally activated network (page 5 of 11) High relative Modulated or Entrez Gene Name Description Affymetrix Probeset ID expression Associated Family ID guanine nucleotide binding protein (G GNB5 protein), beta 5 207124_s_at Highest sensitivity Modulated enzyme 10681 guanine nucleotide binding protein (G GNG2 protein), gamma 2 224964_s_at Lowest sensitivity Modulated enzyme 54331 glycerol-3-phosphate dehydrogenase 2 GPD2 (mitochondrial) 210007_s_at Highest sensitivity Modulated enzyme 2820 G protein-coupled receptor 37 (endothelin G-protein GPR37 receptor type B-like) NA NA Associated coupled 2861

GRAMD3 GRAM domain containing 3 218706_s_at Highest sensitivity Modulated other 65983 H19, imprinted maternally expressed H19 untranslated mRNA NA NA Associated other 283120 hypoxia-inducible factor 1, alpha subunit transcription HIF1A (basic helix-loop-helix transcription factor) NA NA Associated regulator 3091

Histone h3 NA NA Associated group

HK2 hexokinase 2 NA NA Associated kinase 3099 heterogeneous nuclear ribonucleoprotein U HNRPU (scaffold attachment factor A) 236244_at Highest sensitivity Modulated transporter 3192 transcription HOXA9 homeobox A9 NA NA Associated regulator 3205 transcription HOXB2 homeobox B2 205453_at Highest sensitivity Modulated regulator 3212 transcription HOXB3 homeobox B3 228904_at Highest sensitivity Modulated regulator 3213 transcription HOXB4 homeobox B4 231767_at Highest sensitivity Modulated regulator 3214 v-Ha-ras Harvey rat sarcoma viral oncogene HRAS homolog NA NA Associated enzyme 3265

Hsp70 NA NA Associated group

Hsp90 NA NA Associated group

HSPA1A heat shock 70kDa protein 1A NA NA Associated other 3303 heat shock 70kDa protein 5 (glucose- HSPA5 regulated protein, 78kDa) 211936_at Highest sensitivity Modulated other 3309

HSPG2 heparan sulfate proteoglycan 2 (perlecan) NA NA Associated other 3339

IER2 immediate early response 2 NA NA Associated other 9592

IFNA4 interferon, alpha 4 NA NA Associated cytokine 3441 transmembran IFNAR1 interferon (alpha, beta and omega) receptor 1 NA NA Associated e receptor 3454 transmembran IFNAR2 interferon (alpha, beta and omega) receptor 2 204786_s_at Highest sensitivity Modulated e receptor 3455

IFNG interferon, gamma NA NA Associated cytokine 3458 transmembran IFNGR1 interferon gamma receptor 1 NA NA Associated e receptor 3459

IGF2 insulin-like growth factor 2 (somatomedin A) NA NA Associated growth factor 3481 insulin-like growth factor 2 mRNA binding IGF2BP3 protein 3 203819_s_at Lowest sensitivity Modulated other 10643

IGH@ immunoglobulin heavy locus NA NA Associated other 3492

IGFBP4 insulin-like growth factor binding protein 4 NA NA Associated other 3487 Supplementary Table 5. Proteins identified in basally activated network (page 6 of 11) High relative Modulated or Entrez Gene Name Description Affymetrix Probeset ID expression Associated Family ID

IGK@ immunoglobulin kappa locus NA NA Associated other 50802

IGKC immunoglobulin kappa constant 211644_x_at Lowest sensitivity Modulated other 3514

IGLL1 immunoglobulin lambda-like polypeptide 1 NA NA Associated other 3543 transcription IKZF1 IKAROS family zinc finger 1 (Ikaros) 227344_at Highest sensitivity Modulated regulator 10320 transmembran IL10RA interleukin 10 receptor, alpha NA NA Associated e receptor 3587 transmembran IL12RB1 interleukin 12 receptor, beta 1 NA NA Associated e receptor 3594

