Table 2

Genes identified by SAM as being significantly decreased by MMC/5FU treatment

The dataset was divided into pre-treatment and during treatment samples from the 15 patients treated with MMC/5FU for whom we had pre- and during treatment profiles and analyzed using SAM (9). The table lists genes by general function that were significantly decreased by >2-fold during treatment. Italic text indicates genes previously reported to be c-MYC-regulated (19–23). A = genes with cDNA duplicate spots, B = genes with triplicate cDNA spots.

Protein—synthesis
AA496880 Ribosomal protein L5 (RPL5)
AA629808 Ribosomal protein L6 (RPL6)
H23422 Ribosomal protein L7a (RPL7A)
T67270 Ribosomal protein L10 (RPL10)
R01139 Ribosomal protein L10a (RPL10A)
AA680244 Ribosomal protein L11 (RPL11)
AA434088 Ribosomal protein L15 (RPL15)
AA775874 Ribosomal protein L18 (RPL18)
AA083485 Ribosomal protein L19 (RPL19)
AA464743 Ribosomal protein L21 (RPL21)
AA633768 Ribosomal protein L24 (RPL24)
AA599178 Ribosomal protein L27a (RPL27A)
AA775364 Ribosomal protein L30 (RPL30)
W15277 Ribosomal protein L31 (RPL31)
AA625634 Ribosomal protein L35 (RPL35)
AA873351 Ribosomal protein L35A (RPL35A)
AA490011 Ribosomal protein L38 (RPL38)
AA888182 Ribosomal protein S4 (RPS4X)
T69468 Ribosomal protein S4 (RPS4Y)
AA683050 Ribosomal protein S8 (RPS8)
AA629641 Ribosomal protein S13 (RPS13)
AA872341 Ribosomal protein S15a (RPS15A)
AA66830 Ribosomal protein S16 (RPS16)
AA634008 Ribosomal protein S23 (RPS23)
 AA625632Ribosomal protein S27a (RPS27A)
AA856556 Ribosomal protein S28 (RPS28)
 AA411343Ribosomal protein S29 (RPS29)
 R51607Translation initiation factor (EIF1)
 R93621Eukaryotic translation initiation factor 2 sub. 2 (EIF2S2)
 R54097Eukaryotic translation initiation factor 2 sub. 2 (EIF2S2)A
 AA668703Eukaryotic translation initiation factor 3 sub. 4 (EIF3S4)
 AA669674Eukaryotic translation initiation factor 3 sub. 6 (EIF3S6)
AA598863 Eukaryotic translation initiation fact. 3 sub. 8 (EIF3S8)
H09590 Eukaryotic translation initiation factor 4A1 (EIF4A1) A
R43973 Eukaryotic translation elongation factor 1 γ(EEF1G) A
R43766 Eukaryotic translation elongation factor 2 (EEF2)
 AA629909Glycyl-tRNA synthetase (GARS)
AA410636 Isoleucine-tRNA synthetase (IARS)
 AA486220Lysyl-tRNA synthetase (KARS)
 AA634166Glutaminyl-tRNA synthetase (QARS)
RNA processing
R37286 H’geneous nuclear ribonucleoprotein A1 (HNRPA1) A
AA126911 H’geneous nuclear ribonucleoprotein A1 (HNRPA1)
 W72693H’geneous nuclear ribonucleoprotein A, B (HNRPAB)
 W02101H’geneous nuclear ribonucleoprotein A2, B1 (HNRPA2B1)
 H05899H’geneous nuclear ribonucleoprotein C1, C2 (HNRPC)A
 AA487442Heterogeneous nuclear ribonucleoprotein G (HNRPG)
 AA599116Small nuclear ribonucleoprotein B, B1 (SNRPB)
 T62529Small nuclear ribonucleoprotein D2 (SNRPD2)
 AA678021Small nuclear ribonucleoprotein E (SNRPE)
 AA668189Small nuclear ribonucleoprotein F (SNRPF)
AA133577 Small nuclear ribonucleoprotein G (SNRPG)
AA454585 Splicing factor arginine, serine-rich 2 (SFRS2)
AA663986 Fibrillarin (FBL)
AA476294 Nucleolin (NCL)
