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66 Affy U133A 2.0 microarrays hybridized with total RNA from epithelial and stromal cells that were laser captured from normal breast tissue (n=5) and invasive breast cancer (n=28).
GSE10797
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Casey T, Bond J, Tighe S, Hunter T et al. Molecular signatures suggest a major role for stromal cells in development of invasive breast cancer. Breast Cancer Res Treat 2008 Mar 29.
Pub Med
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66 Affy U133A 2.0 microarrays hybridized with total RNA from epithelial and stromal cells that were laser captured from normal breast tissue (n=5) and invasive breast cancer (n=28).
GSE10797Entrez
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Casey T, Bond J, Tighe S, Hunter T et al. Molecular signatures suggest a major role for stromal cells in development of invasive breast cancer. Breast Cancer Res Treat 2008 Mar 29.
Pub Med
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18 Affy U133A microarrays hybridized with mRNA from estrogen receptor-positive MCF-7 cells, stably transfected with the aromatase gene (known as MCF-7aro cells), after tretment with testosterone, 17?-
GSE2225
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Itoh T, Karlsberg K, Kijima I, Yuan YC et al. Letrozole-, anastrozole-, and tamoxifen-responsive genes in MCF-7aro cells: a microarray approach. Mol Cancer Res 2005 Apr;3(4):203-18.
Pub Med
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12 Affy U133A microarrays hybridized with mRNA from MDA-MB-231 Breast Cancer Cells expressing either wild-type estrogen receptor or the mutant estrogen recepor L540Q when treated with estradiol for 1
GSE1045
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Acevedo et al. (2004) Selective Recognition of Distinct Classes of Coactivators by a Ligand-Inducible Activation Domain. Molecular Cell 13: 725-738, 2004
Pub Med
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36 Affy U133A 2.0 microarrays hybridized with total RNA isolated from the control and treated cells.
GSE2225Entrez
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Itoh T, Karlsberg K, Kijima I, Yuan YC et al. Letrozole-, anastrozole-, and tamoxifen-responsive genes in MCF-7aro cells: a microarray approach. Mol Cancer Res 2005 Apr;3(4):203-18.
Pub Med
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96 Affy U133A microarrays hybridized with mRNA from primary breast tumors.
GSE2294
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Yu K, et al. (2006) A modular analysis of breast cancer reveals a novel low-grade molecular signature in estrogen receptor-positive tumors. Clin.Cancer Res 12: 3288-3296, 2006
Pub Med
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121 Affy U133A microarrays hybridized with mRNA from subpopulations of MDA-MB-231 that exhibit different metastatic tropisms when injected into immuno-deficient mice. Also, a cohort of primary breast
GSE2603
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Minn AJ, et al. (2005) Genes that mediate breast cancer metastasis to lung. Nature 436: 518-524, 2005.
Pub Med
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121 Affy U133A microarrays hybridized with mRNA from subpopulations of MDA-MB-231.
GSE2603Entrez
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Minn AJ, et al. (2005) Genes that mediate breast cancer metastasis to lung. Nature 436: 518-524, 2005.
Pub Med
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12 Affy U133A microarrays hybridized with mRNA from MDA-MB-231 Breast Cancer Cells expressing either wild-type estrogen receptor or the mutant estrogen recepor L540Q when treated with estradiol for 1
GSE2034
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Acevedo et al. (2004) Selective Recognition of Distinct Classes of Coactivators by a Ligand-Inducible Activation Domain. Molecular Cell 13: 725-738, 2004
Pub Med
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159 Affy U133A microarrays hybridized with mRNA from primary breast tumors.
GSE1456
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Pawitan Y, et al. (2005) Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast Cancer Res 7: R953-R964.
Pub Med
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12 Affy U133A microarrays hybridized with mRNA from three human ER+ breast cancer cell lines--MCF-7, T47-D, BT-474--grown with or without estradiol (E2).