IL13 interleukin 13 NA NA Associated cytokine 3596 transmembran IL13RA1 interleukin 13 receptor, alpha 1 NA NA Associated e receptor 3597

IL15 interleukin 15 NA NA Associated cytokine 3600

IL27 interleukin 27 NA NA Associated cytokine 246778 transmembran IL27RA interleukin 27 receptor, alpha 222062_at Highest sensitivity Modulated e receptor 9466

IL4 interleukin 4 NA NA Associated cytokine 3565 transmembran IL4R interleukin 4 receptor NA NA Associated e receptor 3566 transmembran IL7R interleukin 7 receptor NA NA Associated e receptor 3575 transmembran IL9R interleukin 9 receptor NA NA Associated e receptor 3581 transcription ILF3 interleukin enhancer binding factor 3, 90kDa 208931_s_at Highest sensitivity Modulated regulator 3609

IRS2 insulin receptor substrate 2 NA NA Associated other 8660 ISL1 transcription factor, LIM/homeodomain, transcription ISL1 (islet-1) NA NA Associated regulator 3670 transmembran ITGB1 integrin, beta 1 NA NA Associated e receptor 3688

ITGB6 integrin, beta 6 NA NA Associated other 3694

ITGB8 integrin, beta 8 226189_at Highest sensitivity Modulated other 3696

JAK1 Janus kinase 1 (a protein tyrosine kinase) 201648_at Lowest sensitivity Modulated kinase 3716

Jnk NA NA Associated group v-Ki-ras2 Kirsten rat sarcoma viral oncogene KRAS homolog NA NA Associated enzyme 3845

KSR1 kinase suppressor of ras 1 NA NA Associated kinase 8844

LAMA1 laminin, alpha 1 NA NA Associated other 284217 laminin, alpha 2 (merosin, congenital LAMA2 muscular dystrophy) NA NA Associated other 3908

LAMA4 laminin, alpha 4 NA NA Associated enzyme 3910

LAMB1 laminin, beta 1 NA NA Associated other 3912

LAMA5 laminin, alpha 5 NA NA Associated other 3911 Supplementary Table 5. Proteins identified in basally activated network (page 7 of 11) High relative Modulated or Entrez Gene Name Description Affymetrix Probeset ID expression Associated Family ID

LAMB3 laminin, beta 3 NA NA Associated transporter 3914

LAMC1 laminin, gamma 1 (formerly LAMB2) 200771_at Highest sensitivity Modulated other 3915

LAMC2 laminin, gamma 2 NA NA Associated other 3918

LAMP3 lysosomal-associated membrane protein 3 205569_at Lowest sensitivity Modulated other 27074 lectin, galactoside-binding, soluble, 1 LGALS1 (galectin 1) NA NA Associated other 3956 leukemia inhibitory factor (cholinergic LIF differentiation factor) NA NA Associated cytokine 3976 transmembran LIFR leukemia inhibitory factor receptor alpha NA NA Associated e receptor 3977

LMO2 LIM domain only 2 (rhombotin-like 1) 244367_at Highest sensitivity Modulated other 4005

LOXL4 lysyl oxidase-like 4 227145_at Highest sensitivity Modulated enzyme 84171 leucine rich repeat containing 8 family, LRRC8C member C 223533_at Highest sensitivity Modulated other 84230 lymphotoxin beta (TNF superfamily, member LTB 3) 207339_s_at Lowest sensitivity Modulated cytokine 4050

LXN latexin 218729_at Highest sensitivity Modulated other 56925 v-maf musculoaponeurotic fibrosarcoma MAFB oncogene homolog B (avian) Associated other 9935

MAGEF1 melanoma antigen family F, 1 218176_at Highest sensitivity Modulated other 64110

