Table 1

Expression of HER2/neu ErbB-2 Breast Cancer Signature genes in MAM-1 Co-cultures and the Bam1a cell line
		Expression Relative to Universal Mouse RNA^a
Agilent Accession	Genbank Accession	MAM	Bam1a	Gene Description and Symbol
Genes present in the tumor-specific HER-2/neu-Induced Gene Expression Signature described by Astolfi

A_51_P184886	NM_011920	5.27	19.10	Mus musculus ATP-binding cassette, sub-family G (WHITE), member 2 (Abcg2), mRNA [NM_011920]
A_52_P336142	NM_011920	4.90	17.77	Mus musculus ATP-binding cassette, sub-family G (WHITE), member 2 (Abcg2), mRNA [NM_011920]
A_51_P342567	NM_031185	9.10	6.60	Mus musculus A kinase (PRKA) anchor protein (gravin) 12 (Akap12), mRNA [NM_031185]
A_51_P445166	NM_019959	11.89	17.02	Mus musculus C1q and tumor necrosis factor related protein 1 (C1qtnf1), mRNA [NM_019959]
A_51_P455647	NM_009801	7.56	9.21	Mus musculus carbonic anhydrase 2 (Car2), mRNA [NM_009801]
A_51_P303160	NM_007482	14.32	23.23	Mus musculus arginase 1, liver (Arg1), mRNA [NM_007482]
A_52_P159232	NM_011926	20.60	24.52	Mus musculus CEA-related cell adhesion molecule 1 (Ceacam1), mRNA [NM_011926]
A_51_P183446	NM_001039185	10.69	12.16	Mus musculus CEA-related cell adhesion molecule 1, mRNA (cDNA clone MGC:18556 IMAGE:4218391), complete cds [BC016891]
A_51_P171728	NM_011926	9.77	12.34	Mus musculus CEA-related cell adhesion molecule 1 (Ceacam1), mRNA [NM_011926]
A_52_P240706	NM_007543	23.70	31.29	Mus musculus CEA-related cell adhesion molecule 2 (Ceacam2), mRNA [NM_007543]
A_51_P362066	NM_007695	8.34	3.89	Mus musculus chitinase 3-like 1 (Chi3l1), mRNA [NM_007695]
A_51_P495049	NM_009897	10.34	11.46	Mus musculus creatine kinase, mitochondrial 1, ubiquitous (Ckmt1), mRNA [NM_009897]
A_51_P343309	NM_009908	5.83	10.54	Mus musculus cytidine monophospho-N-acetylneuraminic acid synthetase (Cmas), mRNA [NM_009908]
A_52_P197963	NM_009936	7.33	10.23	Mus musculus procollagen, type IX, alpha 3 (Col9a3), mRNA [NM_009936]
A_52_P507877	NM_007729	41.31	30.23	Mus musculus procollagen, type XI, alpha 1 (Col11a1), mRNA [NM_007729]
A_51_P459477	NM_007729	34.68	28.45	Mus musculus procollagen, type XI, alpha 1 (Col11a1), mRNA [NM_007729]
A_51_P227280	NM_007786	53.04	56.89	Mus musculus casein kappa (Csnk), mRNA [NM_007786]
A_51_P227275	NM_007786	26.87	32.53	Mus musculus casein kappa (Csnk), mRNA [NM_007786]
A_52_P51078	NM_007801	23.49	35.47	Mus musculus cathepsin H (Ctsh), mRNA [NM_007801]
A_51_P275976	NM_010070		3.24	Mus musculus docking protein 1 (Dok1), mRNA [NM_010070]
A_52_P366842	NM_010070	2.49	4.94	Mus musculus docking protein 1 (Dok1), mRNA [NM_010070]
A_51_P158037	NM_013505	11.59	12.52	Mus musculus desmocollin 2 (Dsc2), mRNA [NM_013505]
A_52_P157158	NM_013505	42.42	46.62	Mus musculus desmocollin 2 (Dsc2), mRNA [NM_013505]
A_52_P252931	NM_013505	107.26	265.33	Mus musculus desmocollin 2 (Dsc2), mRNA [NM_013505]
A_51_P502614	NM_026268	4.28	6.46	Mus musculus dual specificity phosphatase 6 (Dusp6), mRNA [NM_026268]
A_51_P455866	NM_010125	27.80	29.60	Mus musculus E74-like factor 5 (Elf5), mRNA [NM_010125]
A_51_P307979	NM_007960		2.46	Mus musculus ets variant gene 1 (Etv1), mRNA [NM_007960]
A_51_P246166	NM_007969	10.06	10.23	Mus musculus extracellular proteinase inhibitor (Expi), mRNA [NM_007969]
A_52_P329207	NM_007969	13.14	12.84	Mus musculus extracellular proteinase inhibitor (Expi), mRNA [NM_007969]
A_51_P329394	NM_008034	6.64	8.48	Mus musculus folate receptor 1 (adult) (Folr1), mRNA [NM_008034]
A_52_P377791	NM_008557	30.34	40.63	Mus musculus FXYD domain-containing ion transport regulator 3 (Fxyd3), mRNA [NM_008557]
A_51_P282538	NM_008077	28.43	73.47	Mus musculus glutamic acid decarboxylase 1 (Gad1), mRNA [NM_008077]
A_52_P144310	NM_008077	27.33	68.46	Mus musculus glutamic acid decarboxylase 1 (Gad1), mRNA [NM_008077]
