Supplementary Table 1c: Additional genes differentially expressed between MMTV-PyMT mouse mammary tumors and normal mouse mammary tissue identified by olionucleotide (Affymetrix) microarray.

I/LnJ NZB/B MOLF/ LP/J Affymetrix Chromo FVB/N Accession Unigene Gene Description F1 1NJ F1 Ei F1 F1 ID some J Ratio Ratio Ratio Ratio Ratio 94628_r_at AF039064 7 Mm.8025 Abpa androgen binding , alpha 230.72 194.01 71.01 13.00 87.43

160647_at AF079834 Mm.20289 Car6 carbonic anhydrase 7 123.64 61.82 21.86 17.15 73.52

102931_at V00856 11 Mm.3992 Wap whey acidic protein 71.01 55.72 45.25 55.72 100.43

103465_f_at U60438 7 Mm.200941 Saa2 serum amyloid A 3 36.76 42.22 40.79 163.14 115.36

99952_at X93035 1 Mm.4376 Chi3l1 chitinase 3-like 2 22.63 22.63 23.43 12.55 18.38

103905_at AI314958 Mm.21397 2310047E01Rik RIKEN cDNA 2310047E01 gene 13.45 12.55 15.45 14.42 13.93

96518_at AU017197 11 Mm.203700 AU017197 expressed sequence AU017198 13.00 17.75 19.03 21.11 19.03

102338_at AF031147 Mm.10812 Pde9a phosphodiesterase 9A 12.55 19.03 32.00 28.84 16.00

102801_at L24430 3 Mm.14096 AI461847 expressed sequence AI461848 11.71 11.31 9.85 3.48 7.21 S100 calcium binding protein A8 103448_at M83218 3 Mm.21567 S100a8 10.93 3.86 9.85 8.28 4.44 (calgranulin A) fatty acid-Coenzyme A ligase, long chain 104017_at AB033887 Mm.143689 Facl4 10.56 5.28 2.64 3.86 3.86 5 92994_at M87863 15 Mm.5074 Lalba , alpha 10.56 13.45 10.20 10.56 18.38 Mus musculus, clone MGC:8305 103517_at AA822898 Mm.197519 10.20 10.20 19.70 10.20 9.51 IMAGE:3593825, mRNA, complete cds 92927_at L10426 12 Mm.4866 Etv1 ets variant gene 2 10.20 9.85 10.20 9.85 10.20 phosphatidylinositol 3-kinase, regulatory 96592_at U50413 13 Mm.3058 Pik3r1 8.28 10.93 6.50 8.00 7.21 subunit, polypeptide 1 (p85 alpha) ESTs, Weakly similar to SH2/SH3 102979_at AI835278 Mm.18929 SHB 7.73 6.50 4.44 6.28 9.19 adaptor protein [M.musculus] 100484_at X66473 9 Mm.5022 Mmp13 matrix metalloproteinase 14 7.46 7.73 13.93 12.55 6.50

94384_at X67644 Mm.25613 Ier3 immediate early response 4 7.46 6.50 4.14 6.28 6.96

102381_at AA619207 Mm.12166 AU018108 expressed sequence AU018109 7.21 5.46 6.28 5.46 5.46

92779_f_at Z22552 M.musculus membrane glycoprotein gene 7.21 6.28 24.25 4.76 28.84

93435_at D89669 2 Mm.6575 Cyp24 cytochrome P450, 25 7.21 9.19 9.85 11.71 16.00

162475_f_at AV092014 7 Mm.21855 Pglyrp peptidoglycan recognition protein 6.96 5.46 28.84 32.00 46.85

93785_at M64782 7 Mm.2135 Folr1 folate receptor 1 (adult) 6.73 9.51 4.00 5.86 6.28 Mus musculus, clone MGC:8060 93928_f_at AF043689 Mm.1232 6.50 8.88 17.15 3.36 22.63 IMAGE:3587523, mRNA, complete cds 99963_at U07861 7 Mm.4417 Zfp101 zinc finger protein 102 6.50 6.06 6.28 8.28 4.76