GSE3529
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Rae JM, et al. (2005) GREB 1 is a critical regulator of hormone dependent breast cancer growth. Breast Cancer Res Treat. 92: 141-149, 2005.
Pub Med
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189 Affy U133A microarrays hybridized with mRNA from primary breast tumors.
GSE2990
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Sotiriou,C. et al.(2006) Gene Expression Profiling in Breast Cancer: Understanding the Molecular Basis of Histologic Grade To Improve Prognosis. JNCI Cancer Spectrum 98[4], 262-272.
Pub Med
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10 Affy U133A microarrays hybridized with mRNA of 5 matched Ductal Carcinomas in Situ and Invasive Breast Tumors.
GSE3893
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Schuetz CS, et al. (2006) Progression-Specific Genes Identified by Expression Profiling of Matched Ductal Carcinomas In situ and Invasive Breast Tumors, Combining Laser Capture Microdissection and Oli
Pub Med
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251 Affy U133A microarrays hybridized with mRNA from primary breast tumors.
GSE3494Entrez
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Miller,L.D. et al. (2005) From The Cover: An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proceedings of the Nati
Pub Med
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Using Affymetrix GeneChip Human Genome U133 Array Set HG-U133A, we applied LCM to obtain samples enriched in tumor epithelium and stroma from 15 IBC and 35 non-IBC cases to study the relative contribu
GSE5847
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Boersma BJ, Reimers M, Yi M, Ludwig JA et al. A stromal gene signature associated with inflammatory breast cancer. Int J Cancer 2008 Mar 15;122(6):1324-32.
Pub Med
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105 Affy U133A microarrays hybridized with mRNA from MCF-7 Breast Cancer Cells expressing either estrogen receptor beta (AdERb) or no insert (Ad) when treated with ither vehicle control (veh), 6nM 17
GSE9936
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Chang EC, Charn TH, Park SH, Helferich WG et al. Estrogen Receptors alpha and beta as determinants of gene expression: influence of ligand, dose, and chromatin binding. Mol Endocrinol 2008 May;22(5):1
Pub Med
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198 Affy U133A microarrays hybridized with mRNA from primary breast tumors used to validate the 76-gene signature (VERIDEX). No replicate, no reference sample.
GSE7390
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Desmedt C, Piette F, Loi S, Wang Y et al. Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series.
Pub Med
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116 Affy U133A microarrays hybridized with mRNA extracted from the paired biopsies taken from the same subjects both pretreatment and after 10-14 days Letrozol, 2.5 mg/day, oral
GSE5462
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Miller WR, Larionov AA, Renshaw L, Anderson TJ et al. Changes in breast cancer transcriptional profiles after treatment with the aromatase inhibitor, letrozole. Pharmacogenet Genomics 2007 Oct;17(10):
Pub Med
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| coming soon |
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200 Affy U133A microarrays hybridized with mRNA from untreated Breast Cancer Cells
GSE11121
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Schmidt M, Böhm D, von Törne C, Steiner E et al. The humoral immune system has a key prognostic impact in node-negative breast cancer. Cancer Res 2008 Jul 1;68(13):5405-13.
Pub Med
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6 Affy U133A microarrays hybridized with mRNA isolated from human mammary epithelial cells, human MDA-MB-436 cells and HCC1954 cells.
GSE1299
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Mecham BH, Klus GT, Strovel J, Augustus M et al. Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression meas
Pub Med
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17 Affy U133A microarrays hybridized with mRNA from MCF-7 Breast Cancer Cells expressing either estrogen receptor beta (AdERb) or no insert (Ad) at multiplicity of infection (moi) of 10 when treated
GSE4025
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Frasor J, Chang EC, Komm B, Lin CY et al. Gene expression preferentially regulated by tamoxifen in breast cancer cells and correlations with clinical outcome. Cancer Res 2006 Jul 15;66(14):7334-40.