AA894577 Nucleolar protein (NOP56)
 AA402440Exportin (XPOT)
 H29485La autoantigen (SSB)
 AA490047Poly(rC)-binding protein 1 (PCBP1)
 W728163′ pre-RNA cleavage stimulation factor sub. 1 (CSTF1)
Metabolism—oxidative phosphorylation
 AA708298ATP synthase H+ transporting, mitochon. F1 β (ATP5B)
 AA644234ATP synthase H+ transporting, mitochon. F1γ1 (ATP5C1)
 AA453765ATP synthase H+ transporting mitochon. F0 β1 (ATP5F1)
 AA431433ATP synthase H+ transporting, mitochon. F0 ε (ATP5I)
 AA873577ATP synthase H+ transporting mitochon. F1 O (ATP5O)
AA482243 Cytochrome c oxidase subunit VIA 1 (COX6A1)
Protein—turnover
AA047338 Proteasome alpha subunit type 6 (PSMA6)
AA863149 Proteasome alpha subunit type 7 (PSMA7)
AA489343 Proteasome subunit beta type 7 (PSMB7)
 T68758Proteasome subunit beta type 1 (PSMB1)
 N53065Proteasome subunit beta type 2 (PSMB2)
 AA864479Proteasome subunit beta type 5 (PSMB5)
 H05893Proteasome 26S subunit non-ATPase 2 (PSMD2)
 T47815Proteasome activator subunit 1 (PSME1)
 H65395Proteasome activator subunit 2 (PSME2)
 AA430504Ubiquitin carrier protein E2-C (UBCH10)
 N33920Ubiquitin D (UBD)
 AA676484Calpain, small subunit (CAPNS1)
 H22919Cystatin B (CSTB)
 AA486275Proteinase inhibitor clade B member 1 (SERPINB1)
 AA410517Proteinase inhibitor clade B member 6 (SERPINB6)
 AA845156Serine protease inhibitor, Kazal type 1 (SPINK1)
Protein—folding
AA448396 Heat shock 10kD protein 1 (HSPE1)
AA629567 Heat shock cognate 71 (HSPA8)
R44334 Heat shock 90 beta (HSPCB) A
 AA411202Activator of Hsp90 ATPase (AHA1)
 AA669341p23 co-chaperone (P23)
R60933 Chaperonin containing TCP1 gamma subunit 3 (CCT3)
 AA598637Chaperonin containing TCP1 subunit 4 (CCT4)
 AA87269Chaperonin containing TCP1 subunit 6A (CCT6A)
 H07880Chaperonin containing TCP1 subunit 6A (CCT6A)A
R43360 Signal recognition particle 9kD (SRP9)
 AA486261Signal sequence receptor delta (SSR4)
AA664241 Nascent-polypeptide-associated complex alpha (NACA)
AA598758 Tumor rejection antigen 1 (GRP94)
 R78585Calumenin (CALU)
 AA126265Calnexin (CANX)
 AA625981FK506-binding protein 1A (FKBP1A)
RNA transcription
 H20856Basic transcription factor 2 (BTF2)
 R83000Basic transcription factor 3 (BTF3)
 AA115186General transcription factor II-I (GTF2I)
N74956 RNA polymerase II polypeptide B (POLR2B)
AA873691 RNA polymerase II polypeptide L (POLR2L)
 AA136533Transcription elongation factor B peptide 1-like (TCEB1L)
 AA630017Transcription elongation factor B polypeptide 2 (TCEB2)
 AA099534Activated RNA pol. II transcription cofactor 4 (PC4)
 AA600217Activating transcription factor 4 (ATF4)
AA455300 Cold shock domain associated (CSDA)
 AA112660Forkhead box F1 (FKHL5)
 AA894687Interleukin-enhancer binding factor 2 (ILF2)
 AA664389Transforming growth factor beta-stimulated ptn (TSC22)
AA599175 Y-box binding protein 1 (YBP1)
 AA773894Zinc finger protein 43 (HTF6)
Metabolism—glycolysis
AA775241 Aldolase A (ALDOA)
H16958 Glyceraldehyde-3-phosphate dehydrogenase (GAPD) A
H05914 Lactate dehydrogenase A (LDHA) A
 AA599187Phosphoglycerate kinase 1 (PGK1)
 AA663983Triosephosphate isomerase 1 (TPI1)