97413_at AI121305 Mm.29959 1600029D21Rik RIKEN cDNA 1600029D21 gene 6.28 7.73 5.86 8.00 9.19

99126_at L04961 Mm.4095 Xist inactive X specific transcripts 6.28 6.50 6.73 3.36 5.28 Mouse endogenous proviral superantigen 92780_f_at M90535 (Mtv-7 sag), and envelope protein (env) 6.06 6.73 11.31 4.29 16.00 gene 102197_at AJ222586 Mm.9901 Nucb2 nucleobindin 3 5.66 5.46 4.59 5.46 6.96 potassium intermediate/small 102198_at AF042487 Mm.9911 Kcnn4 conductance calcium-activated channel, 5.46 6.06 3.14 4.76 5.28 subfamily N, member 5 Mus musculus, clone IMAGE:3963643, 104643_at AI850846 Mm.31267 5.28 5.86 3.48 3.86 4.92 mRNA, partial cds 104156_r_at U19118 1 Mm.2706 Atf3 activating transcription factor 4 5.10 4.44 10.20 13.00 8.88

93097_at U51805 10 Mm.154144 Arg1 arginase 1, liver 5.10 4.59 5.28 8.57 9.85

97420_at AW230891 11 Mm.176946 Lrg-pending leucine-rich alpha-2-glycoprotein 5.10 6.73 5.86 4.00 6.06

103506_f_at AW228162 18 Mm.4163 Dsc2 desmocollin 3 4.76 3.73 4.00 5.10 5.86

93013_at AF077861 12 Mm.1466 Idb2 inhibitor of DNA binding 3 4.76 3.86 3.48 4.29 5.28

94350_f_at U12961 8 Mm.252 Nqo1 NAD(P)H dehydrogenase, quinone 2 4.76 4.76 6.73 4.00 3.14 ESTs, Weakly similar to TYROSINE- 93479_at AW122413 Mm.218274 4.44 4.59 7.21 6.73 6.28 PROTEIN KINASE JAK3 [M.musculus] 94351_r_at U12961 8 Mm.252 Nqo1 NAD(P)H dehydrogenase, quinone 2 4.44 5.10 7.46 4.59 3.73

94821_at AW123880 11 Mm.22718 Xbp1 X-box binding protein 2 4.44 3.14 3.86 5.28 4.76

96123_at X99347 2 Mm.218846 Lbp lipopolysaccharide binding protein 4.29 3.73 4.92 5.28 3.86

99993_at U77083 9 Mm.4487 Anpep alanyl (membrane) aminopeptidase 4.29 4.76 4.76 3.86 6.28

101446_at AF004428 10 Mm.7821 Tpd52l1 tumor protein D52-like 2 4.14 4.92 4.14 5.46 6.06

94493_at AF095905 5 Mm.28921 Cldn3 claudin 4 4.14 4.76 3.36 4.00 5.10 102934_s_a cell division cycle 25 homolog C (S. L16926 18 Mm.16857 Cdc25c 4.00 3.14 3.48 2.73 3.73 t cerevisiae) lysine oxoglutarate reductase, 103389_at AJ224761 6 Mm.18651 Lorsdh 4.00 4.76 4.92 3.25 4.14 saccharopine dehydrogenase 97527_at AA681998 Mm.326 1110038L14Rik RIKEN cDNA 1110038L14 gene 4.00 3.48 2.64 3.25 3.03

99561_f_at AF087825 11 Mm.42189 Cldn7 claudin 8 4.00 3.73 2.83 4.00 4.14

100333_at M13521 7 Mm.200941 Saa2 serum amyloid A 3 3.73 4.59 7.21 25.99 23.43

160604_at AF045017 13 Mm.12949 Foxc1 forkhead box C2 3.73 3.73 6.50 3.36 4.92 DNA segment, Chr 6, Wayne State 95541_at AW125506 6 Mm.27673 D6Wsu176e 3.73 3.14 2.46 3.36 2.93 University 176, expressed ESTs, Weakly similar to T47140 96748_i_at AA619554 Mm.28958 hypothetical protein DKFZp761K1115.1 3.73 4.14 2.55 3.25 2.93 [H.sapiens] 99663_g_at AI194767 Mm.4379 Pcnt pericentrin 3.73 3.48 3.25 4.00 3.36

