Table S1. List of Genes Differentially Expressed in YB-1 siRNA-Transfected MCF-7 Cells Unigene Accession Symbol Description Mean fold change Hs.17466 NM_004585 RARRES3 retinoic acid receptor responder (tazarotene induced) 3 3.57 Hs.64746 NM_004669 CLIC3 chloride intracellular channel 3 3.33 Hs.516155 NM_001747 CAPG capping protein (actin filament), gelsolin-like 2.88 Hs.926 NM_002463 MX2 myxovirus (influenza virus) resistance 2 (mouse) 2.72 Hs.643494 NM_005410 SEPP1 selenoprotein P, plasma, 1 2.70 Hs.267038 BC017500 POF1B premature ovarian failure 1B 2.67 Hs.20961 U63917 GPR30 G protein- coupled receptor 30 2532.53 Hs.199877 BE645967 CPNE4 copine IV 2.49 Hs.632177 NM_017458 MVP major vault protein 2.48 Hs.528836 AA005023 NOD27 nucleotide-binding oligomerization domains 27 2.43 Hs.360940 AL589866 dJ222E13.1 kraken-like 2.40 Hs.515575 AI743780 PLAC2 placenta-specific 2 2.37 Hs.25674 AI827820 MBD2 methyl-CpG binding domain protein 2 2.36 Hs.12229 AA149594 TIEG2 TGFB inducible early growth response 2 2.33 Hs.482730 AA053711 EDIL3 EGF-like repeats and discoidin I-like domains 3 2.32 Hs. 370771 NM_000389 CDKN1A cyclin- depen dent kinase in hibitor 1A (p 21, Cip 1) 2282.28 Hs.469175 AI341537 JFC1 NADPH oxidase-related, C2 domain-containing protein 2.28 Hs.514821 AF043341 CCL5 chemokine (C-C motif) ligand 5 2.27 Hs.591292 NM_023915 GPR87 G protein-coupled receptor 87 2.26 Hs.500483 NM_001613 ACTA2 actin, alpha 2, smooth muscle, aorta 2.24 Hs.632824 NM_006729 DIAPH2 diaphanous homolog 2 (Drosophila) 2.22 Hs.369430 NM_000919 PAM peptidylglycine alpha-amidating monooxygenase 2.19 Hs.528605 BF478120 RECQL5 RecQ protein-like 5 2.19 Hs.501778 AA083478 TRIM22 tripartite motif-containing 22 2.15 Hs.275243 NM_014624 S100A6 S100 calcium binding protein A6 (calcyclin) 2.14 Hs.500761 NM_004207 SLC16A3 solute carrier family 16 (monocarboxylic acid transporters), member 3 2.14 Hs.81337 NM_009587 LGALS9 lectin, galactoside-binding, soluble, 9 (galectin 9) 2.14 Hs.69771 NM_001710 BF B-factor, properdin 2.13 Hs.508829 BE675995 SPEC2 non-kinase Cdc42 effector protein SPEC2 2.12 Hs.8364 AV707102 PDK4 pyruvate dehydrogenase kinase, isoenzyme 4 2.12 Hs.47061 AB018265 ULK1 unc-51-like kinase 1 (C. elegans) 2.09 Hs.89603 AI610869 MUC1 mucin 1, transmembrane 2.09 Hs.591598 BC002637 TRB2 tribbles homolog 2 2.08 Hs.524672 BC001638 ASCL1 achaete-scute complex-like 1 (Drosophila) 2.07 Hs.497599 NM_004184 WARS tryptophanyl-tRNA synthetase 2.06 Hs.244139 X83493 TNFRSF6 tumor necrosis factor receptor superfamily, member 6 2.06 Hs.524348 AA404269 PRICKLE1 prickle-like 1 (Drosophila) 2.05 Hs.46732 NM_000898 MAOB monoamine oxidase B 2.05 Hs.409602 AW043713 SULF1 sulfatase 1 2.05 Hs.511265 AL036088 SEMA6D sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D 2.02 Hs.438823 AI431931 HIMAP2 immunity associated protein 2 2.01 Hs.512682 NM_001712 CEACAM1 carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein) 