Mapk NA NA Associated group

MAPK1 mitogen-activated protein kinase 1 NA NA Associated kinase 5594

MARCKSL1 MARCKS-like 1 NA NA Associated other 65108

MATK megakaryocyte-associated tyrosine kinase NA NA Associated kinase 4145

MBP myelin basic protein NA NA Associated other 4155 membrane-bound transcription factor MBTPS1 peptidase, site 1 201620_at Highest sensitivity Modulated peptidase 8720 MCM2 minichromosome maintenance MCM2 deficient 2, mitotin (S. cerevisiae) NA NA Associated enzyme 4171 MCM5 minichromosome maintenance MCM5 deficient 5, cell division cycle 46 NA NA Associated enzyme 4174 minichromosome maintenance deficient 6 MCM6 homolog (S. cerevisiae) NA NA Associated enzyme 4175

Mek NA NA Associated group

MGMT O-6-methylguanine-DNA methyltransferase 204880_at Lowest sensitivity Modulated enzyme 4255

MGST3 microsomal glutathione S-transferase 3 201403_s_at Highest sensitivity Modulated enzyme 4259

MHC Class I NA NA Associated complex transcription MKL1 megakaryoblastic leukemia (translocation) 1 NA NA Associated regulator 57591 transcription MKL2 MKL/myocardin-like 2 218259_at Highest sensitivity Modulated regulator 57496 membrane metallo-endopeptidase (neutral MME endopeptidase, enkephalinase) NA NA Associated peptidase 4311 Supplementary Table 5. Proteins identified in basally activated network (page 8 of 11) High relative Modulated or Entrez Gene Name Description Affymetrix Probeset ID expression Associated Family ID transcription MNT MAX binding protein NA NA Associated regulator 4335 transcription MSC musculin (activated B-cell factor-1) 209928_s_at Highest sensitivity Modulated regulator 9242 mutS homolog 2, colon cancer, nonpolyposis MSH2 type 1 (E. coli) NA NA Associated enzyme 4436

MSI2 musashi homolog 2 (Drosophila) 243579_at Highest sensitivity Modulated other 124540

MT1E metallothionein 1E (functional) NA NA Associated other 4493 5,10-methenyltetrahydrofolate synthetase (5- MTHFS formyltetrahydrofolate cyclo-ligase) 203433_at Highest sensitivity Modulated enzyme 10588

MUTYH mutY homolog (E. coli) 207727_s_at Highest sensitivity Modulated enzyme 4595 v-myc myelocytomatosis viral oncogene transcription MYC homolog (avian) NA NA Associated regulator 4609 v-myc myelocytomatosis viral related transcription MYCN oncogene, neuroblastoma derived (avian) NA NA Associated regulator 4613 transcription MYOD1 myogenic differentiation 1 NA NA Associated regulator 4654

NET1 neuroepithelial cell transforming gene 1 201830_s_at Highest sensitivity Modulated other 10276

NID1 nidogen 1 202007_at Highest sensitivity Modulated other 4811 nuclear receptor subfamily 6, group A, ligand- NR6A1 member 1 NA NA Associated dependent 2649

NRG1 neuregulin 1 206343_s_at Highest sensitivity Modulated growth factor 3084

NRN1 neuritin 1 218625_at Highest sensitivity Modulated other 51299 G-protein OGFR opioid growth factor receptor 211513_s_at Highest sensitivity Modulated coupled 11054

P38 MAPK NA NA Associated group p70 S6k NA NA Associated group

PCNA proliferating cell nuclear antigen NA NA Associated other 5111 programmed cell death 4 (neoplastic PDCD4 transformation inhibitor) NA NA Associated other 27250

Pdgf NA NA Associated complex protein disulfide isomerase family A, member PDIA4 4 208658_at Highest sensitivity Modulated enzyme 9601 platelet/endothelial cell adhesion molecule PECAM1 (CD31 antigen) 208983_s_at Highest sensitivity Modulated other 5175

PENK proenkephalin NA NA Associated other 5179 transcription PHB prohibitin NA NA Associated regulator 5245

PHYH phytanoyl-CoA 2-hydroxylase 203335_at Highest sensitivity Modulated enzyme 5264

