Supplemental Table S3. List of the genes down-regulated 1-2 days following CTX treatment Parametric Gene symbol Description EntrezID p-value* BAG2 BCL2-associated athanogene 2 9532 6.20E-06 MCM6 MCM6 minichromosome maintenance deficient 6 4175 6.87E-05 BLMH bleomycin hydrolase 642 7.17E-05 UBB ubiquitin B 7314 7.46E-05 STMN1 stathmin 1/oncoprotein 18 3925 9.12E-05 PTBP2 polypyrimidine tract binding protein 2 58155 9.69E-05 KLRC4 killer cell lectin-like receptor subfamily K, member 1 22914 1.41E-04 LRBA LPS-responsive vesicle trafficking, beach and anchor containing 987 1.81E-04 MCL1 myeloid cell leukemia sequence 1 (BCL2-related) 4170 1.84E-04 RNF10 ring finger protein 10 9921 1.91E-04 GO67 golgin-67 23015 2.11E-04 HMGN2P18 high mobility group nucleosomal binding domain 2 pseudogene 18 648822 2.19E-04 C9orf78 chromosome 9 open reading frame 78 51759 2.20E-04 CCND2 cyclin D2 894 2.21E-04 YES1 v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1 7525 2.44E-04 PSME4 proteasome (prosome, macropain) activator subunit 4 23198 2.50E-04 HARS2 histidyl-tRNA synthetase 2 92675 2.50E-04 NSUN2 NOL1/NOP2/Sun domain family, member 2 54888 2.65E-04 EML4 echinoderm microtubule associated protein like 4 27436 2.88E-04 EEF1G eukaryotic translation elongation factor 1 gamma 1937 3.05E-04 CREM cAMP responsive element modulator 1390 3.08E-04 FBXO7 F-box protein 7 25793 3.08E-04 SLC25A37 mitochondrial solute carrier protein 51312 3.41E-04 IGHG1 immunoglobulin heavy constant gamma 1 (G1m marker) 3500 3.56E-04 IGJ immunoglobulin J polypeptide, linker protein for immunoglobulin alpha 3512 3.57E-04 and mu polypeptides C20orf3 chromosome 20 open reading frame 3 57136 3.65E-04 SFRS5 splicing factor, arginine/serine-rich 5 6430 3.68E-04 BM02 ubiquitin-fold modifier 1 51569 3.70E-04 OSBPL9 oxysterol binding protein-like 9 114883 3.76E-04 TRGV9 similar to T-cell receptor gamma chain C region PT-gamma-1/2 442532 3.89E-04 PHIP pleckstrin homology domain interacting protein 55023 4.02E-04 EIF4A2 eukaryotic translation initiation factor 4A, isoform 2 1974 4.20E-04 ARL7 ADP-ribosylation factor-like 7 10123 4.29E-04 RABGGTB Rab geranylgeranyltransferase, beta subunit 5876 4.53E-04 OGT O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N- 8473 4.56E-04 acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase) UTX ubiquitously transcribed tetratricopeptide repeat, X chromosome 7403 4.60E-04 RAB2B RAB2B, member RAS oncogene family 84932 4.66E-04 GGH gamma-glutamyl hydrolase (conjugase, folylpolygammaglutamyl 8836 4.88E-04 hydrolase) RFPL3S RFPL3 antisense RNA 1 (non-protein coding) 10737 4.99E-04 CCDC16 hypothetical protein MGC20398 91603 5.04E-04 HSPA14 heat shock 70kDa protein 14 51182 5.16E-04 TCP4 activated RNA polymerase II transcription cofactor 4 10923 5.17E-04 TARBP1 TAR (HIV) RNA binding protein 1 6894 5.28E-04 SP100 SP100 nuclear antigen 6672 5.28E-04 ILF2 interleukin enhancer binding factor 2, 45kDa 3608 5.32E-04 CYBA cytochrome b-245, alpha polypeptide 1535 5.72E-04 SMARCC1 SWI/SNF related, matrix associated, actin dependent regulator of 6599 5.74E-04 chromatin, subfamily c, member 1 CTCF CCCTC-binding factor (zinc finger protein) 10664 5.78E-04 LOC120364 similar to Hnrpa1 protein 120364 