TY - JOUR AU - Polyak, K. PY - 2011 DA - 2011// TI - Heterogeneity in breast cancer JO - J Clin Invest VL - 121 UR - https://doi.org/10.1172/JCI60534 DO - 10.1172/JCI60534 ID - Polyak2011 ER - TY - JOUR AU - Schnitt, S. J. PY - 2010 DA - 2010// TI - Classification and prognosis of invasive breast cancer: from morphology to molecular taxonomy JO - Mod Pathol: Official J US Can Acad Pathol, Inc VL - 23 Suppl 2 UR - https://doi.org/10.1038/modpathol.2010.33 DO - 10.1038/modpathol.2010.33 ID - Schnitt2010 ER - TY - JOUR AU - Lehmann, B. D. AU - Bauer, J. A. AU - Chen, X. AU - Sanders, M. E. AU - Chakravarthy, A. B. AU - Shyr, Y. PY - 2011 DA - 2011// TI - Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies JO - J Clin Invest VL - 121 UR - https://doi.org/10.1172/JCI45014 DO - 10.1172/JCI45014 ID - Lehmann2011 ER - TY - JOUR AU - Khatri, P. AU - Sirota, M. AU - Butte, A. J. PY - 2012 DA - 2012// TI - Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges JO - PLoS Comput Biol VL - 8 UR - https://doi.org/10.1371/journal.pcbi.1002375 DO - 10.1371/journal.pcbi.1002375 ID - Khatri2012 ER - TY - JOUR AU - Hofree, M. AU - Shen, J. P. AU - Carter, H. AU - Gross, A. AU - Ideker, T. PY - 2013 DA - 2013// TI - Network-based stratification of tumor mutations JO - Nat. Methods VL - 10 UR - https://doi.org/10.1038/nmeth.2651 DO - 10.1038/nmeth.2651 ID - Hofree2013 ER - TY - JOUR AU - Draghici, S. AU - Khatri, P. AU - Tarca, A. L. AU - Amin, K. AU - Done, A. AU - Voichita, C. PY - 2007 DA - 2007// TI - A systems biology approach for pathway level analysis JO - Genome Res. VL - 17 UR - https://doi.org/10.1101/gr.6202607 DO - 10.1101/gr.6202607 ID - Draghici2007 ER - TY - JOUR AU - Barabási, A. -. L. AU - Gulbahce, N. AU - Loscalzo, J. PY - 2011 DA - 2011// TI - Network medicine: a network-based approach to human disease JO - Nat Rev Genet VL - 12 UR - https://doi.org/10.1038/nrg2918 DO - 10.1038/nrg2918 ID - Barabási2011 ER - TY - STD TI - Rahnenführer J, Domingues FS, Maydt J, Lengauer T. Calculating the Statistical Significance of Changes in Pathway Activity From Gene Expression Data. Stat Appl Genet Mol Biol. 2004; 3(1). doi:10.2202/1544-6115.1055. 00005. Accessed 2013-04-24. ID - ref8 ER - TY - JOUR AU - Tarca, A. L. AU - Draghici, S. AU - Khatri, P. AU - Hassan, S. S. AU - Mittal, P. AU - Kim, J. -. S. PY - 2009 DA - 2009// TI - A novel signaling pathway impact analysis JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btn577 DO - 10.1093/bioinformatics/btn577 ID - Tarca2009 ER - TY - JOUR AU - Haynes, W. A. AU - Higdon, R. AU - Stanberry, L. AU - Collins, D. AU - Kolker, E. PY - 2013 DA - 2013// TI - Differential Expression Analysis for Pathways JO - PLoS Comput Biol VL - 9 UR - https://doi.org/10.1371/journal.pcbi.1002967 DO - 10.1371/journal.pcbi.1002967 ID - Haynes2013 ER - TY - JOUR AU - Subramanian, A. AU - Tamayo, P. AU - Mootha, V. K. AU - Mukherjee, S. AU - Ebert, B. L. AU - Gillette, M. A. PY - 2005 DA - 2005// TI - Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles JO - Proc Nat Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0506580102 