Supplemental Data Table 1: Experimental Setup

Correlation Array Reverse Fluor Array Extraction Coefficient Print Batch (Y/N) mean (range) DLD1-I.1 I A N DLD1-I.2 I B N 0.86 DLD1-I.3 I C N (0.79-0.90) DLD1-I.4 I C Y DLD1 DLD1-II.1 II D N DLD1-II.2 II E N 0.86 DLD1-II.3 II F N (0.74-0.94) DLD1-II.4 II F Y DLD1+3-II.1 II A N DLD1+3-II.2 II A N 0.85 DLD1 + 3 DLD1+3-II.3 II B N (0.64-0.95) DLD1+3-II.4 II B Y DLD1+7-I.1 I A N DLD1+7-I.2 I A N 0.79 DLD1 + 7 DLD1+7-I.3 I B N (0.68-0.90) DLD1+7-I.4 I B Y DLD1+13-I.1 I A N DLD1+13-I.2 I A N 0.88 DLD1 + 13 DLD1+13-I.3 I B N (0.84-0.91) DLD1+13-I.4 I B Y hTERT-HME-I.1 I A N hTERT-HME-I.2 I B N 0.85 hTERT-HME hTERT-HME-I.3 I C N (0.80-0.92) hTERT-HME-I.4 I C Y hTERT-HME+3-I.1 I A N hTERT-HME+3-I.2 I B N 0.84 hTERT-HME + 3 hTERT-HME+3-I.3 I C N (0.74-0.90) hTERT-HME+3-I.4 I C Y

Supplemental Data Table 2: Average expression profiles by arm

DLD1 hTERT-HME Ratio.7 Ratio.1 Ratio.3 Ratio.3 Chrom. Ratio.0 p.7vs0 p.13vs0 p.3vs0 Ratio.0 p.3vs0 vs0 3vs0 vs0 vs0 1p 1.00 1.04 0.0013 1.03 - 0.98 0.0293 1.00 1.02 - 1q 0.92 1.02 - 0.99 - 1.02 - 0.96 1.02 - 2p 1.03 1.05 - 1.00 - 1.00 - 1.01 0.96 0.0059 2q 0.95 1.02 - 1.01 - 0.99 - 0.99 1.01 - 3p 0.95 0.97 - 0.98 - 1.13 0.0009 0.96 1.22 <0.0001 3q 0.89 0.99 - 1.01 - 1.20 <0.0001 1.01 1.18 0.0010 4p 1.00 1.02 - 1.00 - 1.00 - 1.08 0.95 - 4q 1.05 0.96 - 0.97 - 0.97 - 1.12 0.97 - 5p 0.92 0.89 0.0411 0.98 - 1.01 - 0.89 1.05 - 5q 0.94 1.02 - 0.99 - 1.02 - 1.01 0.98 - 6p 0.88 1.08 0.0027 0.99 - 0.98 - 0.87 1.00 - 6q 1.02 1.01 - 1.06 - 1.00 - 1.06 0.91 0.0317 7p 0.95 1.14 <0.0001 0.98 - 1.00 - 0.95 1.00 - 7q 0.81 1.22 <0.0001 0.98 - 0.98 - 0.86 1.03 - 8p 0.88 1.07 0.0159 1.07 0.0063 1.04 - 1.04 0.99 - 8q 0.96 1.00 - 0.99 - 1.00 - 0.99 0.98 - 9p 1.05 1.01 - 1.02 - 0.95 - 1.10 1.01 - 9q 0.94 1.00 - 0.99 - 0.99 - 0.92 1.00 - 10p 0.90 1.04 - 1.02 - 1.04 0.0221 0.90 1.03 - 10q 1.05 1.00 - 0.98 - 0.98 - 1.08 1.01 - 11p 0.94 1.04 - 0.98 - 1.03 - 0.91 1.01 - 11q 0.92 1.00 - 0.96 - 0.98 - 0.97 0.98 - 12p 0.82 1.06 - 0.96 - 0.96 - 0.81 1.02 - 12q 0.96 1.04 0.0183 1.00 - 1.02 - 0.98 0.98 - 13q 0.99 1.01 - 1.26 0.0009 1.04 - 1.11 0.99 - 14q 0.92 1.02 - 1.01 - 1.02 - 0.93 1.00 - 15q 0.90 1.03 - 1.02 - 1.01 - 0.97 1.01 - 16p 0.93 1.05 - 0.99 - 0.97 - 0.85 1.00 - 16q 0.92 1.05 - 1.03 - 1.00 - 0.88 0.99 - 17p 1.07 1.08 - 1.00 - 0.98 - 1.05 0.98 - 17q 0.98 1.05 - 1.03 - 1.00 - 0.96 0.98 - 18p 1.03 0.96 - 1.02 - 0.97 - 1.02 0.96 - 18q 1.03 1.03 - 1.04 - 1.02 - 1.27 0.93 0.0483 19p 0.94 1.00 - 0.95 - 0.99 - 0.88 1.02 - 19q 0.93 1.03 - 0.95 - 0.98 - 0.98 1.01 - 20p 0.94 0.97 - 0.99 - 0.99 - 1.06 1.00 20q 0.84 1.02 - 1.02 - 0.99 - 0.88 1.00 21q 0.90 1.05 - 1.03 - 0.99 - 0.87 1.00 22q 0.94 1.04 - 0.98 - 0.97 - 0.91 1.00 Xp 0.89 0.97 0.0157 1.01 - 0.99 - 0.89 1.01 Xq 0.72 1.08 0.0265 0.98 - 0.98 - 0.82 1.03 Yq 1.30 0.93 - 0.99 - 0.69 <0.0001 0.97 0.96

For each chromosome arm, the average expression ratio for all on that arm relative to the reference RNA pool is given for the parental line (Ratio.0). The average chromosome arm expression ratios (relative to the same reference RNA for each chromosome transfer clone) are then normalized to the parental ratio value (Ratio.7vs0, Ratio.13vs0, Ratio.3vs.0) and their respective p-values from two-sample t-tests calculated. Ratio values having a p-value < 0.001 were considered significant and are in bold. P-values >0.05 are not reported. Supplemental Data Table 3: Genes significantly altered in expression in DLD1+7 a

Upregulated genes Ratio.7vs0 Map Gene Description 12.40 7p21.2 TWIST twist homolog (acrocephalosyndactyly 3; Saethre-Chotzen syndrome) (Drosophila) 5.57 6p21.2 CDKN1A "cyclin-dependent kinase inhibitor 1A (p21, Cip1)" 5.16 6p21.2 CDKN1A "cyclin-dependent kinase inhibitor 1A (p21, Cip1)" 4.94 18 ESTs 4.89 Xq22.3 DSIPI "delta sleep inducing peptide, immunoreactor" 4.79 Incyte EST 4.78 4q13-q21 IL8 interleukin 8 4.68 15q26.1 IDH2 " 2 (NADP+), mitochondrial" 4.68 18q12.1 DSC2 desmocollin 2 3.99 12q13 NR4A1 "nuclear receptor subfamily 4, group A, member 1" 3.91 15q15 CKMT1 "creatine kinase, mitochondrial 1 (ubiquitous)" 3.82 22q13.1 LGALS1 "lectin, galactoside-binding, soluble, 1 (galectin 1)" 3.71 10p15-p14 AKR1C1 "aldo-keto reductase family 1, member C1 (dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase)" 3.71 1p22 CTBS "chitobiase, di-N-acetyl-" 3.55 1p33 TSPAN-1 tetraspan 1 3.55 12q22- PAH phenylalanine hydroxylase q24.2 3.46 15q23 TSPAN-3 tetraspan 3 3.45 Xq28 ZNF185 zinc finger 185 (LIM domain) 3.39 Xq11-q12 HEPH hephaestin 3.35 19q13.11 FXYD3 FXYD domain containing ion transport regulator 3 3.33 1 Human hbc647 mRNA sequence. 3.32 10q25 DUSP5 dual specificity phosphatase 5 3.30 5q31.2 KIAA0416 KIAA0416 protein 3.30 14q21-q22 PYGL ", glycogen; liver (Hers disease, glycogen storage disease type VI)" 3.26 7q21.3- NPTX2 neuronal pentraxin II q22.1 3.21 15q23 TSPAN-3 tetraspan 3 3.15 7q32.3 SMO smoothened homolog (Drosophila) 3.14 7q21 GNAI1 "guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1" 3.13 7q21.3- NPTX2 neuronal pentraxin II q22.1 3.12 1q25.2- PTGS2 prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase q25.3 and cyclooxygenase) 3.08 22q12.2 LIF leukemia inhibitory factor (cholinergic differentiation factor) 3.05 1pter- KIAA0237 KIAA0237 gene p22.2 3.05 12p13.2- KLRC4 "killer cell lectin-like receptor subfamily C, member 4" p12.3 3.00 11p13 CD44 CD44 antigen (homing function and Indian blood group system) 2.98 7q22 TRIP6 thyroid hormone receptor interactor 6 2.97 6p25 SERPINB6 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 