Supplemental Table 1: Expression of the probe set IDs that characterize MUC1-CD- induced tumorigenesis and designation of a 93-gene subset prognostic in breast and lung cancers. Ratio = in vivo / in vitro. PS = 93-gene prognostic subset. Probe Set ID Gene Symbol Ratio PS Description 1383355_at ABCA1 0.429 ATP-binding cassette, sub-family A (ABC1), member 1 1379402_at ABCC4 0.473 ATP-binding cassette, sub-family C (CFTR/MRP), member 4 1382137_at ABHD3 0.075 abhydrolase domain containing 3 1372462_at ACAT2 0.155 * acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl Coenzyme A thiolase) 1367854_at ACLY 0.47 ATP citrate lyase 1370939_at ACSL1 0.201 acyl-CoA synthetase long-chain family member 1 1368177_at ACSL3 0.275 acyl-CoA synthetase long-chain family member 3 1369928_at ACTA1 1230.193 actin, alpha 1, skeletal muscle 1398836_s_at ACTB 2.378 * actin, beta 1389785_at ACY3 19.369 aspartoacylase (aminocyclase) 3 1370071_at ADA 2.259 * adenosine deaminase 1368021_at ADH1C 0.274 alcohol dehydrogenase 1C (class I), gamma polypeptide 1369711_at AGTR2 4.292 angiotensin II receptor, type 2 1398288_at AGTR2 7.511 angiotensin II receptor, type 2 1368558_s_at AIF1 1036.083 * allograft inflammatory factor 1 1388924_at ANGPTL4 2.191 angiopoietin-like 4 1386344_at ANKH 2.936 * ankylosis, progressive homolog (mouse) 1393439_a_at ANKH 3.117 * ankylosis, progressive homolog (mouse) 1369249_at ANKH 3.194 * ankylosis, progressive homolog (mouse) 1385709_x_at ANKH 3.615 * ankylosis, progressive homolog (mouse) 1367664_at ANKRD1 0.096 ankyrin repeat domain 1 (cardiac muscle) 1367665_at ANKRD1 0.241 ankyrin repeat domain 1 (cardiac muscle) 1395552_s_at ANKRD13C 0.483 ankyrin repeat domain 13C 1367974_at ANXA3 0.338 annexin A3 1368587_at APOC1 62.15 * apolipoprotein C-I 1370862_at APOE 113.465 apolipoprotein E 1369625_at AQP1 61.367 aquaporin 1 (Colton blood group) 1368266_at ARG1 4.735 arginase, liver 1393345_at ASPH 0.374 aspartate beta-hydroxylase 1393581_at ASPM 0.407 * asp (abnormal spindle) homolog, microcephaly associated (Drosophila) 1380726_at ASPN 18.803 * asporin 1381504_at ASPN 22.117 * asporin 1367945_at ATOX1 2.068 ATX1 antioxidant protein 1 homolog (yeast) 1387184_at AXIN2 12.576 axin 2 (conductin, axil) BAIAP1 1381871_at PREDICTED 0.408 BAI1-associated protein 1 (predicted) 1375941_at BAIAP2L1 6.253 * BAI1-associated protein 2-like 1 1370823_at BAMBI 0.222 BMP and activin membrane-bound inhibitor homolog (Xenopus laevis) 1389095_at BOC 0.377 Boc homolog (mouse) 1371833_at BRI3 2.064 brain protein I3 1383926_at BUB1B 0.428 * BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast) 1392938_s_at C11ORF17 0.491 chromosome 11 open reading frame 17 1376645_at C13ORF33 5.143 chromosome 13 open reading frame 33 1392547_at C15ORF48 4.758 chromosome 15 open reading frame 48 1376652_at C1QA 22.574 * complement component 1, q subcomponent, A chain 1372202_at C2ORF49 0.497 chromosome 2 open reading frame 49 1398387_at C4ORF18 13.167 chromosome 4 open reading frame 18 1371412_a_at C5ORF13 31.172 * chromosome 5 open reading frame 13 1380872_at C6ORF168 0.498 chromosome 6 open reading frame 168 1393452_at CA9 0.255 * carbonic anhydrase IX 1388460_at