Metabolism—other
 T59245Methionine adenosyltransferase II alpha (MAT2A)
 AA487466Ornithine decarboxylase antizyme 1 (OAZ1)
 R58991Spermidine, spermine N1-acetyltransferase (SAT)A
 AA679907Isocitrate dehydrogenase 2 (IDH2)
 AA487521Mitochon. glutamic-oxaloacetic transminase 2 (GOT2)
 R15814Malate dehydrogenase 1 (MDH1)A
 AA676223Acyl-Coenzyme A oxidase 3 pristanoyl (ACOX3)
 T65790Farnesyl diphosphate synthase (FDPS)
 R43558Mitochondrial enoyl Coenzyme A hydratase (ECHS1)
 N71160Cytochrome c oxidase subunit VIb (COX6B)
 AA456931Cytochrome c oxidase subunit VIC (COX6C)
 AA862813Cytochrome c oxidase subunit VIII (COX8)
R53311 Cytochrome c (HCS)
 AA111999 NADH dehydrogenase 1 alpha 1 (NDUFA1)
 AA680322NADH dehydrogenase 1 alpha subcomplex 4 (NDUF4)
 AA127014NADH dehydrogenase Fe-S protein 8 (NDUFS8)
 AA922326NADH dehydrogenase flavoprotein 2 (NDUFV2)
 AA663058Ubiquinol-cytochrome c reductase core ptn II (UQCRC2)
 R12802Ubiquinol-cytochrome c reductase core ptn II (UQCRC2)
AA404486 Adenine nucleotide translocator 2 (ANT2)
AA663439 Adenine nucleotide translocator 3 (ANT3)
R61295 Adenine nucleotide translocator 3 (ANT3) A
AA044059 Voltage-dependent anion channel 1 (VDAC1)
 AA486200Mitochondrial phosphate carrier (PHC)
Signal transduction
 R37953Adenylyl cyclase-associated protein (CAP)
 AA863086Adenosine A3 receptor (ADORA3)
 AA857163Amphiregulin (AREG)
 AA679177Butyrate-induced transcript 1 (HSPC112)
N21624 14-3-3 epsilon (YWHAE)
 AA63399714-3-3 tau (YWHAQ)
 AA464731Calgizzarin (S100A11)
 R44288Calmodulin 2 (CALM2)A
 AA774638Casein kinase 2 beta (CSNK2B)
 AA451935Fibroblast growth factor 2-interacting factor (AP15L1)
 R43581Guanine nucleotide binding α stimulating 1 (GNAS1)A
R96220 Guanine nucleotide binding β2-like 1 (GNB2L1)
 H05619GDNF family receptor alpha 2 (GFRA2)
AA453749 Hepatoma-derived growth factor (HDGF)
T57556 Histidine triad nucleotide-binding protein (HINT)
 AA157813Interferon, alpha-inducible protein 27 (IFI27)
 AA419251Interferon induced transmembrane protein 1 (IFITM1)
 AA862371Interferon induced transmembrane protein 2 (IFITM2)
 AA464417Interferon induced transmembrane protein 3 (IFITM3)
 AA412053p24 transmembrane 4 superfamily (CD9)
AA485909 Prostatic binding protein (PBP)
 N33955Protein phosphatase ID (PM1D)
 AA406362Prostaglandin E receptor 3 (PTGER3)
W47485 Sigma receptor (SR-BP1)
 AA045699Transmembrane 4 superfamily member 3 (TM4SF3)
Transport
 R49530Accessory proteins BAP31, BAP29 (BAP31)A
 AA625628Accessory proteins BAP31, BAP29 (BAP31)
 H11049ADP-ribosylation factor 1 (ARF1)A
 T71316ADP-ribosylation factor 4 (ARF4)
 AA873355ATPase, Na+, K+ transporting alpha 1 (ATP1A1)
 AA113872Clathrin light polypeptide (CLTA)
 N20335Clathrin, light polypeptide (CLTB)
 AA485913Chloride intracellular channel 1 (CLIC1)
 AA676460Karyopherin alpha 2 (KPNA2)
 T70031Neutral amino acid transporter 5 (SLC1A5)
 AA464528Proteolipid protein 2 (PLP2)
 AA444051S100 calcium-binding protein A10 (S100A10)
AA775415 Sentrin 2 (SMT3H2)
 AA664077Vacuolar ATPase (ATP6S14)
Miscellaneous and unknown function