99926_at AB001489 1 Mm.4317 Pigr polymeric immunoglobulin receptor 3.73 5.46 4.14 5.46 6.28

102052_at AA871791 9 Mm.10297 1300003D03Rik RIKEN cDNA 1300003D03 gene 3.61 3.25 2.55 3.25 5.46 DNA segment, Chr 9, ERATO Doi 280, 161075_at AI226337 9 Mm.6407 D9Ertd280e 3.61 4.29 4.44 3.36 3.03 expressed 97825_at AI854029 10 Mm.28209 Perp-pending p53 apoptosis effector related to Pmp23 3.61 4.00 3.14 3.48 3.48 UDP-N-acetyl-alpha-D- 99011_at U70538 2 Mm.38441 Galnt3 galactosamine:polypeptide N- 3.61 2.93 2.55 2.55 3.14 acetylgalactosaminyltransferase 4 100127_at M35523 2 Mm.4757 Crabp2 cellular retinoic acid binding protein II 3.48 5.66 2.93 5.10 4.29 serine/threonine kinase 39, STE20/SPS1 160806_at AF099988 2 Mm.29404 Stk39 3.48 3.03 2.30 2.73 2.64 homolog (yeast) 160829_at U44088 Mm.3117 Tdag T-cell death associated gene 3.48 3.36 2.93 2.83 4.44 93220_at Z35168 Mm.155579 Col4a5 procollagen, type IV, alpha 6 3.48 4.44 3.48 3.86 2.46

92325_at AI326889 Mm.181833 8430404F20Rik RIKEN cDNA 8430404F20 gene 3.36 4.29 3.61 3.86 3.61 Mus musculus, clone MGC:8060 92778_i_at Z22552 Mm.1232 3.36 3.61 4.59 2.93 8.57 IMAGE:3587523, mRNA, complete cds 97415_at M89777 13 Mm.29968 Rab3d RAB3D, member RAS oncogene family 3.36 4.44 2.83 2.93 3.36

100283_at AW125812 15 Mm.1493 Sox10 SRY-box containing gene 11 3.25 3.03 3.25 3.03 3.61 Cbp/p300-interacting transactivator, with 101973_at Y15163 10 Mm.9524 Cited2 3.14 3.61 3.03 3.03 3.25 Glu/Asp-rich carboxy-terminal domain, 3 FXYD domain-containing ion transport 103059_at X93038 Mm.1662 Fxyd3 3.14 3.03 2.73 2.64 4.00 regulator 4 104099_at AF076482 7 Mm.21855 Pglyrp peptidoglycan recognition protein 3.14 2.64 11.71 13.93 16.56

92903_at X78197 1 Mm.4795 Tcfap2b transcription factor AP-2 beta 3.14 3.36 5.66 2.55 3.61

97206_at AW230369 2 Mm.104955 Spint1 serine protease inhibitor, Kunitz type 2 3.14 5.10 3.73 4.59 5.46

102856_at AF047389 15 Mm.1493 Sox10 SRY-box containing gene 11 3.03 3.61 3.14 2.93 3.61

93736_at AF090686 11 Mm.20948 Tcn2 transcobalamin 3 3.03 2.73 2.93 2.64 2.93

96065_at D88769 3 Mm.2632 Lxn latexin 3.03 3.25 2.64 3.48 2.64 tumor-associated calcium signal 160651_at AI563854 Mm.154045 Tacstd2 2.93 4.00 2.55 5.86 6.50 transducer 3 160973_at AA590345 16 Mm.24491 AA408511 expressed sequence AA408512 2.83 2.55 2.30 2.14 2.93