DO - 10.1073/pnas.0506580102 ID - Subramanian2005 ER - TY - JOUR AU - Donato, M. AU - Xu, Z. AU - Tomoiaga, A. AU - Granneman, J. G. AU - MacKenzie, R. G. AU - Bao, R. PY - 2013 DA - 2013// TI - Analysis and correction of crosstalk effects in pathway analysis JO - Genome Res VL - 23 UR - https://doi.org/10.1101/gr.153551.112 DO - 10.1101/gr.153551.112 ID - Donato2013 ER - TY - JOUR AU - Network, T. C. G. A. PY - 2012 DA - 2012// TI - Comprehensive molecular portraits of human breast tumours JO - Nature VL - 490 UR - https://doi.org/10.1038/nature11412 DO - 10.1038/nature11412 ID - Network2012 ER - TY - JOUR AU - Richardson, A. L. AU - Wang, Z. C. AU - De Nicolo, A. AU - Lu, X. AU - Brown, M. AU - Miron, A. PY - 2006 DA - 2006// TI - X chromosomal abnormalities in basal-like human breast cancer JO - Cancer cell VL - 9 UR - https://doi.org/10.1016/j.ccr.2006.01.013 DO - 10.1016/j.ccr.2006.01.013 ID - Richardson2006 ER - TY - JOUR AU - Network, T. C. G. A. R. PY - 2011 DA - 2011// TI - Integrated genomic analyses of ovarian carcinoma JO - Nature VL - 474 UR - https://doi.org/10.1038/nature10166 DO - 10.1038/nature10166 ID - Network2011 ER - TY - JOUR AU - Cerami, E. G. AU - Gross, B. E. AU - Demir, E. AU - Rodchenkov, I. AU - Babur, O. AU - Anwar, N. PY - 2011 DA - 2011// TI - Pathway Commons, a web resource for biological pathway data JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkq1039 DO - 10.1093/nar/gkq1039 ID - Cerami2011 ER - TY - JOUR AU - Kelder, T. AU - van Iersel, M. P. AU - Hanspers, K. AU - Kutmon, M. AU - Conklin, B. R. AU - Evelo, C. T. PY - 2012 DA - 2012// TI - WikiPathways: building research communities on biological pathways JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr1074 DO - 10.1093/nar/gkr1074 ID - Kelder2012 ER - TY - JOUR AU - Cowley, M. J. AU - Pinese, M. AU - Kassahn, K. S. AU - Waddell, N. AU - Pearson, J. V. AU - Grimmond, S. M. PY - 2012 DA - 2012// TI - PINA v2.0: mining interactome modules JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr967 DO - 10.1093/nar/gkr967 ID - Cowley2012 ER - TY - JOUR AU - Laakso, M. AU - Hautaniemi, S. PY - 2010 DA - 2010// TI - Integrative platform to translate gene sets to networks JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq277 DO - 10.1093/bioinformatics/btq277 ID - Laakso2010 ER - TY - JOUR AU - Ovaska, K. AU - Laakso, M. AU - Haapa-Paananen, S. AU - Louhimo, R. AU - Chen, P. AU - Aittomäki, V. PY - 2010 DA - 2010// TI - Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme JO - Genome Med VL - 2 UR - https://doi.org/10.1186/gm186 DO - 10.1186/gm186 ID - Ovaska2010 ER - TY - JOUR AU - Edgar, R. AU - Domrachev, M. AU - Lash, A. E. PY - 2002 DA - 2002// TI - Gene Expression Omnibus: NCBI gene expression and hybridization array data repository JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.1.207 DO - 10.1093/nar/30.1.207 ID - Edgar2002 ER - TY - JOUR AU - Irizarry, R. A. AU - Hobbs, B. AU - Collin, F. AU - Beazer-Barclay, Y. D. AU - Antonellis, K. J. AU - Scherf, U. PY - 2003 DA - 2003// TI - Exploration, normalization, and