2.01 Hs.33446 BC027893 NR5A2 nuclear receptor subfamily 5, group A, member 2 2.00 Hs.133998 NM_014171 CRIPT postsynaptic protein CRIPT 0.50 Hs.592117 AF275260 CXCL16 chemokine (C-X-C motif) ligand 16 0.50 Hs.278277 NM_000436 OXCT 3-oxoacid CoA transferase 0.50 Hs.23348 BC001441 SKP2 S-phase kinase-associated protein 2 (p45) 0.50 Hs.460184 AI936566 MCM4 MCM4 minichromosome maintenance deficient 4 (S. cerevisiae) 0.50 Hs.435237 NM_000082 CKN1 Cockayne syndrome 1 (classical) 0.50 Hs.473163 BC004248 BMP7 bone morphogenetic protein 7 (osteogenic protein 1) 0.50 Hs.370834 NM_ 014109 PRO2000 PRO2000 protein 0.50 Hs.585782 BE000929 MSI2 musashi homolog 2 (Drosophila) 0.50 Hs.182625 AW291083 VAPB VAMP (vesicle-associated membrane protein)-associated protein B and C 0.50 Hs.179565 NM_002388 MCM3 MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) 0.50 Hs.478673 AF167343 IL1RAP interleukin 1 receptor accessory protein 0.50 Hs.55028 NM_018455 BM039 uncharacterized bone marrow protein BM039 0.50 Hs.507076 BC004815 ACADS acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain 0.50 Hs.121028 NM_018123 ASPM synonyms: MCPH5, FLJ10517, FLJ10549 0.49 Hs.118631 NM_003920 TIMELESS timeless homolog (Drosophila) 0.49 Hs.591697 NM_002358 MAD2L1 MAD2 mitotic arrest deficient-like 1 (yeast) 0490.49 Hs.592340 AL534416 ZFP161 zinc finger protein 161 homolog (mouse) 0.49 Hs.591015 AW575374 ELK3 ELK3, ETS-domain protein (SRF accessory protein 2) 0.49 Hs.297324 NM_000362 TIMP3 tissue inhibitor of metalloproteinase 3 (Sorsby fundus dystrophy, pseudoinflammatory) 0.49 Hs.177576 AW006441 MGAT4A mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme A 0.49 Hs.58919 NM_001392 DTNA; DRP3; D synonyms: DTN, DRP3, D18S892E 0.49 Hs.513645 NM_001211 BUB1B BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast) 0.49 Hs.304792 AL136616 PROSC proline synthetase co-transcribed homolog (bacterial) 0.49 Hs.293917 NM_025263 PRR3 proline-rich polypeptide 3 0.49 Table S1. (Continued) Unigene Accession Symbol Description Mean fold change Hs.376064 NM_006392 NOL5A nucleolar protein 5A (56kDa with KKE/D repeat) 0.49 Hs.482526 AV720650 TINP1 TGF beta-inducible nuclear protein 1 0.49 Hs.472227 NM_006466 POLR3F polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa 0.49 Hs.382306 BF700678 CDK8 cyclin-dependent kinase 8 0.49 Hs.1973 U17105 CCNF cyclin F 0.49 Hs.24529 NM_001274 CHEK1 CHK1 checkpoint homolog (S. pombe) 0.49 Hs.591209 NM_006260 DNAJC3 DnaJ (Hsp40) homolog, subfamily C, member 3 0.49 Hs.497893 AI963713 ENAH enabled homolog (Drosophila) 0.49 Hs.445711 AA888858 PDE3B phosphodiesterase 3B, cGMP-inhibited 0.49 Hs.466391 AB006572 RMP Homo sapiens RMP mRNA for RPB5 meidating protein, complete cds. 0.49 Hs.211580 NM_005931 MICB MHC class I polypeptide-related sequence B 0.49 Hs.514527 BQ021146 BIRC5 baculoviral IAP repeat-containing 5 (survivin) 0.49 Hs.19400 AF080398 MAD2L2 