6" 2.97 19q13.32 FOSB FBJ murine osteosarcoma viral oncogene homolog B 2.93 7p12 GBAS glioblastoma amplified sequence 2.84 17p11.2 ALDH3A2 "aldehyde dehydrogenase 3 family, member A2" 2.84 8q24.13 C8FW phosphoprotein regulated by mitogenic pathways 2.83 5q12.1- SNK serum-inducible kinase q13.2 2.82 8p12-p11 DUSP4 dual specificity phosphatase 4 2.79 1q21 MCL1 myeloid cell leukemia sequence 1 (BCL2-related) 2.77 20q12 SDC4 "syndecan 4 (amphiglycan, ryudocan)" 2.77 17q22 ABCC3 "ATP-binding cassette, sub-family C (CFTR/MRP), member 3" 2.75 1q32.3 ATF3 activating transcription factor 3 2.74 2p21 CYP1B1 "cytochrome P450, family 1, subfamily B, polypeptide 1" 2.73 4p16 S100P S100 calcium binding protein P 2.69 7q36.1 RARRES2 retinoic acid receptor responder (tazarotene induced) 2 2.68 1p36.3 EGFL3 "EGF-like-domain, multiple 3" 2.67 10p15-p14 AKR1C4 "aldo-keto reductase family 1, member C4 (chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4)" 2.63 2q32.1 SSFA2 sperm specific antigen 2 2.61 "trefoil factor 1 (breast cancer, estrogen-inducible sequence expressed in)" 2.61 15q13-q14 SGNE1 "secretory granule, neuroendocrine protein 1 (7B2 protein)" 2.59 16q13 MT1B metallothionein 1B (functional) 2.59 16q13 MT1E metallothionein 1E (functional) 2.56 7q22 PCOLCE procollagen C-endopeptidase enhancer 2.56 "Human DNA sequence from clone 742C19 on chromosome 22q12.3-13.1. Contains a pseudogene similar to Cytochrome C Oxidase Polypeptide VB and (parts of) up to four novel genes, two with homology to Phorbolin genes and one a novel Chro" 2.55 4q28-q32 SLC7A11 "solute carrier family 7, (cationic amino acid transporter, y+ system) member 11" 2.54 19q13.3 KLK1 "kallikrein 1, renal/pancreas/salivary" 2.53 1q31 RGS2 "regulator of G-protein signalling 2, 24kDa" 2.52 22q12.3 TIMP3 "tissue inhibitor of metalloproteinase 3 (Sorsby fundus dystrophy, pseudoinflammatory)" 2.50 11q12-q13 AHNAK AHNAK nucleoprotein (desmoyokin) 2.49 3q26.2 EIF5A2 eukaryotic translation initiation factor 5A2 2.46 21q22.3 TFF3 trefoil factor 3 (intestinal) 2.45 16p13.3 RGS11 regulator of G-protein signalling 11 2.44 19p13.3 LDLR low density lipoprotein receptor (familial hypercholesterolemia) 2.43 9q34.1 STOM stomatin 2.43 16p13.3 ABCA3 "ATP-binding cassette, sub-family A (ABC1), member 3" 2.42 6p21.3 IER3 immediate early response 3 2.42 1p32.3 C1orf34 open reading frame 34 2.42 17q21.2 KRT20 keratin 20 2.42 12p12.3- MGST1 microsomal glutathione S- 1 p12.1 2.41 7q21.3 ASNS asparagine synthetase 2.41 19p13.3 CIRBP cold inducible RNA binding protein 2.41 Incyte EST 2.40 7q21 STEAP six transmembrane epithelial antigen of the prostate 2.37 7q31.1 CAV2 caveolin 2 2.36 17q25 LGALS3BP "lectin, galactoside-binding, soluble, 3 binding protein" 2.35 12q13 IGFBP6 insulin-like growth factor binding protein 6 2.31 Xp11.2 RBM3 RNA binding motif protein 3 2.29 1q24-q25 ABL2 "v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)" 2.28 8p22-p21.3 DLC1 deleted in liver cancer 1 2.27 12p13 KLRC3 "killer cell lectin-like receptor subfamily C, member 3" 2.27 7q11.23 PMS2L9 postmeiotic segregation increased 2-like 9 2.26 7q11.23 PTPN12 "protein tyrosine phosphatase, non-receptor type 12" 2.25 7p13-p12 HUS1 HUS1 checkpoint homolog (S. pombe) 2.25 17p13.3 ABR active BCR-related gene 2.25 7q11.23 BCL7B B-cell CLL/lymphoma 7B 2.24 19q12 DKFZP762D096 hypothetical protein DKFZp762D096 2.23 15q22.3- NEO1 neogenin homolog 1 (chicken) q23 2.22 3q13.13 TACTILE "T cell activation, increased late expression" 2.22 5q31 SEPP1 "selenoprotein P, plasma, 1" 2.22 Xp11.4- GAGE2 G antigen 2 p11.2 2.22 10q21.1 EGR2 "early growth response 2 (Krox-20 homolog, Drosophila)" 2.21 Xq28 EMD emerin (Emery-Dreifuss muscular dystrophy) 2.21 2q32 KLF7 Kruppel-like factor 7 (ubiquitous) 2.20 2q22.1 KYNU kynureninase (L-kynurenine ) 2.19 22q12.2 TCN2 transcobalamin II; macrocytic anemia 2.19 19q13.1 CLC Charot-Leyden crystal protein 2.18 22q12.2 NIPSNAP1 nipsnap homolog 1 (C. elegans) 2.18 1p33 MUF1 MUF1 protein 2.18 6p21.3- PGC progastricsin (pepsinogen C) p21.1 2.18 21 "ESTs, Highly similar to A Chain A, Cyclophilin A (E.C.5.2.1.8) Complexed With Dimethyl-Cyclosporin A [H.sapiens]" 2.18 8q22.2 TIEG TGFB inducible early growth response 2.17 7q31.1 HBP1 HMG-box containing protein 1 2.17 17q12- IGFBP4 insulin-like growth factor binding protein 4 q21.1 2.17 21q22.3 C21orf2 chromosome 21 open reading frame 2 2.15 19p13 FSTL3 follistatin-like 3 (secreted glycoprotein) 2.15 12p13 C3F putative protein similar to nessy (Drosophila) 2.15 12q14.1- TM4SF3 transmembrane 4 superfamily member 3 q21.1 2.14 2q37.3 PER2 period homolog 2 (Drosophila) 2.14 2cen-q24 CAPG "capping protein (actin filament), gelsolin-like" 2.13 11 "Human clone 137308 mRNA, partial cds." 2.13 7q31.1 ZNF277 zinc finger protein (C2H2 type) 277 2.13 7q21.3-q22 SERPINE1 "serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1" 2.12 Xq28 ZNF185 zinc finger protein 185 (LIM domain) 2.12 7p14-cen BLVRA biliverdin reductase A 2.11 8p23.2 KIAA0711 KIAA0711 gene product 2.10 20p11.23- ACAS2L acetyl-Coenzyme A synthetase 2 (AMP forming)-like p11.21 2.10 7q21 STEAP2 six transmembrane epithelial antigen of prostate 2 2.10 1q21.1 TXNIP thioredoxin interacting protein 2.10 7q36.3 KIAA0010 ubiquitin-protein isopeptide (E3) 2.10 22q11 E2F6 E2F transcription factor 6 2.09 7p12.3 LOC285958 hypothetical protein LOC285958 2.08 1q21 S100A4 "S100 calcium binding protein A4 (calcium protein, calvasculin, metastasin, murine placental homolog)" 2.08 7q11.23 MK-STYX map kinase phosphatase-like protein MK-STYX 2.08 7q21.3- DSS1 Deleted in split-hand/split-foot 1 region q22.1 2.06 16q13 MT1F metallothionein 1F (functional) 2.06 12 "Homo sapiens cDNA: FLJ20869 fis, clone ADKA02377." 