5.97E-04 PAPD1 PAP associated domain containing 1 55149 6.01E-04 TAF1B TATA box binding protein (TBP)-associated factor, RNA polymerase I, B 9014 6.02E-04 RNPC1 RNA-binding region (RNP1, RRM) containing 1 55544 6.08E-04 SRPRB signal recognition particle receptor, B subunit 58477 6.17E-04 PNRC2 proline-rich nuclear receptor coactivator 2 55629 6.20E-04 RPA1 replication protein A1, 70kDa 6117 6.24E-04 C1QBP complement component 1, q subcomponent binding protein 708 6.25E-04 OCC-1 hypothetical protein 387882 6.28E-04 LCOR ligand-dependent corepressor 84458 6.31E-04 EIF3J eukaryotic translation initiation factor 3, subunit 1 alpha, 35kDa 8669 6.47E-04 WDR40A WD repeat domain 40A 25853 6.50E-04 YLPM1 YLP motif containing 1 56252 6.66E-04 NPM1 nucleophosmin (nucleolar phosphoprotein B23, numatrin) 4869 6.69E-04 KLRK1 killer cell lectin-like receptor subfamily K, member 1 22914 6.78E-04 MIR membrane-associated ring finger (C3HC4) 8, E3 ubiquitin protein ligase 220972 6.85E-04 DKC1 dyskeratosis congenita 1, dyskerin 1736 6.96E-04 C1orf63 HT014 57095 7.03E-04 OSTF1 osteoclast stimulating factor 1 26578 7.12E-04 OPTN optineurin 10133 7.18E-04 BXDC5 RNA processing factor 1 80135 7.28E-04 SFPQ splicing factor proline/glutamine-rich (polypyrimidine tract binding protein 6421 7.66E-04 associated) PPHLN1 periphilin 1 51535 7.72E-04 EIF3S10 eukaryotic translation initiation factor 3, subunit 10 theta, 150/170kDa 8661 8.20E-04 RRM2 ribonucleotide reductase M2 polypeptide 6241 8.24E-04 ARID4A AT rich interactive domain 4A (RBP1-like) 5926 8.25E-04 TRIM37 tripartite motif-containing 37 4591 8.30E-04 VRK1 vaccinia related kinase 1 7443 8.32E-04 MED6 mediator of RNA polymerase II transcription, subunit 6 homolog (yeast) 10001 8.38E-04 PAFAH1B1 platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit 45kDa 5048 8.42E-04 RP11-78J21.1 hypothetical protein LOC144983 144983 8.47E-04 C14orf87 chromosome 14 open reading frame 87 51218 8.95E-04 PSME4 proteasome (prosome, macropain) activator subunit 4 23198 8.97E-04 NOP5 nucleolar protein NOP5/NOP58 51602 9.51E-04 C3orf17 chromosome 3 open reading frame 17 25871 9.94E-04 FAM82C hypothetical protein FLJ10579 55177 9.95E-04 GPX7 glutathione peroxidase 7 2882 1.00E-03 ETS1 v-ets erythroblastosis virus E26 oncogene homolog 1 (avian) 2113 1.01E-03 CD69 CD69 antigen (p60, early T-cell activation antigen) 969 1.02E-03 OR1E3P olfactory receptor, family 1, subfamily E, member 1 8387 1.04E-03 MRFAP1L1 PP784 protein 114932 1.04E-03 MMD2 monocyte to macrophage differentiation-associated 23531 1.04E-03 G3B2 Ras-GTPase activating protein SH3 domain-binding protein 2 9908 1.05E-03 CD28 CD28 antigen (Tp44) 940 1.09E-03 FTS fused toes homolog (mouse) 64400 1.10E-03 C10orf45 chromosome 10 open reading frame 45 83641 1.10E-03 ALAS2 aminolevulinate, delta-, synthase 2 212 1.10E-03 USP7 ubiquitin specific protease 7 (herpes virus-associated) 7874 1.11E-03 P15RS hypothetical protein FLJ10656 55197 1.12E-03 PDXDC1 KIAA0251 protein 23042 1.13E-03 NP_055462 limkain b1 9665 1.14E-03 SBDS Shwachman-Bodian-Diamond syndrome 51119 1.14E-03 MPHOSPH9 M-phase phosphoprotein 9 10198 1.16E-03 WDR60 hypothetical protein FLJ10300 55112 1.21E-03 SLC35D2 solute carrier family 