MAD2 mitotic arrest deficient-like 2 (yeast) 0.49 Hs.519993 D81048 NRM nurim (nuclear envelope membrane protein) 0.49 Hs.168799 BC001650 METTL3 methyltransferase like 3 0.48 Hs.615092 NM_ 016359 NUSAP1 nucleolar and spppindle associated protein 1 0.48 Hs.523680 BE795648 SSRP1 structure specific recognition protein 1 0.48 Hs.137516 NM_022116 FIGNL1 fidgetin-like 1 0.48 Hs.162777 NM_002692 POLE2 polymerase (DNA directed), epsilon 2 (p59 subunit) 0.48 Hs.276905 BF108964 MASTL microtubule associated serine/threonine kinase-like 0.48 Hs.159274 AF053970 ODF2 outer dense fiber of sperm tails 2 0.48 Hs.405467 NM_018248 FLJ10858 DNA glycosylase hFPG2 0.48 Hs.491682 U34994 PRKDC protein kinase, DNA-activated, catalytic polypeptide 0.48 Hs.479069 AF086924 PPP2R2C protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), gamma isoform 0.48 Hs.591322 NM_002916 RFC4 replication factor C (activator 1) 4, 37kDa 0.48 Hs.201897 NM_002689 POLA2 polymerase (DNA-directed), alpha (70kD) 0.48 Hs.532799 AF360549 BRIP1 BRCA1 interacting protein C-terminal helicase 1 0.48 Hs.18616 NM_017760 MTB more than blood homolog 0.48 Hs.184339 NM_014791 MELK maternal embryonic leucine zipper kinase 0.48 Hs.421956 AF225416 Spc25 kinetochore protein Spc25 0.48 Hs.279766 NM_012310 KIF4A kinesin family member 4A 0.48 Hs.594234 U88989 EIF4EBP2 eukaryotic translation initiation factor 4E binding protein 2 0.47 Hs.477879 NM_002105 H2AFX H2A histone family, member X 0.47 Hs.130031 N21108 TRIO triple functional domain (PTPRF interacting) 0470.47 Hs.478000 BF512200 MBNL1 muscleblind-like (Drosophila) 0.47 Hs.1600 BF197357 CCT5 chaperonin containing TCP1, subunit 5 (epsilon) 0.47 Hs.84113 AF213033 CDKN3 cyclin-dependent kinase inhibitor 3 (CDK2-associated dual specificity phosphatase) 0.47 Hs.422662 NM_003384 VRK1 vaccinia related kinase 1 0.47 Hs.146688 AF010316 PTGES prostaglandin E synthase 0.47 Hs.8878 NM_004523 KIF11 kinesin family member 11 0.47 Hs.592016 W74442 POLG polymerase (DNA directed), gamma 0.47 Hs.572318 NM_017858 FLJ20516 timeless-interacting protein 0.47 Hs. 195464 AI625550 FLNA filam in A, a lp ha (ac tin bin ding pro te in 280) 0470.47 Hs.286233 NM_017425 SPA17 sperm autoantigenic protein 17 0.47 Hs.521640 NM_002874 RAD23B RAD23 homolog B (S. cerevisiae) 0.47 Hs.144407 NM_018283 NUDT15 nudix (nucleoside diphosphate linked moiety X)-type motif 15 0.47 Hs.156346 AU159942 TOP2A topoisomerase (DNA) II alpha 170kDa 0.47 Hs.7753 U67280 CALU calumenin 0.47 Hs.145575 AF044221 UBL3 ubiquitin-like 3 0.47 Hs.445898 AW592266 MYBL1 v-myb myeloblastosis viral oncogene homolog (avian)-like 1 0.47 Hs.592248 AF220509 TAF9L TAF9-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31kDa 0.47 Hs.239 NM_021953 FOXM1 forkhead box M1 0.47 Hs.656 AF277724 CDC25C cell division cycle 25C 0.46 Hs.191334 NM_003362 UNG uracil-DNA glycosylase 0.46 Hs.85951 AW242820 XPOT exportin, tRNA (nuclear export