summaries of high density oligonucleotide array probe level data JO - Biostatistics (Oxford, England) VL - 4 UR - https://doi.org/10.1093/biostatistics/4.2.249 DO - 10.1093/biostatistics/4.2.249 ID - Irizarry2003 ER - TY - JOUR AU - Huang, D. W. AU - Sherman, B. T. AU - Lempicki, R. A. PY - 2009 DA - 2009// TI - Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources JO - Nat Protoc VL - 4 UR - https://doi.org/10.1038/nprot.2008.211 DO - 10.1038/nprot.2008.211 ID - Huang2009 ER - TY - JOUR AU - Benjamini, Y. AU - Hochberg, Y. PY - 1995 DA - 1995// TI - Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing JO - Journal of the Royal Statistical Society. Series B (Methodological) VL - 57 ID - Benjamini1995 ER - TY - JOUR AU - Ossovskaya, V. AU - Wang, Y. AU - Budoff, A. AU - Xu, Q. AU - Lituev, A. AU - Potapova, O. PY - 2011 DA - 2011// TI - Exploring Molecular Pathways of Triple-Negative Breast Cancer JO - Genes Cancer VL - 2 UR - https://doi.org/10.1177/1947601911432496 DO - 10.1177/1947601911432496 ID - Ossovskaya2011 ER - TY - JOUR AU - Podo, F. AU - Buydens, L. M. C. AU - Degani, H. AU - Hilhorst, R. AU - Klipp, E. AU - Gribbestad, I. S. PY - 2010 DA - 2010// TI - Triple-negative breast cancer: Present challenges and new perspectives JO - Mol Oncol VL - 4 UR - https://doi.org/10.1016/j.molonc.2010.04.006 DO - 10.1016/j.molonc.2010.04.006 ID - Podo2010 ER - TY - JOUR AU - Hwang, K. -. T. AU - Woo, J. W. AU - Shin, H. C. AU - Kim, H. S. AU - Ahn, S. K. AU - Moon, H. -. G. PY - 2012 DA - 2012// TI - Prognostic influence of BCL2 expression in breast cancer JO - Int J Cancer J Int Du Cancer VL - 131 UR - https://doi.org/10.1002/ijc.27539 DO - 10.1002/ijc.27539 ID - Hwang2012 ER - TY - JOUR AU - Nakshatri, H. AU - Badve, S. PY - 2007 DA - 2007// TI - FOXA1 as a therapeutic target for breast cancer JO - Expert Opin Ther Targets VL - 11 UR - https://doi.org/10.1517/14728222.11.4.507 DO - 10.1517/14728222.11.4.507 ID - Nakshatri2007 ER - TY - JOUR AU - Hollmén, M. AU - Määttä, J. A. AU - Bald, L. AU - Sliwkowski, M. X. AU - Elenius, K. PY - 2009 DA - 2009// TI - Suppression of breast cancer cell growth by a monoclonal antibody targeting cleavable ErbB4 isoforms JO - Oncogene VL - 28 UR - https://doi.org/10.1038/onc.2008.481 DO - 10.1038/onc.2008.481 ID - Hollmén2009 ER - TY - JOUR AU - Frings, O. AU - Augsten, M. AU - Tobin, N. P. AU - Carlson, J. AU - Paulsson, J. AU - Pena, C. PY - 2013 DA - 2013// TI - Prognostic Significance in Breast Cancer of a Gene Signature Capturing Stromal PDGF Signaling JO - Am J Pathol VL - 182 UR - https://doi.org/10.1016/j.ajpath.2013.02.018 DO - 10.1016/j.ajpath.2013.02.018 ID - Frings2013 ER - TY - JOUR AU - Wäsch, R. AU - Robbins, J. A. AU - Cross, F. R. PY - 2009 DA - 2009// TI - The emerging role of APC/CCdh1 in controlling differentiation, genomic stability and tumor suppression JO - Oncogene VL - 29 UR - https://doi.org/10.1038/onc.2009.325 DO - 10.1038/onc.2009.325 ID - Wäsch2009 ER - TY - JOUR AU - Yan, X. AU - Chua, M. -. S. AU - He, J. AU - So, S. K. PY - 2008 DA - 2008// TI - Small interfering