CAPG 2.226 capping protein (actin filament), gelsolin-like caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, 1369186_at CASP1 3.525 * convertase) 1387818_at CASP4 2.542 caspase 4, apoptosis-related cysteine peptidase 1367995_at CAT 0.476 catalase 1374280_at CBLN2 2.379 cerebellin 2 precursor 1372493_at CCDC23 2.296 coiled-coil domain containing 23 1389490_at CD248 175.045 CD248 molecule, endosialin 1367929_at CD59 5.888 CD59 molecule, complement regulatory protein 1367679_at CD74 84.03 * CD74 molecule, major histocompatibility complex, class II invariant chain 1394113_at CDC20 9.104 * cell division cycle 20 homolog (S. cerevisiae) 1368642_at CDH2 0.448 cadherin 2, type 1, N-cadherin (neuronal) 1368642_at CDH2 0.448 cadherin 2, type 1, N-cadherin (neuronal) 1368623_at CEACAM9 23.097 CEA-related cell adhesion molecule 9 1389542_at CENPE 0.406 * centromere protein E, 312kDa 1382613_at CEP152 0.341 centrosomal protein 152kDa Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal 1367602_at CITED2 0.319 domain, 2 Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal 1367601_at CITED2 0.406 domain, 2 1370719_a_at CLCC1 0.459 chloride channel CLIC-like 1 1388939_at COL15A1 6.409 * collagen, type XV, alpha 1 1379345_at COL15A1 8.411 * collagen, type XV, alpha 1 1388143_at COL18A1 2.882 * collagen, type XVIII, alpha 1 collagen, type III, alpha 1 (Ehlers-Danlos syndrome type IV, autosomal 1370959_at COL3A1 2.856 * dominant) 1368347_at COL5A3 93.714 * collagen, type V, alpha 3 1371349_at COL6A1 377.152 * collagen, type VI, alpha 1 1371369_at COL6A2 741.288 collagen, type VI, alpha 2 1389966_at COL6A3 48.366 collagen, type VI, alpha 3 1368418_a_at CP 9.699 * ceruloplasmin (ferroxidase) 1368419_at CP 10.325 * ceruloplasmin (ferroxidase) 1386921_at CPE 2.567 * carboxypeptidase E 1367604_at CRIP2 3.915 cysteine-rich protein 2 1398286_at CSAD 2.094 cysteine sulfinic acid decarboxylase 1370169_at CSDE1 2.105 cold shock domain containing E1, RNA-binding 1370855_at CST3 2.693 * cystatin C (amyloid angiopathy and cerebral hemorrhage) 1367838_at CTH 0.085 cystathionase (cystathionine gamma-lyase) catenin (cadherin-associated protein), delta 2 (neural plakophilin-related 1383575_at CTNND2 0.225 * arm-repeat protein) 1397808_at CTSC 2.245 * cathepsin C 1368280_at CTSC 5.157 * cathepsin C 1386899_at CTSH 3.191 * cathepsin H 1387005_at CTSS 10.002 * cathepsin S 1367979_s_at CYP51A1 0.342 cytochrome P450, family 51, subfamily A, polypeptide 1 1370956_at DCN 18.931 * decorin 1387111_at DDAH1 0.092 dimethylarginine dimethylaminohydrolase 1 1372012_at DHCR24 0.415 24-dehydrocholesterol reductase 1368189_at DHCR7 0.163 * 7-dehydrocholesterol reductase 1373407_at DIP 3.857 death-inducing-protein 1372658_at DMN 0.288 desmuslin 1387905_at DNAJC12 0.458 * DnaJ (Hsp40) homolog, subfamily C, member 12 1387905_at DNAJC12 0.458 * DnaJ (Hsp40) homolog, subfamily C, member 12 1374585_at ECHDC1 0.47 * enoyl Coenzyme A hydratase domain containing 1 1383747_at ECT2 0.485 * epithelial cell transforming sequence 2 oncogene 1388600_at EFHC1 0.371 EF-hand domain (C-terminal) containing 1 1398063_x_at EG209324 310.182 predicted gene, EG209324 1368321_at EGR1 4.258 