35, member D2 11046 1.21E-03 CRY1 cryptochrome 1 (photolyase-like) 1407 1.22E-03 SH3YL1 SH3 domain containing, Ysc84-like 1 (S. cerevisiae) 26751 1.25E-03 HNRNPA1P7 heterogeneous nuclear ribonucleoprotein A1 pseudogene 7 388275 1.27E-03 TMTC4 hypothetical protein FLJ14624 84899 1.27E-03 DNHD2 hypothetical protein FLJ40427 201625 1.28E-03 LOC93622 hypothetical protein BC006130 93622 1.30E-03 TARDBP TAR DNA binding protein 23435 1.30E-03 KCY UMP-CMP kinase 51727 1.31E-03 ZMYM2 zinc finger protein 198 7750 1.36E-03 CDK5RAP3 CDK5 regulatory subunit associated protein 3 80279 1.36E-03 IGKC immunoglobulin kappa constant 3514 1.36E-03 GLS glutaminase 2744 1.37E-03 TGIF TGFB-induced factor (TALE family homeobox) 7050 1.40E-03 ZNF433 zinc finger protein 433 163059 1.40E-03 KIAA1627 KIAA1627 protein 57721 1.40E-03 LPIN1 lipin 1 23175 1.41E-03 ERH enhancer of rudimentary homolog (Drosophila) 2079 1.41E-03 CLDND1 chromosome 3 open reading frame 4 56650 1.42E-03 ARFGAP3 ADP-ribosylation factor GTPase activating protein 3 26286 1.44E-03 TXNDC5 thioredoxin domain containing 5 81567 1.46E-03 FNBP1 formin binding protein 1 23048 1.47E-03 ENC1 ectodermal-neural cortex (with BTB-like domain) 8507 1.48E-03 GBAS glioblastoma amplified sequence 2631 1.49E-03 CBFB core-binding factor, beta subunit 865 1.50E-03 SNCA synuclein, alpha (non A4 component of amyloid precursor) 6622 1.51E-03 ATRX alpha thalassemia/mental retardation syndrome X-linked 546 1.52E-03 NOLA1 nucleolar protein family A, member 1 (H/ACA small nucleolar RNPs) 54433 1.52E-03 hCG15200 similar to eukaryotic translation initiation factor 3, subunit 5 epsilon, 339799 1.53E-03 47kDa; eukaryotic translation initiation factor 3, subunit 5 (epsilon, 47kD); eIF3-epsilon ANKRD27 ankyrin repeat domain 27 (VPS9 domain) 84079 1.53E-03 CPNE3 copine III 8895 1.55E-03 CHD4 chromodomain helicase DNA binding protein 4 1108 1.56E-03 HNRNPU-AS1 HNRNPU antisense RNA 1 (non-protein coding) 284702 1.59E-03 IPO11 importin 11 51194 1.60E-03 SBDS Shwachman-Bodian-Diamond syndrome 51119 1.61E-03 C1orf156 hypothetical protein MGC9084 92342 1.61E-03 TERF2IP telomeric repeat binding factor 2, interacting protein 54386 1.61E-03 UHRF2 ubiquitin-like, containing PHD and RING finger domains, 2 115426 1.62E-03 DHX9 DEAH (Asp-Glu-Ala-His) box polypeptide 9 1660 1.62E-03 YARS2 CGI-04 protein 51067 1.62E-03 SRSF6 serine/arginine-rich splicing factor 6 6431 1.63E-03 C14orf11 chromosome 14 open reading frame 11 55837 1.64E-03 C19orf13 chromosome 19 open reading frame 13 26065 1.64E-03 KIAA0052 KIAA0052 23517 1.65E-03 PDCD4 programmed cell death 4 (neoplastic transformation inhibitor) 27250 1.66E-03 YTHDC1 splicing factor YT521-B 91746 1.66E-03 MED10 hypothetical protein MGC5309 84246 1.67E-03 THG1L interphase cyctoplasmic foci protein 45 54974 1.68E-03 SUCLG2 succinate-CoA ligase, GDP-forming, beta subunit 8801 1.69E-03 TGFBR3 transforming growth factor, beta receptor III (betaglycan, 300kDa) 7049 1.69E-03 RPL22 ribosomal protein L22 6146 1.70E-03 ATAD2 ATPase family, AAA domain containing 2 29028 1.74E-03 NUP133 nucleoporin 133kDa 55746 1.78E-03 USP1 ubiquitin specific protease 1 7398 1.81E-03 ZNF550 zinc finger protein 550 162972 1.84E-03 MAK3 Mak3 homolog (S.