98485_at AI850288 7 Mm.35465 1300002E07Rik RIKEN cDNA 1300002E07 gene 2.83 2.93 2.93 3.48 4.29 5430432M24Ri 103343_at AI845815 Mm.18228 RIKEN cDNA 5430432M24 gene 2.73 2.55 2.30 2.46 2.64 k 92851_at U49430 9 Mm.13787 Cp 2.73 3.86 3.14 2.83 3.48

100566_at L12447 1 Mm.218877 Igfbp5 insulin-like growth factor binding protein 6 2.64 2.46 3.03 3.86 3.73

101521_at AB013819 11 Mm.8552 Birc5 baculoviral IAP repeat-containing 6 2.64 2.46 2.22 3.14 2.93

102255_at AB015978 15 Mm.10760 Osmr oncostatin receptor 2.64 3.86 3.36 2.46 3.03

94465_g_at AF029347 8 Mm.28842 Clcn3 chloride channel 4 2.64 2.46 3.48 2.55 3.03

92639_at U80932 2 Mm.11738 Stk6 serine/threonine kinase 7 2.55 2.14 3.36 2.73 3.61

102064_at L28095 9 Mm.1051 Casp1 caspase 2 2.46 2.93 2.30 2.93 2.30

96343_at AI836968 7 Mm.143830 Actn4 alpha actinin 5 2.46 2.30 2.64 2.93 2.73

100024_at AI641895 5 Mm.46014 shrm shroom 2.38 2.55 3.61 2.55 2.93

101410_at AB000713 5 Mm.7339 Cldn4 claudin 5 2.38 3.36 2.55 2.73 3.36 DnaJ (Hsp40) homolog, subfamily C, 102414_i_at U28423 Mm.12616 Dnajc3 2.38 2.93 2.83 2.30 3.25 member 4 99440_at Y07686 4 Mm.4025 Nfib nuclear factor I/B 2.30 2.55 2.38 2.46 2.30 CCAAT/enhancer binding protein 92925_at M61007 2 Mm.4863 Cebpb 2.22 2.55 2.64 2.73 2.83 (C/EBP), beta 103709_at AA763466 11 Mm.22621 Col1a1 procollagen, type I, alpha 2 0.47 0.45 0.44 0.39 0.39 succinate-CoA ligase, GDP-forming, 96268_at AI840979 6 Mm.29845 Suclg1 0.47 0.42 0.41 0.41 0.47 alpha subunit L-3-hydroxyacyl-Coenzyme A 95485_at D29639 Mm.2491 Hadhsc 0.44 0.42 0.41 0.38 0.39 dehydrogenase, short chain 93278_at M91458 4 Mm.1779 Scp2 sterol carrier protein 2, liver 0.39 0.41 0.33 0.44 0.38 101897_g_a M63697 3 Mm.157907 Cd1d2 CD1d2 antigen 0.38 0.39 0.37 0.35 0.34 t 3-hydroxyisobutyryl-Coenzyme A 103939_at AW121399 Mm.25250 Hibch 0.38 0.44 0.37 0.28 0.35 hydrolase 98859_at M99054 9 Mm.46354 Acp5 acid phosphatase 5, tartrate resistant 0.37 0.34 0.38 0.31 0.35

94806_at AW125336 14 Mm.22676 Pdhb pyruvate dehydrogenase (lipoamide) beta 0.37 0.35 0.27 0.33 0.35

101039_at X04647 8 Mm.181021 Col4a2 procollagen, type IV, alpha 3 0.35 0.35 0.35 0.29 0.31

95058_f_at AW121984 Mm.29153 2610205H19Rik RIKEN cDNA 2610205H19 gene 0.35 0.37 0.37 0.38 0.34

99637_at AF011450 4 Mm.4352 Col15a1 procollagen, type XV 0.34 0.39 0.26 0.23 0.31 glycerol-3-phosphate acyltransferase, 101867_at U11680 19 Mm.87773 Gpam 0.33 0.32 0.37 0.38 0.39 mitochondrial 104313_at AI842432 4 Mm.22403 2610020G18Rik RIKEN cDNA 2610020G18 gene 0.33 0.32 0.41 0.39 0.37