RNA targeting CDC25b inhibits liver tumor growth in vitro and in vivo JO - Molecular Cancer VL - 7 UR - https://doi.org/10.1186/1476-4598-7-19 DO - 10.1186/1476-4598-7-19 ID - Yan2008 ER - TY - JOUR AU - Nakayama, N. AU - Nakayama, K. AU - Shamima, Y. AU - Ishikawa, M. AU - Katagiri, A. AU - Iida, K. PY - 2010 DA - 2010// TI - Gene amplification CCNE1 is related to poor survival and potential therapeutic target in ovarian cancer JO - Cancer VL - 116 ID - Nakayama2010 ER - TY - JOUR AU - Gonzalez, S. AU - Klatt, P. AU - Delgado, S. AU - Conde, E. AU - Lopez-Rios, F. AU - Sanchez-Cespedes, M. PY - 2006 DA - 2006// TI - Oncogenic activity of Cdc6 through repression of the INK4/ARF locus JO - Nature VL - 440 UR - https://doi.org/10.1038/nature04585 DO - 10.1038/nature04585 ID - Gonzalez2006 ER - TY - JOUR AU - Nisman, B. AU - Allweis, T. AU - Kaduri, L. AU - Maly, B. AU - Gronowitz, S. AU - Hamburger, T. PY - 2010 DA - 2010// TI - Serum thymidine kinase 1 activity in breast cancer JO - Cancer Biomarkers: Sect A Dis Markers VL - 7 ID - Nisman2010 ER - TY - JOUR AU - Zhang, K. AU - Hu, S. AU - Wu, J. AU - Chen, L. AU - Lu, J. AU - Wang, X. PY - 2009 DA - 2009// TI - Overexpression of RRM2 decreases thrombspondin-1 and increases VEGF production in human cancer cells in vitro and in vivo: implication of RRM2 in angiogenesis JO - Mol Cancer VL - 8 UR - https://doi.org/10.1186/1476-4598-8-11 DO - 10.1186/1476-4598-8-11 ID - Zhang2009 ER - TY - JOUR AU - Liu, H. AU - Kato, Y. AU - Erzinger, S. A. AU - Kiriakova, G. M. AU - Qian, Y. AU - Palmieri, D. PY - 2012 DA - 2012// TI - The role of MMP-1 in breast cancer growth and metastasis to the brain in a xenograft model JO - BMC cancer VL - 12 UR - https://doi.org/10.1186/1471-2407-12-583 DO - 10.1186/1471-2407-12-583 ID - Liu2012 ER - TY - JOUR AU - Parker, J. S. AU - Mullins, M. AU - Cheang, M. C. U. AU - Leung, S. AU - Voduc, D. AU - Vickery, T. PY - 2009 DA - 2009// TI - Supervised risk predictor of breast cancer based on intrinsic subtypes JO - J Clin Oncol: Official J Am Soc Clin Oncol VL - 27 UR - https://doi.org/10.1200/JCO.2008.18.1370 DO - 10.1200/JCO.2008.18.1370 ID - Parker2009 ER - TY - JOUR AU - Kreike, B. AU - Kouwenhove, M. V. AU - Horlings, H. AU - Weigelt, B. AU - Peterse, H. AU - Bartelink, H. PY - 2007 DA - 2007// TI - Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas JO - Breast Cancer Res VL - 9 UR - https://doi.org/10.1186/bcr1771 DO - 10.1186/bcr1771 ID - Kreike2007 ER - TY - JOUR AU - Oakman, C. AU - Viale, G. AU - Di Leo, A. PY - 2010 DA - 2010// TI - Management of triple negative breast cancer JO - Breast VL - 19 UR - https://doi.org/10.1016/j.breast.2010.03.026 DO - 10.1016/j.breast.2010.03.026 ID - Oakman2010 ER - TY - JOUR AU - Gazinska, P. AU - Grigoriadis, A. AU - Brown, J. P. AU - Millis, R. R. AU - Mera, A. AU - Gillett, C. E. PY - 2013 DA - 2013// TI - Comparison of basal-like triple-negative breast cancer defined by morphology, immunohistochemistry and transcriptional profiles JO - Mod Pathol: Official J US Can Acad Pathol, Inc VL - 26 UR - https://doi.org/10.1038/modpathol.2012.244 