A_51_P486810	NM_030677	13.90	14.97	Mus musculus glutathione peroxidase 2 (Gpx2), mRNA [NM_030677]
A_51_P258409	NM_010423	13.98	30.78	Mus musculus hairy/enhancer-of-split related with YRPW motif 1 (Hey1), mRNA [NM_010423]
A_51_P365152	NM_010474	23.53	48.48	Mus musculus heparan sulfate (glucosamine) 3-O-sulfotransferase 1 (Hs3st1), mRNA [NM_010474]
A_52_P281702	NM_010518	2.12	3.08	Mus musculus insulin-like growth factor binding protein 5 (Igfbp5), mRNA [NM_010518]
A_51_P204153	NM_010518	4.25	10.70	Mus musculus insulin-like growth factor binding protein 5 (Igfbp5), mRNA [NM_010518]
A_51_P510156	NM_008491	9.56	10.11	Mus musculus lipocalin 2 (Lcn2), mRNA [NM_008491]
A_52_P153864	NM_010723	2.77	3.75	Mus musculus LIM domain only 4 (Lmo4), mRNA [NM_010723]
A_51_P394190	NM_010723	3.05	4.24	Mus musculus LIM domain only 4 (Lmo4), mRNA [NM_010723]
A_52_P415168	NM_019394	8.35	8.26	Mus musculus melanoma inhibitory activity 1 (Mia1), mRNA [NM_019394]
A_52_P415167	NM_019394	18.65	22.26	Mus musculus melanoma inhibitory activity 1 (Mia1), mRNA [NM_019394]
A_52_P174346	NM_019394	7.84	8.15	Mus musculus melanoma inhibitory activity 1 (Mia1), mRNA [NM_019394]
A_51_P220062	NM_008609	10.60	15.42	Mus musculus matrix metalloproteinase 15 (Mmp15), mRNA [NM_008609]
A_51_P139780	NM_009402	6.81	7.64	Mus musculus peptidoglycan recognition protein 1 (Pglyrp1), mRNA [NM_009402]
A_51_P195958	NM_009344	3.26	6.05	Mus musculus pleckstrin homology-like domain, family A, member 1 (Phlda1), mRNA [NM_009344]
A_52_P418791	NM_011254	15.11	16.38	Mus musculus retinol binding protein 1, cellular (Rbp1), mRNA [NM_011254]
A_51_P423484	NM_011254	8.26	7.45	Mus musculus retinol binding protein 1, cellular (Rbp1), mRNA [NM_011254]
A_52_P197215	NM_028777	2.76	4.29	Mus musculus SEC14-like 1 (S. cerevisiae) (Sec14l1), mRNA [NM_028777]
A_52_P197223	NM_028777	3.32	5.72	Mus musculus SEC14-like 1 (S. cerevisiae) (Sec14l1), mRNA [NM_028777]
A_51_P268094	NM_009255	22.21	38.32	Mus musculus serine (or cysteine) proteinase inhibitor, clade E, member 2 (Serpine2), mRNA [NM_009255]
A_52_P637988	NM_009199	40.88	62.00	Mus musculus solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1 (Slc1a1), mRNA [NM_009199]
A_51_P110759	NM_009199	20.06	26.16	Mus musculus solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1 (Slc1a1), mRNA [NM_009199]
A_52_P426605	NM_021301	23.10	30.57	Mus musculus solute carrier family 15 (H+/peptide transporter), member 2 (Slc15a2), mRNA [NM_021301]
A_51_P107362	NM_007706	13.23	14.79	Mus musculus suppressor of cytokine signaling 2 (Socs2), mRNA [NM_007706]
A_51_P346704	XM_128139	10.67	11.19	Mus musculus SRY-box containing gene 10, mRNA (cDNA clone MGC:32314 IMAGE:5027211), complete cds. [BC023356]
A_52_P192625	XM_128139	23.80	36.33	Mus musculus SRY-box containing gene 10, mRNA (cDNA clone MGC:32314 IMAGE:5027211), complete cds. [BC023356]
A_52_P161630	NM_145933		4.23	Mus musculus beta galactoside alpha 2,6 sialyltransferase 1 (St6gal1), mRNA [NM_145933]
A_51_P101375	NM_145933	2.35	5.29	Mus musculus beta galactoside alpha 2,6 sialyltransferase 1 (St6gal1), mRNA [NM_145933]
A_51_P183940	NM_016866	2.21	3.02	Mus musculus serine/threonine kinase 39, STE20/SPS1 homolog (yeast) (Stk39), mRNA [NM_016866]
A_52_P447944	NM_008532	5.04	8.96	Mus musculus tumor-associated calcium signal transducer 1 (Tacstd1), mRNA [NM_008532]
A_51_P418820	NM_009335	40.16	37.90	Mus musculus transcription factor AP-2, gamma (Tcfap2c), mRNA [NM_009335]
A_51_P338262	NM_011619	5.37	8.17	Mus musculus troponin T2, cardiac (Tnnt2), mRNA [NM_011619]
A_51_P482503	NM_009413	21.46	34.02	Mus musculus tumor protein D52-like 1 (Tpd52l1), mRNA [NM_009413]
A_51_P506822	NM_011674	42.90	81.82	Mus musculus UDP galactosyltransferase 8A (Ugt8a), mRNA [NM_011674]
A_52_P439263	NM_011674	56.91	70.50	Mus musculus UDP galactosyltransferase 8A (Ugt8a), mRNA [NM_011674]