receptor for tRNAs) 0.46 Hs.532363 NM_152696 HIPK1 homeodomain interacting protein kinase 1 0.46 Hs.244940 AV697515 RDH10 retinol dehydrogenase 10 (all-trans) 0.46 Hs.534040 NM_152903 KBTBD6 kelch repeat and BTB (POZ) domain containing 6 0.46 Hs.319265 NM_003144 SSR1 signal sequence receptor, alpha (translocon-associated protein alpha) 0.46 Hs.386793 NM_002084 GPX3 glutathione peroxidase 3 (plasma) 0.46 Hs.159234 AF080255 TTF2 transcription termination factor, RNA polymerase II 0.46 Hs.508480 AI302106 RAP2A RAP2A, member of RAS oncogene family 0.46 Hs.591637 AA176247 FNBP3 formin binding protein 3 0.46 Hs.30561 NM_012415 RAD54B RAD54 homolog B (S. cerevisiae) 0.46 Hs.115474 NM_002915 RFC3 replication factor C (activator 1) 3, 38kDa 0.46 Hs.89497 NM_005573 LMNB1 lamin B1 0.46 Hs.591939 NM_004879 EI24 etoposide induced 2.4 mRNA 0.46 Hs.118722 AI654093 FUT8 fucosyltransferase 8 (alpha (1,6) fucosyltransferase) 0.45 Table S1. (Continued) Unigene Accession Symbol Description Mean fold change Hs.481186 AA902971 CLCN3 chloride channel 3 0.45 Hs.395482 AA912743 PTK2 PTK2 protein tyrosine kinase 2 0.45 Hs.438289 AF001903 HADHSC L-3-hydroxyacyl-Coenzyme A dehydrogenase, short chain 0.45 Hs.153546 NM_004661 CDC23 CDC23 (cell division cycle 23, yeast, homolog) 0.45 Hs.226755 NM_003405 YWHAH tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide 0.45 Hs.130316 AL110225 DBN1 drebrin 1 0.45 Hs.513867 NM_002208 ITGAE integrin, alpha E (antigen CD103 , human mucosal lymphocyte antigen 1; alpha polypeptide) 0450.45 Hs.292464 NM_030780 MFTC mitochondrial folate transporter/carrier 0.45 Hs.574492 NM_012346 NUP62 nucleoporin 62kDa 0.45 Hs.523855 AI816243 STX12 syntaxin 12 0.45 Hs.241558 AI340270 ARIH2 ariadne homolog 2 (Drosophila) 0.45 Hs.308045 D38553 BRRN1 barren homolog (Drosophila) 0.45 Hs.436031 BF438417 IREB2 iron-responsive element binding protein 2 0.45 Hs.575032 NM_024629 KLIP1 KSHV latent nuclear antigen interacting protein 1 0.44 Hs.402752 AW296067 TAF15 TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa 0.44 Hs. 591925 AF155827 HELLS hlihelicase, l ymph hidoid-specifi c 0440.44 Hs.584807 BC002493 TCF19 transcription factor 19 (SC1) 0.44 Hs.511067 NM_002875 RAD51 RAD51 homolog (RecA homolog, E. coli) (S. cerevisiae) 0.44 Hs.388918 BC032240 RECK reversion-inducing-cysteine-rich protein with kazal motifs 0.44 Hs.7200 AI073943 NEK8 NIMA (never in mitosis gene a)- related kinase 8 0.44 Hs.19114 AI806853 HMGB3 high-mobility group box 3 0.44 Hs.445098 AI810054 DEPDC1 DEP domain containing 1 0.44 Hs.421986 AJ224869 CXCR4 Homo sapiens CXCR4 gene encoding receptor CXCR4. 