Pub Med
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| coming soon |
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24 Affy U133A microarrays hybridized with mRNA from MCF10A-Myc Breast Cancer cells subjected to 72 hrs of growth factor withdrawal followed by treatment with either vehicle (ethanol) or Dex (10-6 M)
GSE4917
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Wu W, Zou M, Brickley DR, Pew T et al. Glucocorticoid receptor activation signals through forkhead transcription factor 3a in breast cancer cells. Mol Endocrinol 2006 Oct;20(10):2304-14.
Pub Med
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289 Affy U133A microarrays hybridized with mRNA from primary invasive breast tumors.
GSE4922
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Ivshina AV, George J, Senko O, Mow B et al. Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer. Cancer Res 2006 Nov 1;66(21):10292-301
Pub Med
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23 Affy U133A microarrays hybridized with mRNA from breast cancer cell lines to identify genes whose expression level correlates with sensitivity of particular drug.
GSE6569
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Huang F, Reeves K, Han X, Fairchild C et al. Identification of candidate molecular markers predicting sensitivity in solid tumors to dasatinib: rationale for patient selection. Cancer Res 2007 Mar 1;6
Pub Med
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12 Affy U133A microarrays hybridized with mRNA from 6 tumorigenic, 3 non tumorigenic samples of breast tumors and 3 normal breast samples.
GSE6883
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Liu R, Wang X, Chen GY, Dalerba P et al. The prognostic role of a gene signature from tumorigenic breast-cancer cells.N Engl J Med 2007 Jan 18;356(3):217-26.
Pub Med
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| coming soon |
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26 Affy U133A microarrays hybridized with mRNA from breast cancer cells
GSE6596
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Klein A, Wessel R, Graessmann M, Jürgens M et al. Comparison of gene expression data from human and mouse breast cancers: identification of a conserved breast tumor gene set. Int J Cancer 2007 Aug 1;
Pub Med
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26 Affy U133A microarrays hybridized with mRNA from six independent cultures:three from MCF7/XBP1 cultures and three from the vector control culturesv
GSE8562
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Gomez BP, Riggins RB, Shajahan AN, Klimach U et al. Human X-box binding protein-1 confers both estrogen independence and antiestrogen resistance in breast cancer cell lines. FASEB J 2007 Dec;21(14):40
Pub Med
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251 Affy U133A microarrays hybridized with mRNA from primary breast tumors.
GSE3494
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Miller,L.D. et al. (2005) From The Cover: An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proceedings of the National Academy of Sciences 102[38], 13550-13555.
Pub Med
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12 Affy U133A microarrays hybridized with mRNA from MCF-7 breast cancer cells co-expressing ERa and ERb after treatment with estrogen
GSE4006
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Chang EC, Frasor J, Komm B, Katzenellenbogen BS. Impact of estrogen receptor beta on gene networks regulated by estrogen receptor alpha in breast cancer cells. Endocrinology 2006 Oct;147(10):4831-42.
Pub Med
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989 Affy microarrays dataset created by combining independent samples from 6 different datasets GSE11121,GSE1456,GSE2990,GSE3494,GSE7390 and GSE9195
JointSurvival
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NA
Pub Med
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122 Agilents G4212A two-channel microarrays of mammary tumors and normal mammary glands from different mouse breast cancer models.
GSE3165gpl891
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Herschkowitz JI, Simin K, Weigman VJ, Mikaelian I et al. Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors. Genome Biol 2007;8(5):R76.
Pub Med
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| coming soon |
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122 Agilents G4212A two-channel microarrays of mammary tumors and normal mammary glands from different mouse breast cancer models.
GSE3165gpl891
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Herschkowitz JI, Simin K, Weigman VJ, Mikaelian I et al. Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors. Genome Biol 2007;8(5):R76.
Pub Med
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| coming soon |
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111 NCI Qiagen Homo sapiens 36K v3 Comparative Genomic Hybridization microarrays comparing breast ductal carcinomas of different grade to normal brease tissue.
