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.