0.44 Hs.194143 NM_007295 BRCA1 breast cancer 1, early onset 0.44 Hs.484782 NM_004401 DFFA DNA fragmentation factor, 45kDa, alpha polypeptide 0.44 Hs.160574 AI202201 JPH1 junctophilin 1 0.44 Hs.460124 BE544837 PHF19 PHD finger protein 19 0.44 Hs.409065 BC000323 FEN1 flap structure-specific endonuclease 1 0.43 Hs.79018 BF000239 CHAF1A chromatin assembly factor 1, subunit A (p150) 0.43 Hs.589594 NM_001533 HNRPL heterogeneous nuclear ribonucleoprotein L 0.43 Hs.577404 AI990326 MPHOSPH9 M-phase phosphoprotein 9 0.43 Hs.471851 BE378479 HDLBP high density lipoprotein binding protein (vigilin) 0.43 Hs.417795 AA706316 ZD52F10 hypothetical gene ZD52F10 0.43 Hs.1770 NM_000234 LIG1 ligase I, DNA, ATP-dependent 0.43 Hs.368982 U13022 CASP2 caspase 2 0.43 Hs.514685 NM_020648 TWSG1 twisted gastrulation homolog 1 (Drosophila) 0.43 Hs.591671 BC001255 NCBP2 nuclear cap binding protein subunit 2, 20kDa 0.43 Hs.471873 NM_012145 DTYMK deoxythymidylate kinase (thymidylate kinase) 0.43 Hs.198365 NM_001724 BPGM 2,3-bisphosphoglycerate mutase 0.43 Hs.514470 BC001075 SLC25A19 solute carrier family 25 (mitochondrial deoxynucleotide carrier), member 19 0.43 Hs.567295 NM_002222 ITPR1 inositol 1,4,5-triphosphate receptor, type 1 0.43 Hs.610775 AW771919 PAI-RBP1 PAI-1 mRNA-binding protein 0.42 Hs.529778 BC005400 FKSG14 leucine zipper protein FKSG14 0.42 Hs.498248 NM_003686 EXO1 exonuclease 1 0.42 Hs.505735 NM_000946 NACA nascent-polypeptide-associated complex alpha polypeptide 0.42 Hs.422688 NM_006048 UBE4B ubiquitination factor E4B (UFD2 homolog, yeast) 0.42 Hs.172052 AL043646 PLK4 polo-like kinase 4 (Drosophila) 0.42 Hs.113876 AW024870 WHSC1 Wolf-Hirschhorn syndrome candidate 1 0.42 Hs.83765 BC000192 DHFR dihydrofolate reductase 0.42 Hs.301804 AB040927 SH3MD2 SH3 multiple domains 2 0.42 Hs.588179 AU148466 KPNB3 karyypopherin ( im portin ) beta 3 0.42 Hs.439643 AW975728 SLC16A7 solute carrier family 16 (monocarboxylic acid transporters), member 7 0.42 Hs.433068 NM_002736 PRKAR2B protein kinase, cAMP-dependent, regulatory, type II, beta 0.42 Hs.446684 NM_012099 ASE-1 CD3-epsilon-associated protein; antisense to ERCC-1 0.42 Hs.106019 AI492873 PPP1R10 protein phosphatase 1, regulatory subunit 10 0.42 Hs.558393 AI692974 RRM1 ribonucleotide reductase M1 polypeptide 0.41 Hs.77254 NM_006807 CBX1 chromobox homolog 1 (HP1 beta homolog Drosophila ) 0.41 Hs.467701 NM_002539 ODC1 ornithine decarboxylase 1 0.41 Hs.591036 NM_020128 MDM1 nuclear protein double minute 1 0.41 Hs.2182 AI224977 PMCH pro-melanin-concentrating hormone 0410.41 Hs.78060 AI798207 PHKB phosphorylase kinase, beta 0.41 Hs.25292 NM_006397 JUNB jun B proto-oncogene 0.41 Hs.447877 NM_004085 TIMM8A translocase of inner mitochondrial membrane 8 homolog A (yeast) 0.41 Hs.506989 BC001866 RFC5 replication factor C (activator 1) 5, 36.5kDa 0.41 Hs.226390 BC001886 RRM2 ribonucleotide reductase M2 polypeptide 0.41 Hs.123253 NM_024745 SHCBP1 likely ortholog of mouse Shc SH2-domain binding protein 1 0.41 Hs.408182 X06268 COL2A1 collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital) 0.40 Hs.591363 NM_007057 ZWINT ZW10 interactor 0.40 Table S1. (Continued) Unigene Accession Symbol Description Mean fold change Hs.482233 AK001166 