2.06 11q22.2- CASP4 "caspase 4, apoptosis-related cysteine protease" q22.3 2.06 zinc finger protein 264 2.06 7q36 INSIG1 insulin induced gene 1 2.05 19q13.4 TNNT1 "troponin T1, skeletal, slow" 2.05 7q32 IRF5 interferon regulatory factor 5 2.05 8p23-p21 EGR3 early growth response 3 2.05 1p32-p31 JUN v-jun sarcoma virus 17 oncogene homolog (avian) 2.05 11q12- PYGM "phosphorylase, glycogen; muscle (McArdle syndrome, glycogen q13.2 storage disease type V)" 2.04 1p36-p31 C1orf8 chromosome 1 open reading frame 8 2.04 7q21-q22 AKAP9 A kinase (PRKA) anchor protein (yotiao) 9 2.04 6p24.1 EDN1 endothelin 1 2.03 8q24 PLEC1 "plectin 1, intermediate filament binding protein 500kDa" 2.03 diaphorase (NADH/NADPH) (cytochrome b-5 reductase) 2.03 4q34-q35 FACL2 "fatty-acid-Coenzyme A ligase, long-chain 2" 2.03 7p22.2 LOC221955 KCCR13L 2.02 1p34 PTPRF "protein tyrosine phosphatase, receptor type, F" 2.02 7p22 LFNG lunatic fringe homolog (Drosophila) 2.02 5q31 ALDH7A1 "aldehyde dehydrogenase 7 family, member A1" 2.02 10p11.23 BMI1 B lymphoma Mo-MLV insertion region (mouse) 2.02 7p12.1 COBL KIAA0633 protein 2.01 6p25 SERPINB1 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 1" 2.00 17q21 CNTNAP1 contactin associated protein 1 2.00 6p21.3 TNXB tenascin XB 2.00 7p22.3 EIF3S9 "eukaryotic translation initiation factor 3, subunit 9 eta, 116kDa" 2.00 20q12- HNF4A "hepatocyte nuclear factor 4, alpha" q13.1 Down regulated genes Ratio.7vs0 Map Gene Description 0.18 3p14.3 CADPS Ca2+-dependent activator protein for secretion 0.28 1q44 ELYS ELYS transcription factor-like protein TMBS62 0.29 4q25-q27 PITX2 paired-like homeodomain transcription factor 2 0.29 Incyte EST 0.33 10p12 NRP1 1 0.33 4q21-q23 ADH1A " 1A (class I), alpha polypeptide" 0.33 3q21-q25 CPA3 carboxypeptidase A3 (mast cell) 0.34 Xp11.23- CLCN5 "chloride channel 5 (nephrolithiasis 2, X-linked, Dent disease)" p11.22 0.37 9q33 TNC (hexabrachion) 0.37 11p13 BDNF brain-derived neurotrophic factor 0.38 12q15 HMGA2 high mobility group AT-hook 2 0.38 8q13.2 FLJ40021 hypothetical protein FLJ40021 0.38 2q24.3 DPP4 "dipeptidylpeptidase 4 (CD26, adenosine deaminase complexing protein 2)" 0.39 Incyte EST 0.41 14q32.33 C14orf2 chromosome 14 open reading frame 2 0.41 X "Homo sapiens cDNA: FLJ21909 fis, clone HEP03834." 0.42 20q12- TNNC2 "troponin C2, fast" q13.11 0.42 5p13 SLC1A3 "solute carrier family 1 (glial high affinity glutamate transporter), member 3" 0.44 3q25.1 P2RY1 "purinergic receptor P2Y, G-protein coupled, 1" 0.44 9 Homo sapiens mRNA; cDNA DKFZp564H1916 (from clone DKFZp564H1916) 0.44 7p14 B1 PTH-responsive osteosarcoma B1 protein 0.44 10q26 GFRA1 GDNF family receptor alpha 1 0.44 3p21.3 ITGA9 ", alpha 9" 0.45 6p21.1- TNFRSF21 "tumor necrosis factor receptor superfamily, member 21" 12.2 0.45 17q11.2 BLMH bleomycin hydrolase 0.45 3p23-p21 SMARCC1 "SWI/SNF related, matrix associated, actin dependent regulator of , subfamily c, member 1" 0.45 19p13.3 GPX4 glutathione peroxidase 4 (phospholipid hydroperoxidase) 0.46 11p13 FSHB "follicle stimulating hormone, beta polypeptide" 0.46 11p15.2- CALCB "calcitonin-related polypeptide, beta" p15.1 0.46 7q11.23 NCF1 "neutrophil cytosolic factor 1 (47kDa, chronic granulomatous disease, autosomal 1)" 0.47 6q24 GRM1 "glutamate receptor, metabotropic 1" 0.47 1p31 MSH4 mutS homolog 4 (E. coli) 0.47 9q22.1 DIRAS2 "DIRAS family, GTP-binding RAS-like 2" 0.47 5 "Homo sapiens cDNA FLJ12815 fis, clone NT2RP2002546." 0.47 1q25 C1orf24 chromosome 1 open reading frame 24 0.47 1q44 KIAA0470 KIAA0470 gene product 0.48 5q13.2 IQGAP2 IQ motif containing GTPase activating protein 2 0.48 5p13 DAB2 "disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)" 0.48 8q11.22 ST18 suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein) 0.49 4q22.1 FAM13A1 "family with sequence similarity 13, member A1" 0.49 7q21.12 MGC26647 hypothetical protein MGC26647 0.49 19 "Homo sapiens cDNA FLJ14241 fis, clone OVARC1000533." 0.49 19p13.3 CLPP "ClpP caseinolytic protease, ATP-dependent, proteolytic subunit homolog (E. coli)" 0.49 6q23 EPB41L2 erythrocyte membrane protein band 4.1-like 2 0.50 5p14-p13 NPR3 natriuretic peptide receptor C/guanylate C (atrionatriuretic peptide receptor C) 0.50 10q23.31 CARP cardiac protein 0.50 10q24 CYP2C9 "cytochrome P450, family 2, subfamily C, polypeptide 9" a For all of the genes in this table, the p-value associated with the approximate z-test of the chromosome transfer clone expression ratio compared to the parental clone expression ratio was less than 0.0001 with the exception of the following genes: ADH1A: "alcohol dehydrogenase 1A (class I), alpha polypeptide" (p=0.0001) C14orf2: chromosome 14 open reading frame 2 (p=0.0051) GFRA1: GDNF family receptor alpha 1 (p=0.0003) CALCB: "calcitonin-related polypeptide, beta" (p=0.0002) NCF1: "neutrophil cytosolic factor 1 (47kDa, chronic granulomatous disease, autosomal 1)" (p=0.0155) GRM1: "glutamate receptor, metabotropic 1" (p=0.0007) DIRAS2: "DIRAS family, GTP-binding RAS-like 2" (p=0.0061) MGC26647: hypothetical protein MGC26647 (p=0.0016) CYP2C9: "cytochrome P450, family 2, subfamily C, polypeptide 9" (p=0.0010) Supplemental Data Table 4: Genes significantly altered in expression in DLD1+13 a