PI3K NA NA Associated complex transcription PIAS2 protein inhibitor of activated STAT, 2 244633_at Highest sensitivity Modulated regulator 9063 phosphoinositide-3-kinase, regulatory subunit PIK3R1 1 (p85 alpha) 212240_s_at Highest sensitivity Modulated kinase 5295

PIP3-E phosphoinositide-binding protein PIP3-E NA NA Associated enzyme 26034 Supplementary Table 5. Proteins identified in basally activated network (page 9 of 11) High relative Modulated or Entrez Gene Name Description Affymetrix Probeset ID expression Associated Family ID transcription PIR pirin (iron-binding nuclear protein) 207469_s_at Highest sensitivity Modulated regulator 8544

Pkc(s) NA NA Associated group phospholipase A2, group IVA (cytosolic, PLA2G4A calcium-dependent) 210145_at Lowest sensitivity Modulated enzyme 5321 transcription PLAGL1 pleiomorphic adenoma gene-like 1 NA NA Associated regulator 5325

PLC gamma NA NA Associated group

PLCE1 phospholipase C, epsilon 1 NA NA Associated enzyme 51196 phospholipase D1, phosphatidylcholine- PLD1 specific 226636_at Highest sensitivity Modulated enzyme 5337

PLDN pallidin homolog (mouse) NA NA Associated other 26258

PP2A NA NA Associated complex protein phosphatase 2 (formerly 2A), PPP2R1B regulatory subunit A (PR 65), beta isoform 202883_s_at Highest sensitivity Modulated phosphatase 5519 protein phosphatase 3 (formerly 2B), catalytic PPP3CA subunit, alpha 202457_s_at Highest sensitivity Modulated phosphatase 5530 protein phosphatase 3 (formerly 2B), PPP3R2 regulatory subunit B NA NA Associated phosphatase 5535

PPT2 palmitoyl-protein thioesterase 2 209490_s_at Highest sensitivity Modulated enzyme 9374

PRNP prion protein (p27-30) 201300_s_at Lowest sensitivity Modulated other 5621 pleckstrin homology, Sec7 and coiled-coil PSCD3 domains 3 Associated other 9265

PSEN2 presenilin 2 (Alzheimer disease 4) Associated other 5664 G-protein PTAFR platelet-activating factor receptor 206278_at Highest sensitivity Modulated coupled 5724 protein tyrosine phosphatase, receptor type, PTPRC C NA NA Associated phosphatase 5788 protein tyrosine phosphatase, receptor type, PTPRK K 203038_at Highest sensitivity Modulated phosphatase 5796

PXN paxillin 201087_at Lowest sensitivity Modulated other 5829

RAB34 RAB34, member RAS oncogene family 224710_at Lowest sensitivity Modulated enzyme 83871

RAB38 RAB38, member RAS oncogene family 219412_at Highest sensitivity Modulated enzyme 23682

Rac NA NA Associated group RAD51 homolog (RecA homolog, E. coli) (S. RAD51 cerevisiae) NA NA Associated enzyme 5888

RAD54B RAD54 homolog B (S. cerevisiae) 219494_at Highest sensitivity Modulated enzyme 25788

Rap1 NA NA Associated group

RAP1GAP RAP1 GTPase activating protein NA NA Associated other 5909 Ras protein-specific guanine nucleotide- RASGRF1 releasing factor 1 NA NA Associated other 5923

Rb NA NA Associated group transcription RB1 retinoblastoma 1 (including osteosarcoma) NA NA Associated regulator 5925 Supplementary Table 5. Proteins identified in basally activated network (page 10 of 11) High relative Modulated or Entrez Gene Name Description Affymetrix Probeset ID expression Associated Family ID v-rel reticuloendotheliosis viral oncogene transcription REL homolog (avian) 206036_s_at Lowest sensitivity Modulated regulator 5966 v-rel reticuloendotheliosis viral oncogene transcription RELA homolog A, nuclear factor of kappa light NA NA Associated regulator 5970