 AA404264Amplified in osteosarcoma (OS4)
 AA457092Chromosome 20 open reading frame 47 (C20ORF47)
 R51835ESTA
 R60313ESTB
AA702548 Etoposide-induced mRNA (PIG8)
 R42479FLJ20528
 H59916FLJ37889
 AA460728FLJ38479
 AA082943Hmd4a12
 N98412Lysozyme (LYZ)
 AA608575Propionyl Coenzyme A carboxylase α polypep. (PCCA)
AA676466 Argininosuccinate synthetase (ASS)
AA644092 Expressed in non-metastatic cells 1 (NME1)
AA496628 Expressed in non-metastatic cells 2 (NME2)
 AA459909Dimerization cofactor of hepatocyte factor 1α (PCBD)
H59231 Meltrin gamma (ADAM9)
 AA463497Membrane cofactor protein (MCP)
 AA683321Prader-Willi, Angelman region 5 (PAR5)
 W92812Pro-platelet basic protein (PPBP)
 AA457719Reticulocalbin 1 (RCN1)
 AA447684Small proline-rich protein 1B (SPRR1B)
 T65736Selenium binding protein 1 (SELENBP1)
 AA400474Zona pellucida binding protein (ZPBP)
Detoxification
 AA136710Glyoxalase I (GLO1)
 AA135152Glutathione peroxidase 2 (GPX2)
AA495936 Microsomal glutathione S-transferase 1 (MGST1)
 W73474Microsomal glutathione S-transferase 2 (MGST2)
 AA775803Peroxiredoxin 1 (PRDX1)
H68845 Peroxiredoxin 2 (PRDX2)
H19203 Peroxiredoxin 3 (PRDX3)
AA459663 Peroxiredoxin 4 (PRDX4)
 T64482S-formylglutathione hydrolase (ESD)
 AA599127Superoxide dismutase 1 (SOD1)
 AA461065Mercaptopyruvate sulfurtransferase (MST)
Chromatin and DNA synthesis
 AA48620770kD Ku antigen (KU70)
 AA77535580kD Ku antigen (KU80)
 AA608557Damage-specific DNA binding protein 1 (DDB1)
 AA683085High-mobility non-histone chromosomal ptn 1 (HMG1)
AA608514 H3 histone 3B (H3,3B)
 AA668811H3 histone 3A (H3F3A)
 AA127093Histone deacetylase 3 (HDAC3)
 AA465203Mitochon. single-stranded DNA-binding protein (SSBP)
AA450265 Proliferating cell nuclear antigen (PCNA)
AA608548 SET translocation (SET)
Cell cycle and proliferation
 N58511Cyclin I (CCNI)
 AA488332Proliferation-associated 2G4 (PA2G4)
AA442991 Prothymosin alpha (PTMA)
 R32848S100 calcium-binding protein P (S100P)
Cytoskeleton
 AA634006Actin alpha 2 (ACTA2)
 R44290Actin beta (ACTB)A
 R42609Actin filament capping protein alpha 2 (CAPZA2)
 R40850Centractin alpha (ACTR1A)A
 H73276Actin related protein 2, 3 complex subunit 3 (ARPC3)
 T65118Catenin alpha 1 (CTNNA1)A
 AA434144Claudin 3 (CLDN3)
 AA644679Cytoplasmic dynein light polypeptide (PIN)
 AA424824destrin (ADF)
 AA664179Keratin 18 (KRT18)
 AA634103Thymosin beta 4 (TMSB4X)
 AA888148Tubulin beta 2 (TUBB2)
Cell surface and adhesion
 AA054073Carcinoembryonic antigen-related cell adhesion 6 (NCA)
 AA130579Galectin 4 (LGALS4)
 AA485353Galectin 6 binding protein (LGALS3BP)
AA629897 Laminin receptor 1 (LAMR1)
 AA458965Natural killer cell transcript 4 (NK4)
 AA486556Target of antiproliferative antibody 1 (CD81)
Immune
 AA670408Beta-2-microglobulin (B2M)
 AA663981Immunoglobulin heavy constant gamma 3 (IGHG3)
 H54023Ig-like receptor subfamily B member 2 (LILRB2)
 AA464246Major histocompatibility complex, class I, C (HLA-C)
 AA702254Major histocompatibility class II DN alpha (HLA-DNA)
 R47979Major histocompatibility class II DR alpha (HLA-DRA)
 AA634028Major histocompatibility class II DP alpha (HLA-DPA)