Upregulated genes Ratio.13vs0 Map Gene Description 20.94 13q13 MAB21L1 mab-21-like 1 (C. elegans) 9.27 13q13.1 SPG20 "spastic paraplegia 20, spartin (Troyer syndrome)" 5.24 13q22 SCEL sciellin 4.38 1 Human hbc647 mRNA sequence. 4.27 1p12 TSPAN-2 tetraspan 2 4.17 6q14-q21 NT5E "5'-nucleotidase, ecto (CD73)" 3.82 19q13.3- KLK10 kallikrein 10 q13.4 3.59 17q22 ABCC3 "ATP-binding cassette, sub-family C (CFTR/MRP), member 3" 3.52 18q12.1 DSC2 desmocollin 2 3.48 19p13.3 FUT3 " 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group included)" 3.32 1p33 TSPAN-1 tetraspan 1 3.29 15q13-q14 SGNE1 "secretory granule, neuroendocrine protein 1 (7B2 protein)" 3.25 13q32 ZIC2 "Zic family member 2 (odd-paired homolog, Drosophila)" 3.23 Xq28 ZNF185 zinc finger protein 185 (LIM domain) 3.07 10q25 DUSP5 dual specificity phosphatase 5 3.06 18 ESTs 3.04 4p16 S100P S100 calcium binding protein P 3.03 4q28-q32 SLC7A11 "solute carrier family 7, (cationic amino acid transporter, y+ system) member 11" 2.79 Xq11-q12 HEPH hephaestin 2.76 1q21.2 FLJ11280 hypothetical protein FLJ11280 2.65 1p32-p31 TACSTD2 tumor-associated calcium signal transducer 2 2.64 13 "ESTs, Weakly similar to cytokine receptor-like factor 2; cytokine receptor CRL2 precusor [Homo sapiens] [H.sapiens]" 2.63 8p22-p21.3 ASAH1 N-acylsphingosine amidohydrolase (acid ceramidase) 1 2.62 6p21.2 CDKN1A "cyclin-dependent kinase inhibitor 1A (p21, Cip1)" 2.55 1p36.12 PRO1489 hypothetical protein PRO1489 2.55 8p23.1 DKFZp761P042 hypothetical protein DKFZp761P0423 2.53 1q23.2 GPA33 glycoprotein A33 (transmembrane) 2.51 2q32.3-q33 NAB1 NGFI-A binding protein 1 (EGR1 binding protein 1) 2.49 3q21.2 FTHFD formyltetrahydrofolate dehydrogenase 2.48 3p21.3 VILL villin-like 2.48 13q21.33 LMO7 LIM domain only 7 2.45 17q21.32 ITGA3 "integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)" 2.44 11p13 CD44 CD44 antigen (homing function and Indian blood group system) 2.44 6p21.2 CDKN1A "cyclin-dependent kinase inhibitor 1A (p21, Cip1)" 2.43 1q32 LAMB3 "laminin, beta 3" 2.42 18q21.3 SERPINB5 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 5" 2.42 22q12.2 LIF leukemia inhibitory factor (cholinergic differentiation factor) 2.42 19p13.1 CYP4F12 "cytochrome P450, family 4, subfamily F, polypeptide 12" 2.41 12p13 SCNN1A "sodium channel, nonvoltage-gated 1 alpha" 2.40 12 "Homo sapiens, clone IMAGE:4471726, mRNA" 2.38 3q28-q29 CLDN1 claudin 1 2.37 3q21.3 MGLL monoglyceride lipase 2.36 1 Homo sapiens (clone B3B3E13) Huntington's disease candidate region mRNA fragment. 2.34 6p21.3 DDR1 "discoidin domain receptor family, member 1" 2.31 1p33 PIK3R3 "phosphoinositide-3-kinase, regulatory subunit, polypeptide 3 (p55, gamma)" 2.31 6q22.1 CT2 carnitine transporter 2 2.28 4p16-p15 HBP17 heparin-binding growth factor binding protein 2.25 14q24 TGFB3 "transforming growth factor, beta 3" 2.25 8q13.2 RDH10 retinol dehydrogenase 10 (all-trans) 2.24 21q22.3 TFF3 trefoil factor 3 (intestinal) 2.24 1p35.3- PTPRU "protein tyrosine phosphatase, receptor type, U" p35.1 2.22 2q24-q31 TANK TRAF family member-associated NFKB activator 2.21 9q31 KLF4 Kruppel-like factor 4 (gut) 2.21 20q12 SDC4 "syndecan 4 (amphiglycan, ryudocan)" 2.21 13q31.2- STK24 "serine/threonine kinase 24 (STE20 homolog, yeast)" q32.3 2.21 2p24.3 VSNL1 visinin-like 1 2.20 15q26.1 IDH2 "isocitrate dehydrogenase 2 (NADP+), mitochondrial" 2.20 1p36.11 CLIC4 chloride intracellular channel 4 2.20 13q34 C13orf11 chromosome 13 open reading frame 11 2.18 6p21.1- PTK7 PTK7 protein tyrosine kinase 7 p12.2 2.18 16q12.2-q13 HERPUD1 "homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1" 2.18 12 Homo sapiens full length insert cDNA clone YW24E06 2.18 1q32 C4BPB "complement component 4 binding protein, beta" 2.17 Xq28 ZNF185 zinc finger protein 185 (LIM domain) 2.16 16q13 GPR56 G protein-coupled receptor 56 2.16 10q23.31 CARP cardiac ankyrin repeat protein 2.15 1q25-q31 LAMC2 "laminin, gamma 2" 2.13 5q31.2 KIAA0416 KIAA0416 protein 2.12 15q11 CYFIP1 cytoplasmic FMR1 interacting protein 1 2.11 10q23-q24 SCD stearoyl-CoA desaturase (delta-9-desaturase) 2.11 4q13.3 ShrmL Shroom-related protein 2.11 21q22.13 SIM2 single-minded homolog 2 (Drosophila) 2.10 2p25 DDEF2 development and differentiation enhancing factor 2 2.09 1p34 PTPRF "protein tyrosine phosphatase, receptor type, F" 2.08 10p12 NEBL nebulette 2.07 14q24.3 C14orf4 chromosome 14 open reading frame 4 2.06 4 "Homo sapiens cDNA FLJ37247 fis, clone BRAMY2006397." 2.05 11 "Homo sapiens cDNA FLJ34459 fis, clone HLUNG2002916, highly similar to SRC CORTACTIN." 2.05 7p14.1 FLJ22313 hypothetical protein FLJ22313 2.05 2cen-q13 INHBB "inhibin, beta B (activin AB beta polypeptide)" 2.05 1q31.3 FLJ10901 hypothetical protein FLJ10901 2.04 16q22.1 CBFB "core-binding factor, beta subunit" 2.04 6p21.1-12.2 TNFRSF21 "tumor necrosis factor receptor superfamily, member 21" 2.03 1q32.1 KIAA0663 KIAA0663 gene product 2.03 13q14.3 ITM2B integral membrane protein 2B 2.02 2q37.3 PER2 period homolog 2 (Drosophila) 2.02 2p21 CYP1B1 "cytochrome P450, family 1, subfamily B, polypeptide 1" 2.01 15q22.3-q23 NEO1 neogenin homolog 1 (chicken) 2.01 20q13.1 CEBPB "CCAAT/enhancer binding protein (C/EBP), beta" 2.01 13 "Human BRCA2 region, mRNA sequence CG011." 2.00 5 "Homo sapiens cDNA FLJ12815 fis, clone NT2RP2002546." 