RETN resistin NA NA Associated other 56729

REV1 REV1 homolog (S. cerevisiae) 232236_at Highest sensitivity Modulated enzyme 51455

Rho (RAS homolog) NA NA Associated group ribosomal protein S6 kinase, 90kDa, RPS6KA2 polypeptide 2 NA NA Associated kinase 6196 transmembran RPSA ribosomal protein SA NA NA Associated e receptor 3921

RRAS related RAS viral (r-ras) oncogene homolog NA NA Associated enzyme 6237

RRM2 ribonucleotide reductase M2 polypeptide NA NA Associated enzyme 6241

RSU1 Ras suppressor protein 1 NA NA Associated other 6251

RTK NA NA Associated group

S100A10 S100 calcium binding protein A10 NA NA Associated other 6281

SDC4 syndecan 4 (amphiglycan, ryudocan) NA NA Associated other 6385

SELS selenoprotein S 223209_s_at Highest sensitivity Modulated other 55829 serpin peptidase inhibitor, clade G (C1 SERPING1 inhibitor), member 1, (angioedema, NA NA Associated other 710

SFTPB surfactant, pulmonary-associated protein B NA NA Associated other 6439

SFTPC surfactant, pulmonary-associated protein C NA NA Associated other 6440 sarcoglycan, alpha (50kDa dystrophin- SGCA associated glycoprotein) NA NA Associated other 6442 sarcoglycan, beta (43kDa dystrophin- SGCB associated glycoprotein) 205120_s_at Highest sensitivity Modulated other 6443 sarcoglycan, delta (35kDa dystrophin- SGCD associated glycoprotein) NA NA Associated other 6444

SH2B1 SH2B adaptor protein 1 NA NA Associated other 25970 solute carrier family 2 (facilitated SLC2A5 glucose/fructose transporter), member 5 204429_s_at Highest sensitivity Modulated transporter 6518

SLC35B1 solute carrier family 35, member B1 202433_at Highest sensitivity Modulated transporter 10237

SNAPAP SNAP-associated protein NA NA Associated other 23557 transcription SOX4 SRY (sex determining region Y)-box 4 NA NA Associated regulator 6659

SPINT2 serine peptidase inhibitor, Kunitz type, 2 NA NA Associated other 10653

SPTBN1 spectrin, beta, non-erythrocytic 1 200671_s_at Highest sensitivity Modulated other 6711 sterol regulatory element binding transcription transcription SREBF1 factor 1 NA NA Associated regulator 6720 transcription SRF serum response factor NA NA Associated regulator 6722 synovial sarcoma, X breakpoint 2 interacting SSX2IP protein 203015_s_at Highest sensitivity Modulated other 117178 Supplementary Table 5. Proteins identified in basally activated network (page 11 of 11) High relative Modulated or Entrez Gene Name Description Affymetrix Probeset ID expression Associated Family ID

Stat NA NA Associated group signal transducer and activator of transcription STAT3 transcription 3 (acute-phase response factor) NA NA Associated regulator 6774

STC2 stanniocalcin 2 203439_s_at Lowest sensitivity Modulated other 8614

STEAP3 STEAP family member 3 218424_s_at Highest sensitivity Modulated transporter 55240 stress-induced-phosphoprotein 1 STIP1 (Hsp70/Hsp90-organizing protein) NA NA Associated other 10963

SYPL1 synaptophysin-like 1 201260_s_at Highest sensitivity Modulated transporter 6856 transcription factor 3 (E2A immunoglobulin transcription TCF3 enhancer binding factors E12/E47) NA NA Associated regulator 6929

TERT telomerase reverse transcriptase NA NA Associated enzyme 7015 transcription factor AP-2 beta (activating transcription TFAP2B enhancer binding protein 2 beta) 1553394_a_at Highest sensitivity Modulated regulator 7021