Genes expressed in common with the mouse orthologs of the human "intrinsic" gene list of published by Sorlie

A_51_P311038	NM_001024139	7.11	9.21	Mus musculus a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 15 (Adamts15), mRNA [NM_001024139]
A_51_P366811	NM_007470	45.17	36.20	Mus musculus apolipoprotein D (Apod), mRNA [NM_007470]
A_51_P163015	NM_172309	2.77	14.02	Mus musculus aryl hydrocarbon receptor nuclear translocator-like 2 (Arntl2), mRNA [NM_172309]
A_51_P455647	NM_009801	7.57	9.21	Mus musculus carbonic anhydrase 2 (Car2), mRNA [NM_009801]
A_51_P302823	NM_019686	4.02	11.39	Mus musculus calcium and integrin binding family member 2 (Cib2), mRNA [NM_019686]
A_51_P165185	NM_016887	11.54	15.50	Mus musculus claudin 7 (Cldn7), mRNA [NM_016887]
A_52_P507877	NM_007729	41.32	30.23	Mus musculus procollagen, type XI, alpha 1 (Col11a1), mRNA [NM_007729]
A_51_P459477	NM_007729	34.69	28.45	Mus musculus procollagen, type XI, alpha 1 (Col11a1), mRNA [NM_007729]
A_51_P502614	NM_026268	4.28	6.46	Mus musculus dual specificity phosphatase 6 (Dusp6), mRNA [NM_026268]
A_51_P116940	NM_007940	15.92	5.95	Mus musculus epoxide hydrolase 2, cytoplasmic (Ephx2), mRNA [NM_007940]
A_51_P455932	NM_007974	12.81	33.87	Mus musculus coagulation factor II (thrombin) receptor-like 1 (F2rl1), mRNA [NM_007974]
A_52_P192418	NM_010175	2.63	4.90	Mus musculus Fas (TNFRSF6)-associated via death domain (Fadd), mRNA [NM_010175]
A_51_P382925	NM_010175	2.16	3.61	Mus musculus Fas (TNFRSF6)-associated via death domain (Fadd), mRNA [NM_010175]
A_52_P100252	NM_007988	3.23	3.40	Mus musculus clone:A630082H08 product:fatty acid synthase, full insert sequence. [AK080374]
A_52_P136162	NM_010206	2.27	4.37	Mus musculus fibroblast growth factor receptor 1 (Fgfr1), mRNA [NM_010206]
A_52_P668810	NM_010206		3.81	Mus musculus fibroblast growth factor receptor 1 (Fgfr1), mRNA [NM_010206]
A_51_P335000	NM_010211		5.05	Mus musculus four and a half LIM domains 1 (Fhl1), mRNA [NM_010211]
A_51_P329394	NM_008034	6.64	8.48	Mus musculus folate receptor 1 (adult) (Folr1), mRNA [NM_008034]
A_52_P217710	NM_008056		3.08	Mus musculus frizzled homolog 6 (Drosophila) (Fzd6), mRNA [NM_008056]
A_51_P282538	NM_008077	28.43	73.47	Mus musculus glutamic acid decarboxylase 1 (Gad1), mRNA [NM_008077]
A_52_P144310	NM_008077	27.33	68.46	Mus musculus glutamic acid decarboxylase 1 (Gad1), mRNA [NM_008077]
A_51_P380005	NM_015736	32.95	69.29	Mus musculus UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (Galnt3), mRNA [NM_015736]
A_51_P379997	NM_015736	38.50	82.09	Mus musculus UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (Galnt3), mRNA [NM_015736]