2.00 1p22 CTBS "chitobiase, di-N-acetyl-" Down regulated genes Ratio.13vs0 Map Gene Description 0.12 3 "Homo sapiens, H4 family, member A, clone MGC:29783 IMAGE:4647914, mRNA, complete cds" 0.22 6p22.2- HIST1H2AE "histone 1, H2ae" p21.1 0.23 12p12.3- MGST1 microsomal glutathione S-transferase 1 p12.1 0.25 7q32 MEST mesoderm specific transcript homolog (mouse) 0.25 1q21.2 HIST2H2AA "histone 2, H2aa" 0.26 6p22-p21.3 HIST1H2AM "histone 1, H2am" 0.26 8p22-p21.3 SLC7A2 "solute carrier family 7 (cationic amino acid transporter, y+ system), member 2" 0.26 6p21.3 HIST1H2AC "histone 1, H2ac" 0.28 1q22 IFI16 "interferon, gamma-inducible protein 16" 0.28 11q13 FAU Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived); ribosomal protein S30 0.31 17q21.3 NME1 "non-metastatic cells 1, protein (NM23A) expressed in" 0.31 11q14.1- CTSC cathepsin C q14.3 0.31 9q34.1 RPL35 ribosomal protein L35 0.32 3 ESTs 0.33 9q34.1 RPL35 ribosomal protein L35 0.33 6p21.31 RPS10 ribosomal protein S10 0.34 14q RPS29 ribosomal protein S29 0.36 4q21 CXCL6 chemokine (C-X-C motif) ligand 6 (granulocyte chemotactic protein 2) 0.36 17q12 PSMB3 "proteasome (prosome, macropain) subunit, beta type, 3" 0.36 4q21-q23 ADH1A "alcohol dehydrogenase 1A (class I), alpha polypeptide" 0.36 4 "Homo sapiens cDNA: FLJ21718 fis, clone COL10356." 0.38 2p25.2 RNF144 ring finger protein 144 0.39 6q12-q13 RIMS1 regulating synaptic membrane exocytosis 1 0.40 7q21.1 ABCB1 "ATP-binding cassette, sub-family B (MDR/TAP), member 1" 0.40 11q22-q23 HSPB2 heat shock 27kDa protein 2 0.40 19q13.3- NR1H2 "nuclear receptor subfamily 1, group H, member 2" 19q13.3 0.41 12pter-p12 CD4 CD4 antigen (p55) 0.41 9q34 RPL12 ribosomal protein L12 0.41 Xq13.1 RPS4X "ribosomal protein S4, X-linked" 0.41 Xp21.1 OTC ornithine carbamoyltransferase 0.42 11q23 ATP5L "ATP synthase, H+ transporting, mitochondrial F0 complex, subunit g" 0.42 12q24.2 COX6A1 cytochrome c oxidase subunit VIa polypeptide 1 0.42 12p13 REA repressor of estrogen receptor activity 0.42 17q21.3 NME2 "non-metastatic cells 2, protein (NM23B) expressed in" 0.42 19p13.3 GNG7 "guanine nucleotide binding protein (G protein), gamma 7" 0.43 5p13 SLC1A3 "solute carrier family 1 (glial high affinity glutamate transporter), member 3" 0.43 19p13.12- NDUFB7 "NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7, p13.11 18kDa" 0.43 16p12.1 MGC5178 hypothetical protein MGC5178 0.43 Incyte EST 0.44 9q31.1 LOC286367 hypothetical protein LOC286367 0.44 11q13 PPP1R14B "protein phosphatase 1, regulatory (inhibitor) subunit 14B" 0.44 12q24.12 HSU79274 protein predicted by clone 23733 0.44 CYP4X1 likely ortholog of rat cytochrome P450 4X1 0.44 6p21.3 HIST1H1D "histone 1, H1d" 0.44 4p16.3 ATP5I "ATP synthase, H+ transporting, mitochondrial F0 complex, subunit e" 0.44 7q11.23 FZD9 frizzled homolog 9 (Drosophila) 0.45 16 NETO2 neuropilin (NRP) and tolloid (TLL)-like 2 0.45 3q12.1 ESDN endothelial and smooth muscle cell-derived neuropilin-like protein 0.45 11q24 DDX25 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 25 0.45 19q13.2 SNRPD2 small nuclear ribonucleoprotein D2 polypeptide 16.5kDa 0.46 8q12 RPS20 ribosomal protein S20 0.46 11q24.1 HSPA8 heat shock 70kDa protein 8 0.46 14q32.33 C14orf2 chromosome 14 open reading frame 2 0.46 19p13 RPL18A ribosomal protein L18a 0.46 3q21-q25 CPA3 carboxypeptidase A3 (mast cell) 0.47 16p12.3 TCEB2 "transcription elongation factor B (SIII), polypeptide 2 (18kDa, elongin B)" 0.48 2p21 SPTBN1 "spectrin, beta, non-erythrocytic 1" 0.48 10q26.3 MGC30006 hypothetical protein MGC30006 0.48 1p22-p21 CNN3 "calponin 3, acidic" 0.48 5p13 RPL37 ribosomal protein L37 0.48 7q11.23 NCF1 "neutrophil cytosolic factor 1 (47kDa, chronic granulomatous disease, autosomal 1)" 0.48 7q21.1 ABCB1 "ATP-binding cassette, sub-family B (MDR/TAP), member 1" 0.48 2q36.1 TUBA1 "tubulin, alpha 1 (testis specific)" 0.48 1p35-p33 EBNA1BP2 EBNA1 binding protein 2 0.48 10p12 NRP1 neuropilin 1 0.48 12q13.13 GDF11 growth differentiation factor 11 0.48 17q23 CA4 carbonic anhydrase IV 0.48 6q14-q15 CNR1 cannabinoid receptor 1 (brain) 0.48 4q12 NMU neuromedin U 0.49 8q22 CBFA2T1 "core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related" 0.49 2 "Homo sapiens, clone IMAGE:5314816, mRNA" 0.49 1p36.1-p35 RPL11 ribosomal protein L11 a For all of the genes in this table, the p-value associated with the approximate z-test of the chromosome transfer clone expression ratio compared to the parental clone expression ratio was less than 0.0001 with the exception of the following genes: OTC: ornithine carbamoyltransferase (p=0.0001) C14orf2: chromosome 14 open reading frame 2 (p=0.0017) NCF1: "neutrophil cytosolic factor 1 (47kDa, chronic granulomatous disease, autosomal 1)" (p=0.0027)

Supplemental Data Table 5: Genes significantly altered in expression in DLD1+3 a

Upregulated genes Ratio.3vs0 Map Gene Description 14.50 5q11.1 ITGA1 "integrin, alpha 1" 13.33 17q21.2 KRT20 keratin 20 11.22 10q23.31 CARP cardiac ankyrin repeat protein 9.43 4p16.3- MSX1 msh homeo box homolog 1 (Drosophila) p16.1 5.93 14q11.2 GZMB "granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)" 5.71 3q12.1 ESDN endothelial and smooth muscle cell-derived neuropilin-like protein 5.55 3q21 MYLK "myosin, polypeptide kinase" 5.25 18q21.3 SERPINB2 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 4.98 1q21 S100A4 "S100 calcium binding protein A4 (calcium protein, calvasculin, metastasin, murine placental homolog)" 4.66 14q22.3 DACT1 "dapper homolog 1, antagonist of beta-catenin (xenopus)" 4.53 15q23 TSPAN-3 tetraspan 3 4.43 3p22-p21.3 CCK cholecystokinin 4.21 3q25.1- SMARCA3 "SWI/SNF related, matrix associated, actin dependent regulator of q26.1 chromatin, subfamily a, member 3" 4.18 3q13 PVRL3 poliovirus receptor-related 3 4.03 13q13- DCAMKL1 doublecortin and CaM kinase-like 1 q14.1 3.87 6q14-q21 NT5E "5'-nucleotidase, ecto (CD73)" 3.63 16q13 MT1F metallothionein 1F (functional) 3.60 16q13 MT1L metallothionein 1L 3.60 