104735_at AI842065 14 Mm.24647 AU046135 expressed sequence AU046136 0.33 0.34 0.29 0.26 0.21

93543_f_at J03952 3 Mm.2011 Gstm1 glutathione S-transferase, mu 2 0.32 0.30 0.33 0.26 0.31

101007_at AI845732 10 Mm.42126 Gprk7 -coupled receptor kinase 8 0.30 0.38 0.29 0.24 0.38

101093_at M15832 8 Mm.738 Col4a1 procollagen, type IV, alpha 2 0.30 0.34 0.38 0.29 0.33 thyroid hormone responsive SPOT14 160306_at X95279 Mm.28585 Thrsp 0.30 0.19 0.26 0.27 0.30 homolog (Rattus) 96870_at AI836740 10 Mm.154581 Aco2 aconitase 2, mitochondrial 0.30 0.37 0.32 0.34 0.42

97160_at X04017 11 Mm.35439 Sparc secreted acidic cysteine rich glycoprotein 0.30 0.28 0.19 0.15 0.20

101964_at U05809 16 Mm.154387 Tkt transketolase 0.29 0.28 0.24 0.28 0.38 acetyl-Coenzyme A dehydrogenase, 92581_at U07159 3 Mm.10530 Acadm 0.28 0.31 0.23 0.23 0.32 medium chain 97944_f_at AF099808 14 Mm.30557 Tcra T-cell receptor alpha chain 0.28 0.30 0.35 0.35 0.35

100538_at M35725 16 Mm.5274 Sod1 superoxide dismutase 1, soluble 0.27 0.33 0.38 0.31 0.39

94056_at M21285 19 Mm.140785 Scd1 stearoyl-Coenzyme A desaturase 2 0.27 0.32 0.27 0.35 0.39

94345_at AI843709 Mm.25142 5133400A03Rik RIKEN cDNA 5133400A03 gene 0.27 0.37 0.26 0.26 0.26 succinate-Coenzyme A ligase, ADP- 93501_f_at AF058955 14 Mm.19154 Sucla2 0.26 0.34 0.28 0.28 0.34 forming, beta subunit CCAAT/enhancer binding protein 98447_at M62362 7 Mm.34537 Cebpa 0.26 0.32 0.24 0.26 0.26 (C/EBP), alpha 93353_at AF013262 10 Mm.18888 Lum lumican 0.25 0.31 0.13 0.15 0.09 pleckstrin homology-like domain, family 98056_at AI846214 1 Mm.34346 Phlda3 0.25 0.23 0.22 0.25 0.26 A, member 4 99669_at X15986 15 Mm.43831 Lgals1 lectin, galactose binding, soluble 2 0.25 0.29 0.18 0.20 0.19

160511_at L12029 6 Mm.465 Sdf1 stromal cell derived factor 2 0.24 0.37 0.26 0.11 0.25

92773_at AF079528 1 Mm.12246 Ier5 immediate early response 6 0.24 0.26 0.21 0.27 0.26 membrane-spanning 4-domains, 104173_at AA797989 19 Mm.4046 Ms4a2 0.23 0.26 0.37 0.26 0.31 subfamily A, member 3 99108_s_at U15012 15 Mm.3986 Ghr growth hormone receptor 0.23 0.22 0.23 0.18 0.11

104605_at AW047554 6 Mm.24126 AI115388 EST AI115389 0.22 0.23 0.21 0.20 0.33 cyclin-dependent kinase inhibitor 1C 95471_at U22399 7 Mm.168789 Cdkn1c 0.22 0.21 0.31 0.38 0.20 (P57) 103422_at M63695 3 Mm.1894 Cd1d1 CD1d1 antigen 0.21 0.22 0.24 0.18 0.18 94438_at AI852672 15 Mm.26550 Pfkm phosphofructokinase, muscle 0.21 0.20 0.26 0.25 0.32 glutathione transferase zeta 1 160350_at AW060750 12 Mm.29652 Gstz1 0.20 0.25 0.21 0.20 0.24 (maleylacetoacetate isomerase) 93534_at X53929 10 Mm.1987 Dcn decorin 0.20 0.29 0.15 0.12 0.15