A_51_P462422	NM_008124		5.07	Mus musculus gap junction membrane channel protein beta 1 (Gjb1), mRNA [NM_008124]
A_52_P16419	NM_010271	2.43	6.66	Mus musculus glycerol-3-phosphate dehydrogenase 1 (soluble) (Gpd1), mRNA [NM_010271]
A_52_P415996	NM_008184		6.29	Mus musculus glutathione S-transferase, mu 6 (Gstm6), mRNA [NM_008184]
A_51_P179664	NM_008185	3.67	6.80	Mus musculus glutathione S-transferase, theta 1 (Gstt1), mRNA [NM_008185]
A_52_P281702	NM_010518	2.12	3.08	Mus musculus insulin-like growth factor binding protein 5 (Igfbp5), mRNA [NM_010518]
A_51_P204153	NM_010518	4.25	10.70	Mus musculus insulin-like growth factor binding protein 5 (Igfbp5), mRNA [NM_010518]
A_52_P401386	NM_010593	3.74	5.28	Mus musculus junction plakoglobin (Jup), mRNA [NM_010593]
A_52_P642488	NM_008430	24.28	26.37	Mus musculus potassium channel, subfamily K, member 1 (Kcnk1), mRNA [NM_008430]
A_51_P307964	NM_010662	3.11	6.39	Mus musculus keratin complex 1, acidic, gene 13 (Krt1-13), mRNA [NM_010662]
A_51_P324814	NM_010664	2.93	3.89	Mus musculus keratin complex 1, acidic, gene 18 (Krt1-18), mRNA [NM_010664]
A_52_P410685	NM_033073	12.42	14.59	Mus musculus keratin complex 2, basic, gene 7 (Krt2-7), mRNA [NM_033073]
A_51_P242400	NM_031170	2.56	3.75	Mus musculus keratin complex 2, basic, gene 8 (Krt2-8), mRNA [NM_031170]
A_51_P174943	NM_008485	6.90	10.66	Mus musculus laminin, gamma 2 (Lamc2), mRNA [NM_008485]
A_51_P220062	NM_008609	10.60	15.42	Mus musculus matrix metalloproteinase 15 (Mmp15), mRNA [NM_008609]
A_51_P514085	NM_013606	3.75	6.35	Mus musculus myxovirus (influenza virus) resistance 2 (Mx2), mRNA [NM_013606]
A_52_P608097	NM_008756	17.70	41.15	Mus musculus occludin (Ocln), mRNA [NM_008756]
A_51_P486150	NM_008756	10.05	12.72	Mus musculus occludin (Ocln), mRNA [NM_008756]
A_52_P458279	NM_011169	15.09	21.23	Mus musculus prolactin receptor (Prlr), mRNA [NM_011169]
A_51_P248345	NM_009334		17.92	Mus musculus transcription factor AP-2 beta (Tcfap2b), transcript variant 1, mRNA [NM_009334]
A_51_P418820	NM_009335	40.16	37.90	Mus musculus transcription factor AP-2, gamma (Tcfap2c), mRNA [NM_009335]
A_51_P240614	NM_008536	3.79	5.43	Mus musculus transmembrane 4 superfamily member 1 (Tm4sf1), mRNA [NM_008536]
A_51_P482503	NM_009413	21.46	34.02	Mus musculus tumor protein D52-like 1 (Tpd52l1), mRNA [NM_009413]
A_51_P106059	NM_009423	2.81	3.48	Mus musculus Tnf receptor associated factor 4 (Traf4), mRNA [NM_009423]
A_52_P78403	NM_009423	2.90	5.78	Mus musculus Tnf receptor associated factor 4 (Traf4), mRNA [NM_009423]

Genes expressed in common with the MMTV/neu mammary tumor gene signature described by Landis