15q23 TSPAN-3 tetraspan 3 3.44 8p22-p21.3 DLC1 deleted in liver cancer 1 3.40 7p21.3 LOC221810 hypothetical protein LOC221810 3.38 10p12 NRP1 neuropilin 1 3.38 3p26 BHLHB2 "basic helix-loop-helix domain containing, class B, 2" 3.37 17q12- IGFBP4 insulin-like growth factor binding protein 4 q21.1 3.36 12q23 ELK3 "ELK3, ETS-domain protein (SRF accessory protein 2)" 3.23 3p21-p14 PTPRG "protein tyrosine phosphatase, receptor type, G" 3.19 6q24-q25 AKAP12 A kinase (PRKA) anchor protein (gravin) 12 3.17 3p21 SCN5A "sodium channel, voltage-gated, type V, alpha polypeptide (long (electrocardiographic) QT syndrome 3)" 3.15 1p31-p22 CYR61 "cysteine-rich, angiogenic inducer, 61" 3.10 3q23 RBP1 "retinol binding protein 1, cellular" 3.08 17q24.3 SLC16A6 "solute carrier family 16 (monocarboxylic acid transporters), member 6" 2.96 10q25 DUSP5 dual specificity phosphatase 5 2.94 7q21.3-q22 SERPINE1 "serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1" 2.94 Xp22.2- GRPR gastrin-releasing peptide receptor p22.13 2.91 16q13 MT1E metallothionein 1E (functional) 2.90 11p13 CD44 CD44 antigen (homing function and Indian blood group system) 2.89 11q23.2 IGSF4 "immunoglobulin superfamily, member 4" 2.82 7q33 CALD1 caldesmon 1 2.80 14q11.2 GZMB "granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)" 2.73 10q26.11 KIAA0417 KIAA0417 gene product 2.70 12q24.11 FLJ33957 hypothetical protein FLJ33957 2.65 3q26.2- CLDN11 claudin 11 (oligodendrocyte ) q26.3 2.64 11p13 PAX6 "paired box gene 6 (aniridia, keratitis)" 2.63 12q24.11 ARK5 KIAA0537 gene product 2.62 12q13.1- DDIT3 DNA-damage-inducible transcript 3 q13.2 2.50 3q26.2 SERPINI1 "serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 1" 2.47 15q22.3- NEO1 neogenin homolog 1 (chicken) q23 2.46 11p14.3 PRMT3 protein arginine N-methyltransferase 3(hnRNP methyltransferase S. cerevisiae)-like 3 2.45 1 "Homo sapiens cDNA FLJ11245 fis, clone PLACE1008629." 2.44 3p14.3- ADAMTS9 "a disintegrin-like and metalloprotease (reprolysin type) with p14.2 thrombospondin type 1 motif, 9" 2.43 5p15.2 SEMA5A "sema domain, seven thrombospondin repeats (type 1 and type 1- like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A" 2.42 15q15 THBS1 thrombospondin 1 2.40 15q22.31 CORO2B "coronin, actin binding protein, 2B" 2.38 10p14 DKFZP761F241 hypothetical protein DKFZp761F241 2.38 3q21-q23 MRPL3 mitochondrial ribosomal protein L3 2.37 16q13 MT1B metallothionein 1B (functional) 2.33 3q26 SKIL SKI-like 2.32 11q13.2 PDE2A "phosphodiesterase 2A, cGMP-stimulated" 2.30 5q32 ATOX1 ATX1 antioxidant protein 1 homolog (yeast) 2.27 14q24.3 NPC2 "Niemann-Pick disease, type C2" 2.23 11p15.1 SAA1 serum amyloid A1 2.22 11q22-q23 TRIM29 tripartite motif-containing 29 2.18 3q27-q28 SIAT1 " 1 (beta-galactoside alpha-2,6-sialyltransferase)" 2.17 3q23-q24 CLSTN2 calsyntenin 2 2.16 8q12 PLAG1 pleiomorphic adenoma gene 1 2.15 6q21 FOXO3A forkhead box O3A 2.15 9q12-q21.2 ANXA1 annexin A1 2.15 12q22 BTG1 "B-cell translocation gene 1, anti-proliferative" 2.14 2q31.1 FLJ23462 duodenal cytochrome b 2.13 5 "Homo sapiens cDNA FLJ12815 fis, clone NT2RP2002546." 2.12 15q22.31 CORO2B "coronin, actin binding protein, 2B" 2.11 15q26.1 FURIN furin (paired basic amino acid cleaving ) 2.11 20q12- TNNC2 "troponin C2, fast" q13.11 2.09 1p22-p21 F3 "coagulation factor III (thromboplastin, )" 2.06 6p21.2 CDKN1A "cyclin-dependent kinase inhibitor 1A (p21, Cip1)" 2.06 10q22 COL13A1 "collagen, type XIII, alpha 1" 2.06 5q12.1- SNK serum-inducible kinase q13.2 2.02 18q21.3 SERPINB8 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 8" 2.01 1cen-qter HSPA6 heat shock 70kDa protein 6 (HSP70B') 2.01 6p22.3 DTNBP1 dystrobrevin binding protein 1 2.00 3q21.2 KIAA1237 KIAA1237 protein Down regulated genes Ratio.3vs0 Map Gene Description 0.13 1p36.3 HKR3 GLI-Kruppel family member HKR3 0.16 7q31.2 CFTR "cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)" 0.22 4q12-q13 CXCL5 chemokine (C-X-C motif) ligand 5 0.23 1 KIAA0485 KIAA0485 protein 0.26 10q24.2- ADD3 adducin 3 (gamma) q24.3 0.29 14q12-q13 FOXA1 forkhead box A1 0.29 13q22 SCEL sciellin 0.30 9p24 SLC1A1 "solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1" 0.32 4q21 CXCL6 chemokine (C-X-C motif) ligand 6 (granulocyte chemotactic protein 2) 0.33 7p21.3 AGR2 anterior gradient 2 homolog (Xenepus laevis) 0.33 17q21.32 ITGB3 "integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)" 0.33 1q32.2 ELF3 "E74-like factor 3 (ets domain transcription factor, epithelial- specific )" 0.33 11p15 MUC5AC "mucin 5, subtypes A and C, tracheobronchial/gastric" 0.34 11q24-q25 RICS Rho GTPase-activating protein 0.35 Yq11.221 EIF1AY "eukaryotic translation initiation factor 1A, Y chromosome" 0.35 2q24.3 DPP4 "dipeptidylpeptidase 4 (CD26, adenosine deaminase complexing protein 2)" 0.35 4q21.1 EREG epiregulin 0.35 12p13 SCNN1A "sodium channel, nonvoltage-gated 1 alpha" 0.36 4p15.1 UGDH UDP-glucose dehydrogenase 0.37 1q21-q22 SELENBP1 selenium binding protein 1 0.37 1p32-p31 TACSTD2 tumor-associated calcium signal transducer 2 0.37 19q13.3- KLK10 kallikrein 10 q13.4 0.38 19q13.11 FXYD3 FXYD domain containing ion transport regulator 3 0.39 8q24.1 SQLE squalene epoxidase 0.39 4q31.23 TRIM2 tripartite motif-containing 2 0.39 "inositol 1,4,5-triphosphate receptor, type 2" 0.40 2q35-q36 VIL1 villin 1 0.40 12 PAMCI peptidylglycine alpha-amidating monooxygenase COOH-terminal interactor 0.40 20q11 ID1 "inhibitor of DNA binding 1, dominant negative helix-loop-helix protein" 0.40 9q34.1 STOM stomatin 0.41 10q25 ABLIM1 actin binding LIM protein 1 