early growth response 1 1387306_a_at EGR2 6.265 early growth response 2 (Krox-20 homolog, Drosophila) 1374224_at EIF2AK4 0.472 eukaryotic translation initiation factor 2 alpha kinase 4 ELOVL family member 6, elongation of long chain fatty acids (FEN1/Elo2, 1394401_at ELOVL6 0.278 SUR4/Elo3-like, yeast) ELOVL family member 6, elongation of long chain fatty acids (FEN1/Elo2, 1388108_at ELOVL6 0.401 SUR4/Elo3-like, yeast) 1397449_at ENAH 0.393 enabled homolog (Drosophila) 1370047_at ENPP1 4.026 * ectonucleotide pyrophosphatase/phosphodiesterase 1 1367905_at ENPP3 3.054 ectonucleotide pyrophosphatase/phosphodiesterase 3 1392607_at EPB41 0.245 erythrocyte membrane protein band 4.1 (elliptocytosis 1, RH-linked) 1388889_at ERMP1 0.236 endoplasmic reticulum metallopeptidase 1 1368078_at ESM1 0.416 endothelial cell-specific molecule 1 1369182_at F3 2.109 * coagulation factor III (thromboplastin, tissue factor) 1374320_at F5 4.42 coagulation factor V (proaccelerin, labile factor) 1367857_at FADS1 0.374 * fatty acid desaturase 1 1376177_at FAM117A 2.936 family with sequence similarity 117, member A 1376831_at FAM64A 0.203 * family with sequence similarity 64, member A 1367708_a_at FASN 0.352 fatty acid synthase 1368829_at FBN1 6.52 * fibrillin 1 1367839_at FDFT1 0.451 farnesyl-diphosphate farnesyltransferase 1 1367667_at FDPS 0.229 * farnesyl diphosphate synthase 1368114_at FGF13 17.214 fibroblast growth factor 13 1372107_at FHL1 0.463 * four and a half LIM domains 1 1373175_at FLJ22662 113.837 hypothetical protein FLJ22662 1375043_at FOS 19.346 * v-fos FBJ murine osteosarcoma viral oncogene homolog 1368947_at GADD45A 2.889 growth arrest and DNA-damage-inducible, alpha 1368332_at GBP2 5.709 * guanylate nucleotide binding protein 2 guanine nucleotide binding protein (G protein), alpha inhibiting activity 1387505_at GNAI1 0.479 polypeptide 1 1387039_at GPC1 2.091 * glypican 1 1368618_at GRB14 0.106 growth factor receptor-bound protein 14 1369113_at GREM1 0.379 gremlin 1, cysteine knot superfamily, homolog (Xenopus laevis) 1370952_at GSTM1 0.399 glutathione S-transferase M1 1370813_at GSTM3 0.355 * glutathione S-transferase M3 (brain) 1367553_x_at HBB 252.236 hemoglobin, beta 1393096_at HCG 21078 0.365 hCG21078 1369204_at HCK 12.989 * hemopoietic cell kinase 1387036_at HES1 2.48 hairy and enhancer of split 1, (Drosophila) 1381428_a_at HFE 3.23 hemochromatosis 1390021_at HIST1H2BG 3.275 histone cluster 1, H2bg 1371332_at HIST1H3J 2.763 histone cluster 1, H3j 1371332_at HIST1H3J 2.763 histone cluster 1, H3j 1369728_at HIST1H4I 4.772 histone cluster 1, H4i 1369728_at HIST1H4I 4.772 histone cluster 1, H4i 1369728_at HIST1H4I 4.772 histone cluster 1, H4i 1369728_at HIST1H4I 4.772 histone cluster 1, H4i 1370383_s_at HLA-DRB1 17.34 * major histocompatibility complex, class II, DR beta 1 1388164_at HLA-E 5.56 * major histocompatibility complex, class I, E 1388213_a_at HLA-E 11.664 * major histocompatibility complex, class I, E 1393629_at HLX 0.378 H2.0-like homeobox 1367932_at HMGCS1 0.363 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble) 1371989_at HMGN3 0.489 high mobility group nucleosomal binding domain 3 1370202_at HRASLS3 6.665 HRAS-like