A_51_P320852	NM_007657	2.52	7.50	Mus musculus CD9 antigen (Cd9), mRNA [NM_007657]
A_51_P242265	NM_009950	2.45	4.36	Mus musculus CASP2 and RIPK1 domain containing adaptor with death domain (Cradd), mRNA [NM_009950]
A_52_P559779	NM_007883	17.30	22.26	Mus musculus desmoglein 2 (Dsg2), mRNA [NM_007883]
A_51_P249848	NM_007883	11.40	13.77	Mus musculus desmoglein 2 (Dsg2), mRNA [NM_007883]
A_52_P88091	NM_007883	22.00	38.20	Mus musculus desmoglein 2 (Dsg2), mRNA [NM_007883]
A_52_P601757	NM_007883	76.45	101.83	Mus musculus desmoglein 2, mRNA (cDNA clone IMAGE:4036406), partial cds [BC034056]
A_51_P502614	NM_026268	4.28	6.46	Mus musculus dual specificity phosphatase 6 (Dusp6), mRNA [NM_026268]
A_51_P246166	NM_007969	10.06	10.23	Mus musculus extracellular proteinase inhibitor (Expi), mRNA [NM_007969]
A_52_P329207	NM_007969	13.14	12.84	Mus musculus extracellular proteinase inhibitor (Expi), mRNA [NM_007969]
A_51_P329394	NM_008034	6.64	8.48	Mus musculus folate receptor 1 (adult) (Folr1), mRNA [NM_008034]
A_51_P352303	NM_011983	5.94	8.58	Mus musculus homer homolog 2 (Drosophila) (Homer2), mRNA [NM_011983]
A_52_P176573	NM_011983	7.52	12.27	Mus musculus homer homolog 2 (Drosophila) (Homer2), mRNA [NM_011983]
A_51_P510156	NM_008491	9.56	10.11	Mus musculus lipocalin 2 (Lcn2), mRNA [NM_008491]
A_52_P382785	NM_033525	3.71	12.17	Mus musculus nephronectin (Npnt), mRNA [NM_033525]
A_51_P289889	NM_033525	3.57	9.38	Mus musculus nephronectin (Npnt), mRNA [NM_033525]
A_52_P17556	NM_134249	6.84	18.37	Mus musculus T-cell immunoglobulin and mucin domain containing 2 (Timd2), mRNA [NM_134249]
A_51_P500906	NM_134249	12.27	24.24	Mus musculus T-cell immunoglobulin and mucin domain containing 2 (Timd2), mRNA [NM_134249]
A_51_P482503	NM_009413	21.46	34.02	Mus musculus tumor protein D52-like 1 (Tpd52l1), mRNA [NM_009413]

Expression of genes associated with the human HER2/neu chromosome 17q amplicon by Bertucci

A_51_P317176	NM_009971	12.40	13.05	Mus musculus colony stimulating factor 3 (granulocyte) (Csf3), mRNA [NM_009971]
A_51_P216179	NM_010152	4.71	8.69	Mus musculus v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) (Erbb2), transcript variant 2, mRNA [NM_010152]
A_51_P230382	NM_008815	2.63	3.66	Mus musculus ets variant gene 4 (E1A enhancer binding protein, E1AF) (Etv4), mRNA [NM_008815]
A_51_P368823	NM_010346	3.09	4.64	Mus musculus growth factor receptor bound protein 7 (Grb7), mRNA [NM_010346]
A_52_P401386	NM_010593	3.74	5.28	Mus musculus junction plakoglobin (Jup), mRNA [NM_010593]
A_52_P567306	NM_010688	2.95	4.98	Mus musculus LIM and SH3 protein 1 (Lasp1), mRNA [NM_010688]
A_51_P182462	NM_010688	2.46	3.44	Mus musculus LIM and SH3 protein 1 (Lasp1), mRNA [NM_010688]
A_51_P387123	NM_011854	2.77	4.06	Mus musculus 2'-5' oligoadenylate synthetase-like 2 (Oasl2), mRNA [NM_011854]

^aAverage fold difference is the ratio (n = 3, p value cutoff > .05) MAM-1 or Bam1a RNA to Universal Mouse RNA. RNA from MAM-1 or Bam1a was labeled in red color (cy5), universal RNA is labeled in green (cy3). Three independent RNA preparations per condition were analyzed on three separate chips and averaged; a confidence cutoff of >0.95 was used for the raw values of red/green before normalization. The fold change (MAM-1 or Bam1a/Universal Mouse) = Normalized ratio value(cy5/cy3). The MAM-1 and Bam1a transcriptomes include genes that are differentially increased relative to the Universal mouse RNA by at least 2-fold.
Piechocki BMC Cancer 2008 8:119 doi:10.1186/1471-2407-8-119