0.41 1p35.3- PTPRU "protein tyrosine phosphatase, receptor type, U" p35.1 0.41 16p13.3 NME4 "non-metastatic cells 4, protein expressed in" 0.42 15q23-q25 ETFA "electron-transfer-flavoprotein, alpha polypeptide (glutaric aciduria II)" 0.42 17p13 CLDN7 claudin 7 0.42 4q11-q12 KIT v- Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog 0.42 13q14 TSC22 transforming growth factor beta-stimulated protein TSC-22 0.42 "trefoil factor 1 (breast cancer, estrogen-inducible sequence expressed in)" 0.42 6q21 AIM1 absent in 1 0.43 9p11.2 PRSS3 "protease, serine, 3 (mesotrypsin)" 0.43 Xp22.32 SLC25A6 "solute carrier family 25 (mitochondrial carrier; adenine nucleotide and Yp translocator), member 6" 0.43 20q12- HNF4A "hepatocyte nuclear factor 4, alpha" q13.1 0.44 4p16 S100P S100 calcium binding protein P 0.44 13q12 PRDX2 peroxiredoxin 2 0.44 9q34.1 CRAT carnitine acetyltransferase 0.44 Xp22.32 KAL1 Kallmann syndrome 1 sequence 0.44 5q23.3 SLC12A2 "solute carrier family 12 (sodium/potassium/chloride transporters), member 2" 0.45 1p36.1-p35 EPHB2 EphB2 0.46 16p11.2 CORO1A "coronin, actin binding protein, 1A" 0.46 14q21-q22 LGALS3 "lectin, galactoside-binding, soluble, 3 (galectin 3)" 0.46 6q22-q23 MYB v-myb myeloblastosis viral oncogene homolog (avian) 0.46 15q21-q22 ANXA2 annexin A2 0.47 11q23 CD3E "CD3E antigen, epsilon polypeptide (TiT3 complex)" 0.47 10p15-p14 AKR1C1 "aldo-keto reductase family 1, member C1 (dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase)" 0.48 6q22 MAN1A1 "mannosidase, alpha, class 1A, member 1" 0.48 T cell receptor beta 0.48 17p11.2 ALDH3A2 "aldehyde dehydrogenase 3 family, member A2" 0.48 "mannosidase, alpha, class 1A, member 1" 0.48 15q26.1 IDH2 "isocitrate dehydrogenase 2 (NADP+), mitochondrial" 0.48 12p11.22 FLJ10462 hypothetical protein FLJ10462 0.49 4q13-q21 AREG amphiregulin (schwannoma-derived growth factor) 0.49 1q32 HF1 H factor 1 (complement) 0.49 16q24.3 RPL13 ribosomal protein L13 0.49 7q21 PEG10 paternally expressed 10 0.49 6q13-15 SH3BGRL2 SH3 domain binding glutamic acid-rich protein like 2 0.49 5 "Homo sapiens cDNA: FLJ21409 fis, clone COL03924." 0.50 4q13-q21 AREG amphiregulin (schwannoma-derived growth factor) a For all of the genes in this table, the p-value associated with the approximate z-test of the chromosome transfer clone expression ratio compared to the parental clone expression ratio was less than 0.0001. Supplemental Data Table 6: Genes significantly altered in expression in hTERT-HME+3 a

Upregulated genes Ratio.3vs0 Map Gene Description 5.21 3p21-p22 PFKFB4 "6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4" 4.94 1p31.1 C1orf29 chromosome 1 open reading frame 29 4.28 Xq27.1-q27.2 CDR1 "cerebellar degeneration-related protein 1, 34kDa" 4.04 5q31.1 EGR1 early growth response 1 3.97 3p11-q11.2 PROS1 protein S (alpha) 3.45 Incyte EST 3.31 7q11.21 AUTS2 autism susceptibility candidate 2 3.29 1q44-qter ZNF238 zinc finger protein 238 3.18 8q22-q23 SDC2 "syndecan 2 (heparan sulfate proteoglycan 1, cell surface- associated, fibroglycan)" 3.17 11q12 FEN1 flap structure-specific endonuclease 1 3.17 3q21 MCM2 "MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)" 3.06 20q12 SLPI secretory leukocyte protease inhibitor (antileukoproteinase) 3.01 heat shock 70kD protein 1 3.00 Incyte EST 2.92 3q13.2 LOC152185 hypothetical protein AY099107 2.87 14q24.3 FOS v-fos FBJ murine osteosarcoma viral oncogene homolog 2.87 1p32 CDKN2C "cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)" 2.87 1p31.1 IFI44 interferon-induced protein 44 2.84 1q42-q43 EXO1 exonuclease 1 2.84 10q21.1 EGR2 "early growth response 2 (Krox-20 homolog, Drosophila)" 2.83 9q13 BTEB1 basic transcription element binding protein 1 2.79 5p13.3 FLJ14054 hypothetical protein FLJ14054 2.75 14q32.1 FBLN5 fibulin 5 2.69 10q21.1 CDC2 "cell division cycle 2, G1 to S and G2 to M" 2.68 19p13.2 ZNF177 zinc finger protein 177 2.61 6p22.2-p22.3 ALDH5A1 "aldehyde dehydrogenase 5 family, member A1 (succinate- semialdehyde dehydrogenase)" 2.61 5p15.2-p13.1 UNG2 uracil-DNA glycosylase 2 2.57 1q21-q22 FY Duffy blood group 2.54 8q13.1 SULF1 sulfatase 1 2.47 5q11.2-q13.2 DHFR dihydrofolate reductase 2.43 20pter-p12 PCNA proliferating cell nuclear antigen 2.39 7q33-q34 PTN "pleiotrophin (heparin binding growth factor 8, neurite growth- promoting factor 1)" 2.39 12q13 IGFBP6 insulin-like growth factor binding protein 6 2.35 9p13-p12 DNAJA1 "DnaJ (Hsp40) homolog, subfamily A, member 1" 2.34 6p21.3 HIST1H2BG "histone 1, H2bg" 2.32 3q26.1 SMC4L1 SMC4 structural maintenance of 4-like 1 (yeast) 2.31 6p21.3 HIST1H1D "histone 1, H1d" 2.31 5p14-p13 NPR3 natriuretic peptide receptor C/ C (atrionatriuretic peptide receptor C) 2.28 12q23.1 NR1H4 "nuclear receptor subfamily 1, group H, member 4" 2.28 Xp22.12 PDK3 "pyruvate dehydrogenase kinase, isoenzyme 3" 2.28 Incyte EST 2.27 3p22-p21.3 PLCD1 "phospholipase C, delta 1" 2.27 6 "Homo sapiens, clone IMAGE:5588650, mRNA" 2.24 11q23 DRD2 dopamine receptor D2 2.24 10q21-q22 ZWINT ZW10 interactor 2.24 2 ESTs 2.24 3q23-q24 PLOD2 "procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2" 2.23 1q21-q23 HIST2H2BE "histone 2, H2be" 2.23 11p15.5 TNNI2 "troponin I, skeletal, fast" 2.22 17q23.2-q25.3 TK1 "thymidine kinase 1, soluble" 2.22 8q12-q13 MCM4 MCM4 minichromosome maintenance deficient 4 (S. cerevisiae) 2.21 3q26.1-q26.2 ECT2 epithelial cell transforming sequence 2 oncogene 2.20 3p26 BHLHB2 "basic helix-loop-helix domain containing, class B, 2" 2.18 7q35 LOC154761 hypothetical protein LOC154761 2.17 1q21-q23 HIST2H2BE "histone 