Tgf beta NA NA Associated group tumor necrosis factor (TNF superfamily, TNF member 2) NA NA Associated cytokine 7124 tumor necrosis factor receptor superfamily, transmembran TNFRSF11B member 11b (osteoprotegerin) NA NA Associated e receptor 4982 tumor necrosis factor (ligand) superfamily, TNFSF13 member 13 210314_x_at Highest sensitivity Modulated cytokine 8741

TOP1 topoisomerase (DNA) I NA NA Associated enzyme 7150 transcription TP53 tumor protein p53 (Li-Fraumeni syndrome) NA NA Associated regulator 7157 transcription TRIM24 tripartite motif-containing 24 213301_x_at Highest sensitivity Modulated regulator 8805

TRIP6 thyroid hormone receptor interactor 6 209129_at Lowest sensitivity Modulated cytokine 7205

Tropomyosin NA NA Associated group

TSPAN NA NA Associated group

TSPAN4 tetraspanin 4 209264_s_at Highest sensitivity Modulated other 7106 upstream binding transcription factor, RNA transcription UBTF polymerase I NA NA Associated regulator 7343

UFD1L ubiquitin fusion degradation 1 like (yeast) NA NA Associated peptidase 7353 vesicle-associated membrane protein 2 VAMP2 (synaptobrevin 2) NA NA Associated other 6844

VCP valosin-containing protein NA NA Associated enzyme 7415

VEGFA vascular endothelial growth factor A NA NA Associated growth factor 7422

ZNF124 zinc finger protein 124 206928_at Highest sensitivity Modulated other 7678

ZNF592 zinc finger protein 592 204473_s_at Highest sensitivity Modulated other 9640 transcription ZNF83 zinc finger protein 83 236346_at Highest sensitivity Modulated regulator 55769 Supplementary Table 6. List of enriched subnetworks contained within large interactome.

p-value Network Proteins contained within network (10-X) Functions enriched in network

(red represents proteins with high relative basal expression in resistant cell lines, green represents proteins with high relative basal expression in sensitive cell lines)

Actin, Adenylate Cyclase, ASF1B, Calcineurin proteins,Calpain, CAPN2, Caspase, Cbp/p300, CCND2, CENPO, DNAJB11,E2f,E2F2,E2F7,ENC1,FCGR2B,GNB5,GNG2,GPR37,Histone 1 30 Cancer,Cell Morphology,Immunological Disease h3,HNRPU,HOXB2,HOXB4,Hsp70,HSPA5,IKZF1,P38 MAPK, PIAS2, PPP3CA, PPP3R2, PRNP, Rb, REL,Tgf beta,TRIM24

Akt,ARF6,ARHGAP5,CALR,CD38,EDN1,FGFR1,Hsp90,JAK1,Jnk,Mapk,MBTPS1,Mek,MGMT,MHC Class 2 I,NET1,NRG1,p70 S6k,Pdgf,PECAM1,PI3K,PIK3R1,Pkc(s),PLA2G4A,PLC 26 Cancer,Cellular Movement,Cell Signaling gamma,PLD1,PP2A,PPP2R1B,PXN,Rac,Rap1,Rho (RAS homolog),RTK,Stat,TRIP6

AIFM2,APEX1,APP,ARMET,ASF1B,BNIP3L,Ck2,COL4A1,E2F4,ENG,FIGNL1,FLNB,FUCA1,GINS1,HIF1A,MC DNA Replication, Recombination, and 3 M2,MCM5,MCM6,MGMT,MME,MSH2,PHB,PSEN2,RAB38,RAD51,RAD54B,RRM2,SSX2IP,STC2,STEAP3,STIP 18 Repair,Cancer,Neurological Disease 1,TOP1,TP53,UBTF,ZNF83

ARRDC3,CCL27,CCR10,CD38,CD247,CEBPE,CISH,CPNE3,CTLA4,CTSC,CUGBP1,ELF3,FCGR2A,FCGR2C, Hematological System Development and Function,Immune 4 GPD2,GRAMD3,HK2,HOXA9,IER2,IL7R,LAMP3,LIF,LIFR,MBP,MSI2,MT1E,MTHFS,NR6A1,PECAM1,PTAFR,P 17 and Lymphatic System Development and Function,Tissue TPRC,SDC4,SOX4,TNF,TNFRSF11B Morphology