XTP1 HBxAg transactivated protein 1 0.40 Hs.436187 NM_004237 TRIP13 thyroid hormone receptor interactor 13 0.40 Hs.19192 AB012305 CDK2 cyclin-dependent kinase 2 0.40 Hs.40499 NM_012242 DKK1 dickkopf homolog 1 (Xenopus laevis) 0.40 Hs.592325 AK022829 XRCC3 X-ray repair complementing defective repair in Chinese hamster cells 3 0.39 Hs.438720 D55716 MCM7 MCM7 minichromosome maintenance deficient 7 (S. cerevisiae) 0.39 Hs. 270845 AW192521 KIF23 kinesi n f amil y memb er 23 0390.39 Hs.198363 AL136840 MCM10 MCM10 minichromosome maintenance deficient 10 (S. cerevisiae) 0.38 Hs.30026 AF277178 HSPC182 HSPC182 protein 0.38 Hs.516578 J03225 TFPI tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor) 0.38 Hs.26516 NM_018154 ASF1B ASF1 anti-silencing function 1 homolog B (S. cerevisiae) 0.38 Hs.495656 AW968555 TBL1X transducin (beta)-like 1X-linked 0.38 Hs.302738 AI718385 SLC26A2 solute carrier family 26 (sulfate transporter), member 2 0.38 Hs.517582 AA807529 MCM5 MCM5 minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae) 0.38 Hs.405958 U77949 CDC6 CDC6 cell division cycle 6 homolog (S. cerevisiae) 0.38 Hs.374378 NM_001826 CKS1B CDC28 protein kinase regulatory subunit 1B 0.38 Hs.408061 NM_001444 FABP5 fatty acid binding protein 5 (psoriasis-associated) 0.38 Hs.567421 BE045993 OIP5 Opa-interacting protein 5 0.37 Hs.289092 AL565621 COTL1 coactosin-like 1 (Dictyostelium) 0.37 Hs.416375 AI341146 E2F7 E2F transcription factor 7 0.37 Hs.436542 AF142573 LOC83690 CocoaCrisp 0.37 Hs.520506 NM_012177 FBXO5 F-box only protein 5 0.37 Hs.444118 NM_005915 MCM6 MCM6 minichromosome maintenance deficient 6 (MIS5 homolog, S. pombe) (S. cerevisiae) 0.36 Hs.632496 AK001261 RAMP RA-regulated nuclear matrix-associated protein 0.36 Hs.470654 AY029179 CDCA7 cell division cycle associated 7 0.36 Hs.75823 BC006471 AF1Q ALL1-fused gene from chromosome 1q 0.36 Hs.541894 AA463221 UNQ2430 ankyrin-related 0.36 Hs.55220 AF095192 BAG2 BCL2-associated athanogene 2 0.36 Hs.433180 BC003186 Pfs2 DNA replication complex GINS protein PSF2 0.36 Hs.515122 BC007986 TK1 thymidine kinase 1, soluble 0.34 Hs.108106 AK025578 UHRF1 ubiquitin-like, containing PHD and RING finger domains, 1 0.34 Hs.488189 AA534860 H2AV H2A histone family, member V 0.33 Hs.9194 NM_016172 UBADC1 ubiquitin associated domain containing 1 0.33 Hs.517228 U90902 TIAM1 T-cell lymphoma invasion and metastasis 1 0.33 Hs.179718 NM_002466 MYBL2 v-myb myeloblastosis viral oncogene homolog (avian)-like 2 0.32 Hs.122908 AF321125 CDT1 DNA replication factor 0.31 Hs.527980 AB049113 DUT dUTP pyrophosphatase 0.31 Hs.477481 NM_004526 MCM2 MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae) 0.30 Hs.534032 M30894 TARP TCR gamma alternate reading frame protein 0.29 Hs.208388 AA579890 FANCD2 Fanconi anemia, complementation group D2 0.28 Hs.597144 N62196 ZNF367 zinc finger protein 367 0.27 Hs.437705 AY137580 CDC25A cell division cycle 25A 0.25