GSE7882
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Pub Med
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| coming soon |
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118 BAC-mediated array CGH microarrays of triple negative breast cancers to study genomic copy number alterations as predictive markers in breast cancer.
GSE10181
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Han W, Jung EM, Cho J, Lee JW et al. DNA copy number alterations and expression of relevant genes in triple-negative breast cancer. Genes Chromosomes Cancer 2008 Jun;47(6):490-9.
Pub Med
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| coming soon |
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220 high resolution CGH arrays of ER negative breast cancer (171 primary breast tumors of relatively small size and low NPI, and 49 breast cancer cell-lines.
GSE8757
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Chin SF, Teschendorff AE, Marioni JC, Wang Y et al. High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biol 2007;8(10):R215.
Pub Med
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| coming soon |
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61 NCI Qiagen Homo sapiens 36K v3 Comparative Genomic Hybridization microarrays comparing breast ductal carcinomas of different grade to normal breast tissue.
GSE7882expression
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Pub Med
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| coming soon |
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50 NCI Qiagen Homo sapiens 36K v3 Comparative Genomic Hybridization microarrays comparing breast ductal carcinomas of different grade to normal breast tissue.
GSE7882cgh
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Pub Med
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| coming soon |
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119 Luminex bead-based microRNA arrays of primary human breast tumors, tumor-derived cell lines and normal breast tissue samples.
GSE7842
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Blenkiron C, Goldstein LD, Thorne NP, Spiteri I et al. MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biol 2007;8(10):R214.
Pub Med
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| coming soon |
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341 Affymetrix GeneChip Human HG-U133A microarrays profiling normal tissue and tumor samples from Breast, Colon, Liver, Lung, Oesophagus and Thyroid
GSE5364
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Yu K, Ganesan K, Tan LK, Laban M et al. A precisely regulated gene expression cassette potently modulates metastasis and survival in multiple solid cancers. PLoS Genet 2008 Jul 18;4(7):e1000129.
Pub Med
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| coming soon |
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35 Affy rat 230A microarrays hybridized with mRNA from primary NMU-induced rat mammary tumors and normal mammary gland tissue
GDS1363
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Chan MM, Lu X, Merchant FM, Iglehart JD et al. Gene expression profiling of NMU-induced rat mammary tumors: cross species comparison with human breast cancer. Carcinogenesis 2005 Aug;26(8):1343-53.
Pub Med
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| coming soon |
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35 Affy rat 230A microarrays hybridized with mRNA from primary NMU-induced rat mammary tumors and normal mammary gland tissue
GDS1363Entrez
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Chan MM, Lu X, Merchant FM, Iglehart JD et al. Gene expression profiling of NMU-induced rat mammary tumors: cross species comparison with human breast cancer. Carcinogenesis 2005 Aug;26(8):1343-53.
Pub Med
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| coming soon |
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10 Affymetrix Rat 230A microarrays hybridized with mRNA from LCM captured mammary epithelium of rats fed a diet containing the soy isoflavone genistein or soy protein isolate.
GDS2616
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Su Y, Simmen FA, Xiao R, Simmen RC. Expression profiling of rat mammary epithelial cells reveals candidate signaling pathways in dietary protection from mammary tumors. Physiol Genomics 2007 Jun 19;30(1):8-16.
Pub Med
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| coming soon |
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73 Affymetrix Rat Genome 230 2.0 microarrays hybridized with mRNA from LCM captured mammary epithelium of 21 and 50 days old female ratss fed different fatty acids diets. Diets were: AIN-93G (reference diet), High- and Low-fat olive oil (HFO,LFO), High- and Low-fat butter (HFB,LFB), High- and Low-fat safflower oil (HFS,LFS). Batch effect has been subtracted from the measurements as described in the paper.
BcercDiets
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Medvedovic M, Gear R, Freudenberg JM, Schneider J, Bornschein R, Yan
M, Mistry MJ, Hendrix H, Karyala S, Halbleib D, Heffelfinger S, Clegg
DJ, Anderson MW. Influence of fatty acid diets on gene expression in
rat mammary epithelial cells. Physiol Genomics. 38(1):80-8. Jun 2009.