ALDH7A1,BZW2,CHI3L2,CNR1,CXCL6,EBI3,ETV5,FER,FEZ1,FKBP5,GAS6,IFNA4,IFNAR1,IFNAR2,IFNG,IFN Cellular Movement,Respiratory Disease,Hematological 5 GR1,IL13,IL27,IL10RA,IL12RB1,IL13RA1,IL27RA,IL4R,IRS2,ISL1,JAK1,OGFR,PENK,SFTPB,SFTPC,SH2B1,S 17 System Development and Function TAT3,VEGFA,ZNF124,ZNF592

ABP1,AMACR,AQP3,ARF6,BLOC1S1,BLOC1S2,BNIP3,C10ORF58,CKS2,CRTAP,DERL1,DSG2,DTNBP1,EG 6 F,ELK3,ERRFI1,FSTL1,IL15,IL9R,KRAS,NRN1,PDCD4,PIP3- 17 Molecular Transport,Protein Trafficking,Cancer E,PLAGL1,PLDN,PSCD3,RPSA,SELS,SLC35B1,SNAPAP,SYPL1,TERT,UFD1L,VAMP2,VCP

AP1B1,AP1G1,AP1G2,AP1M1,AP1M2,AP1S1,AP1S2,AP1S3,ARHGDIA,CRY1,DNTT,EPB41L1,FN1,HOXB4,IG Gene Expression,Cellular Assembly and 7 F2,IGF2BP3,IGH@,IGK@,IGKC,IGLL1,ITGB8,MAGEF1,MGST3,MNT,MSC,MUTYH,MYC,PCNA,PPT2,RB1,REL 17 Organization,Hematological System Development and A,RRM2,SLC2A5,TCF3,TNFSF13 Function

ACP2,ADAM19,BCL3,CCND2,CD226,CITED1,CITED2,CITED4,CMIP,COL4A1,DKFZP564K142,ERBB2,EREG, Cellular Growth and Proliferation,Connective Tissue 8 ESR1,F2,F8,FKBP4,H19,IER2,IGFBP4,IL4,LGALS1,LOXL4,MATK,MYCN,PDIA4,PHB,PHYH,PIR,PTPRK,RAB3 15 Development and Function,Organismal Survival 4,S100A10,SPINT2,TFAP2B,TNFRSF11B

AK3L1,CKM,CMTM3,CREBBP,DDX5,DUSP6,DUSP16,FHL2,GIMAP1,HOXB3,HRAS,ITGB6,KSR1,LRRC8C,LX 9 N,MAFB,MAPK1,MKL1,MKL2,MYOD1,PLCE1,PRNP,RAP1GAP,RASGRF1,RETN,REV1,RPS6KA2,RRAS,RSU 13 Gene Expression,Cell Signaling,Behavior 1,SH2B1,SPTBN1,SREBF1,SRF,Tropomyosin,UBTF

ADAM10,CTNNB1,CXCL13,DAG1,DDX5,DDX17,ELK3,Ets,FGF18,HSPA1A,HSPG2,ILF3,ITGB1,LAMA1,LAMA Tissue Development,Nervous System Development and 10 2,LAMA5,LAMA4,LAMB1,LAMB3,LAMC1,LAMC2,LMO2,LTB,MARCKSL1,NID1,PECAM1,RPSA,SERPING1,SG 10 Function,Skeletal and Muscular System Development and CA,SGCB,SGCD,SOX4,TNF,TSPAN,TSPAN4 Function Supplementary Table 7. Transcription Factor Binding Enrichment Gene Set

Transcription Factor Description BASA TRASA TASA 48 genes 39 genes 121 genes 240 genes P value P value P value P value

Octamer binding transcription Oct-1 factor 0.004 0.0286 0.048 0.007