2, H2be" 2.17 3q21 MYLK "myosin, light polypeptide kinase" 2.16 11q25 KIAA0056 KIAA0056 protein 2.15 3q23-q24 TAZ transcriptional co-activator with PDZ-binding motif (TAZ) 2.15 13q22.1 SPRY2 sprouty homolog 2 (Drosophila) 2.14 X "Phosphoglycerate kinase {alternatively spliced} [human, phosphoglycerate kinase deficient patient with episodes of muscl, mRNA Partial Mutant, 307 nt]" 2.11 17p13.1 STK12 serine/threonine kinase 12 2.11 5q11.2-q13.2 DHFR dihydrofolate reductase 2.10 14q24-q31 PGF "placental growth factor, vascular endothelial growth factor- related protein" 2.10 3 Homo sapiens clone 24627 mRNA sequence 2.08 20q11.2 RBL1 retinoblastoma-like 1 (p107) 2.08 6p22.2-p21.1 HIST1H2AE "histone 1, H2ae" 2.08 3p24.1-p21.2 CELSR3 "cadherin, EGF LAG seven-pass G-type receptor 3 (flamingo homolog, Drosophila)" 2.08 17q21-q22 TOP2A topoisomerase (DNA) II alpha 170kDa 2.06 Xp22.1-p21.3 POLA "polymerase (DNA directed), alpha" 2.06 5q31 PCDHA9 protocadherin alpha 9 2.06 3p22 TGFBR2 "transforming growth factor, beta receptor II (70/80kDa)" 2.06 10q25-qter MKI67 antigen identified by monoclonal antibody Ki-67 2.05 12p13.2-p13.1 PIR51 RAD51-interacting protein 2.05 2q23-q24 PLA2R1 "phospholipase A2 receptor 1, 180kDa" 2.04 10p14-p15 PFKFB3 "6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3" 2.04 3p25-p24 SLC6A6 "solute carrier family 6 (neurotransmitter transporter, taurine), member 6" 2.04 3q27 RFC4 "replication factor C (activator 1) 4, 37kDa" 2.03 3p22-p21.3 XYLB xylulokinase homolog (H. influenzae) 2.03 1p31.1 PTGFR prostaglandin F receptor (FP) 2.03 8q24.2 KHDRBS3 "KH domain containing, RNA binding, signal transduction associated 3" 2.03 1p36.3-p36.2 CORT cortistatin 2.02 3q25.1-q26.1 SMARCA3 "SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3" 2.02 3p12.3 GBE1 "glucan (1,4-alpha-), branching enzyme 1 (glycogen branching enzyme, Andersen disease, glycogen storage disease type IV)" 2.02 6p12 MCM3 MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) 2.01 3p21.3 SLC26A6 "solute carrier family 26, member 6" 2.01 3p21.31 STAB1 stabilin 1 2.01 8q22.1 CCNE2 cyclin E2 2.01 11q12.3 POLA2 "polymerase (DNA-directed), alpha (70kD)" 2.01 11q21-q22 GUCY1A2 "guanylate cyclase 1, soluble, alpha 2" 2.00 1q23.1 RGS4 regulator of G-protein signalling 4 2.00 1q42.1 LBR lamin B receptor Down regulated genes Ratio.3vs0 Map Gene Description 0.17 5q35.2 STC2 stanniocalcin 2 0.20 2q14 IL1A "interleukin 1, alpha" 0.27 Xq21.33-q22.2 ALEX2 armadillo repeat protein ALEX2 0.30 3q28-q29 CLDN1 claudin 1 0.31 20p12.2-p13 C20orf97 chromosome 20 open reading frame 97 0.31 12q13.1-q13.2 DDIT3 DNA-damage-inducible transcript 3 0.31 11q22.3 MMP1 matrix metalloproteinase 1 (interstitial collagenase) 0.32 11q23.2 IGSF4 "immunoglobulin superfamily, member 4" 0.32 4q28-q32 SLC7A11 "solute carrier family 7, (cationic amino acid transporter, y+ system) member 11" 0.32 7q21.3 ASNS asparagine synthetase 0.33 18q21.3 SERPINB2 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 0.33 6q12 ME1 "malic enzyme 1, NADP(+)-dependent, cytosolic" 0.34 9q21.2 PSA phosphoserine aminotransferase 0.35 1q22-q23 RXRG "retinoid X receptor, gamma" 0.38 7 UP 0.38 12q SOCS2 suppressor of cytokine signaling 2 0.38 2q14 IL1B "interleukin 1, beta" 0.38 4q13-q22 ANXA3 annexin A3 0.39 16q24.3 SLC7A5 "solute carrier family 7 (cationic amino acid transporter, y+ system), member 5" 0.40 14q11.2 PCK2 phosphoenolpyruvate carboxykinase 2 (mitochondrial) 0.41 5q11-q12 GZMK "granzyme K (serine protease, granzyme 3; tryptase II)" 0.42 2q23.3 ARHE "ras homolog gene family, member E" 0.43 17q12-q21 KRTHA1 "keratin, hair, acidic, 1" 0.43 4q26-q27 FGF2 fibroblast growth factor 2 (basic) 0.44 11q22 BIRC3 baculoviral IAP repeat-containing 3 0.44 2p15-p13 SLC1A4 "solute carrier family 1 (glutamate/neutral amino acid transporter), member 4" 0.44 19q13.1 SPINT2 "serine protease inhibitor, Kunitz type, 2" 0.44 15q13-q14 SGNE1 "secretory granule, neuroendocrine protein 1 (7B2 protein)" 0.45 11p15.1 HTATIP2 "HIV-1 Tat interactive protein 2, 30kDa" 0.45 8p22-p21.3 SLC7A2 "solute carrier family 7 (cationic amino acid transporter, y+ system), member 2" 0.45 9q33 TNC tenascin C (hexabrachion) 0.45 15q22.32 FLJ11196 acheron 0.45 1q44 ELYS ELYS transcription factor-like protein TMBS62 0.45 transgelin 0.46 6q25.3 SOD2 "superoxide dismutase 2, mitochondrial" 0.46 11q13 SLC3A2 "solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2" 0.47 21q22.2 ETS2 v-ets erythroblastosis virus E26 oncogene homolog 2 (avian) 0.47 1p35.3 MGC16491 hypothetical protein MGC16491 0.47 2p12 MTHFD2 "methylene tetrahydrofolate dehydrogenase (NAD+ dependent), methenyltetrahydrofolate cyclohydrolase" 0.47 8q21 RIPK2 receptor-interacting serine-threonine kinase 2 0.48 18q11.2 LAMA3 "laminin, alpha 3" 0.48 3p24.1 NR1D2 "nuclear receptor subfamily 1, group D, member 2" 0.49 19p13.1 PRKACA "protein kinase, cAMP-dependent, catalytic, alpha" 0.49 12 XPOT "exportin, tRNA (nuclear export receptor for tRNAs)" 0.49 18q12.1-q12.2 DSG3 desmoglein 3 (pemphigus vulgaris antigen) 0.49 7p15 GARS glycyl-tRNA synthetase 0.49 6q21 FYN "FYN oncogene related to SRC, FGR, YES" 0.49 7q22-q31 IFRD1 interferon-related developmental regulator 1 0.50 1q41 TGFB2 "transforming growth factor, beta 2" a For all of the genes in this table, the p-value associated with the approximate z-test of the chromosome transfer clone expression ratio compared to the parental clone expression ratio was less than 0.0001 with the exception of the gene ELYS (transcription factor-like protein TMBS62, p=0.0003).