Pub Med
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| coming soon |
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62 ABI Human Genome Survey Version 2 Microarrays profiling mRNA from whole blood samples from patients with single and double primary tumors and healthy controls
GSE11545
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Pub Med
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| coming soon |
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66 Affymetrix GeneChip Human X3P Array microarrays profiling LCM isolated the epithelial and stroma compartments from 14 fresh frozen primary breast cancer biopsies.
GSE14548
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Ma XJ, Dahiya S, Richardson E, Erlander M, Sgroi DC. Gene expression profiling of the tumor microenvironment during breast cancer progression. Breast Cancer Res. 2009 Feb 2;11(1):R7.
Pub Med
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| coming soon |
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12 Affy U133+2.0 microarrays were hybridized with mRNA from MCF-7 cells stimulated with 100 nM estrogen for 0, 3, 6 or 12 hou
rs.
GSE11324
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Carroll JS, Meyer CA, Song J, Li W et al. Genome-wide analysis of estrogen receptor binding sites. Nat Genet 2006 Nov;38(1
1):1289-97.
Pub Med
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| coming soon |
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66 Affymetrix GeneChip Human X3P Array microarrays profiling LCM isolated the epithelial and stroma compartments from 14 fresh frozen primary breast cancer biopsies. RMA preprocessed using Entrez based custom CDF v11 (`Brainarray` U Michigan).
GSE14548Entrez
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Ma XJ, Dahiya S, Richardson E, Erlander M, Sgroi DC. Gene expression profiling of the tumor microenvironment during breast cancer progression. Breast Cancer Res. 2009 Feb 2;11(1):R7.
Pub Med
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| coming soon |
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12 Affy U133A microarrays profiling time series of finite life span and immortal non-malignant human mammary epithelial cell lines.
EGEOD8096Entrez
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Fournier MV, Martin KJ, Kenny PA, Xhaja K et al. Gene expression signature in organized and growth-arrested mammary acini predicts good outcome in breast cancer. Cancer Res 2006 Jul 15;66(14):7095-102.
Pub Med
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| coming soon |
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6 tissue samples from patients with early stage breast cancer (DCIS) were profiled for DNA methylation compared to normal tissue from same patient using Agilent-014791 Human CpG Island ChIP-on-Chip Microarray 244K (G4492A).
GSE14865
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Pub Med
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| coming soon |
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DNA methylation profiling of ductal carcinoma in situ (DCIS). Methylated genomic fragments from tumor DNA and matching normal control were enriched with the methylated-CpG island recovery assay (MIRA); amplified, labeled and hybridized on Agilent CpG island tiling oligo arrays. MIRA enriched samples from tumor were labeled with Cy5 while MIRA enriched DNA samples from normal tissue were labeled with Cy3. No Background correction, Lowess Normalization within each array, no between array normalization.
GSE14865
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Pub Med
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| coming soon |
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14 Affymetrix mouse MOE430A microarrays hybridized with mRNA from of pre-pubertal, pubertal and post-pubertal mouse mammary gland.
GDS2721
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McBryan J, Howlin J, Kenny PA, Shioda T et al. ERalpha-CITED1 co-regulated genes expressed during pubertal mammary gland development: implications for breast cancer prognosis. Oncogene 2007 Sep 27;26(44):6406-19.
Pub Med
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| coming soon |
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61 Affy U133 Plus 2.0 microarrays profiling mammary epithelim proximal to breast tumors and normal mammary epithelium.
ETABM276Entrez
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Cheng AS, Culhane AC, Chan MW, Venkataramu CR et al. Epithelial progeny of estrogen-exposed breast progenitor cells display a cancer-like methylome. Cancer Res 2008 Mar 15;68(6):1786-96.
Pub Med
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| coming soon |