94057_g_at M21285 19 Mm.140785 Scd1 stearoyl-Coenzyme A desaturase 2 0.19 0.19 0.15 0.16 0.23

100567_at M20497 3 Mm.582 Fabp4 fatty acid binding protein 4, adipocyte 0.19 0.28 0.25 0.25 0.35

93497_at K02782 17 Mm.19131 C3 complement component 4 0.18 0.22 0.23 0.18 0.19

93319_at U20238 Mm.18517 Rasa3 RAS p21 protein activator 4 0.16 0.16 0.26 0.26 0.18

101082_at J02652 9 Mm.148155 Mod1 malic enzyme, supernatant 0.16 0.18 0.19 0.17 0.21

103257_at AA690483 3 Mm.2073 AW109744 expressed sequence AW109745 0.16 0.17 0.20 0.23 0.19

160298_at AW122012 16 Mm.181074 2610001E17Rik RIKEN cDNA 2610001E17 gene 0.16 0.15 0.13 0.15 0.10

101676_at U13705 11 Mm.7156 Gpx3 glutathione peroxidase 4 0.15 0.32 0.19 0.18 0.22

93051_at Z37107 14 Mm.15295 Ephx2 epoxide hydrolase 2, cytoplasmic 0.15 0.18 0.29 0.16 0.22

93826_at AI956230 Mm.205569 2310028N02Rik RIKEN cDNA 2310028N02 gene 0.15 0.18 0.12 0.11 0.20

104606_at M55561 4 Mm.24130 Cd52 CD52 antigen 0.14 0.16 0.19 0.16 0.22

94781_at V00714 11 Mm.196110 Hba-a1 hemoglobin alpha, adult chain 2 0.14 0.23 0.08 0.06 0.05

93100_at X13297 19 Mm.16537 Acta2 actin, alpha 2, smooth muscle, aorta 0.13 0.20 0.29 0.23 0.20

93996_at X01026 7 Mm.21758 Cyp2e1 cytochrome P450, 2e1, ethanol inducible 0.13 0.14 0.12 0.19 0.16 104445_at AW046694 Mm.2935 4631408O11Rik RIKEN cDNA 4631408O11 gene 0.13 0.13 0.14 0.11 0.13

95523_at AI839718 Mm.27579 2900062L11Rik RIKEN cDNA 2900062L11 gene 0.12 0.12 0.10 0.11 0.09 fatty acid Coenzyme A ligase, long chain 94507_at U15977 Mm.28962 Facl2 0.11 0.14 0.14 0.10 0.13 3 101089_at AF002283 Mm.7342 Pdlim3 PDZ and LIM domain 4 0.10 0.15 0.30 0.16 0.15 Mus musculus SMAF1 mRNA, complete 96237_at AI118905 Mm.28800 0.10 0.17 0.13 0.10 0.14 cds 93750_at J04953 2 Mm.21109 Gsn gelsolin 0.05 0.09 0.05 0.05 0.07

99671_at X04673 10 Mm.4407 Adn adipsin 0.05 0.12 0.05 0.08 0.14

160375_at AJ006474 3 Mm.300 Car3 carbonic anhydrase 4 0.03 0.08 0.08 0.04 0.13

100381_at M12347 8 Mm.214950 Acta1 actin, alpha 1, skeletal muscle 0.03 0.15 0.33 0.03 0.44 myosin light chain, alkali, fast skeletal 92541_at X12973 1 Mm.1000 Mylf 0.03 0.08 0.18 0.04 0.23 muscle adipocyte complement related protein of 99104_at U49915 Mm.3969 Acrp30 0.02 0.04 0.03 0.03 0.06 30 kDa myosin, heavy polypeptide 4, skeletal 98488_at AJ223361 11 Mm.35531 Myh4 0.01 0.05 0.15 0.01 0.23 muscle