DO - 10.1038/modpathol.2012.244 ID - Gazinska2013 ER - TY - JOUR AU - Hurtado, A. AU - Holmes, K. A. AU - Ross-Innes, C. S. AU - Schmidt, D. AU - Carroll, J. S. PY - 2011 DA - 2011// TI - FOXA1 is a key determinant of estrogen receptor function and endocrine response JO - Nat Genet VL - 43 UR - https://doi.org/10.1038/ng.730 DO - 10.1038/ng.730 ID - Hurtado2011 ER - TY - JOUR AU - Mehta, R. J. AU - Jain, R. K. AU - Leung, S. AU - Choo, J. AU - Nielsen, T. AU - Huntsman, D. PY - 2012 DA - 2012// TI - FOXA1 is an independent prognostic marker for ER-positive breast cancer JO - Breast Cancer Res Treat VL - 131 UR - https://doi.org/10.1007/s10549-011-1482-6 DO - 10.1007/s10549-011-1482-6 ID - Mehta2012 ER - TY - JOUR AU - Bernardo, G. M. AU - Bebek, G. AU - Ginther, C. L. AU - Sizemore, S. T. AU - Lozada, K. L. AU - Miedler, J. D. PY - 2013 DA - 2013// TI - FOXA1 represses the molecular phenotype of basal breast cancer cells JO - Oncogene VL - 32 UR - https://doi.org/10.1038/onc.2012.62 DO - 10.1038/onc.2012.62 ID - Bernardo2013 ER - TY - JOUR AU - Carey, L. A. AU - Dees, E. C. AU - Sawyer, L. AU - Gatti, L. AU - Moore, D. T. AU - Collichio, F. PY - 2007 DA - 2007// TI - The Triple Negative Paradox: Primary Tumor Chemosensitivity of Breast Cancer Subtypes JO - Clin Cancer Res VL - 13 UR - https://doi.org/10.1158/1078-0432.CCR-06-1109 DO - 10.1158/1078-0432.CCR-06-1109 ID - Carey2007 ER - TY - JOUR AU - Melchor, L. AU - Saucedo-Cuevas, L. P. AU - Muñoz-Repeto, I. AU - Rodríguez-Pinilla, S. M. AU - Honrado, E. AU - Campoverde, A. PY - 2009 DA - 2009// TI - Comprehensive characterization of the DNA amplification at 13q34 in human breast cancer reveals TFDP1 and CUL4a as likely candidate target genes JO - Breast Cancer Res VL - 11 UR - https://doi.org/10.1186/bcr2456 DO - 10.1186/bcr2456 ID - Melchor2009 ER - TY - JOUR AU - Abba, M. C. AU - Fabris, V. T. AU - Hu, Y. AU - Kittrell, F. S. AU - Cai, W. -. W. AU - Donehower, L. A. PY - 2007 DA - 2007// TI - Identification of Novel Amplification Gene Targets in Mouse and Human Breast Cancer at a Syntenic Cluster Mapping to Mouse ch8a1 and Human ch13q34 JO - Cancer Res VL - 67 UR - https://doi.org/10.1158/0008-5472.CAN-06-4672 DO - 10.1158/0008-5472.CAN-06-4672 ID - Abba2007 ER - TY - JOUR AU - Signoretti, S. AU - Di Marcotullio, L. AU - Richardson, A. AU - Ramaswamy, S. AU - Isaac, B. AU - Rue, M. PY - 2002 DA - 2002// TI - Oncogenic role of the ubiquitin ligase subunit Skp2 in human breast cancer JO - J Clin Invest VL - 110 UR - https://doi.org/10.1172/JCI0215795 DO - 10.1172/JCI0215795 ID - Signoretti2002 ER - TY - JOUR AU - Sieuwerts, A. M. AU - Look, M. P. AU - Meijer-van Gelder, M. E. AU - Timmermans, M. AU - Trapman, A. M. A. C. AU - Garcia, R. R. PY - 2006 DA - 2006// TI - Which cyclin E prevails as prognostic marker for breast cancer? Results from a retrospective study involving 635 lymph node-negative breast cancer patients JO - Clin cancer Res: Official J Am Assoc Cancer Res VL - 12 UR - https://doi.org/10.1158/1078-0432.CCR-06-0225 DO - 10.1158/1078-0432.CCR-06-0225 ID - Sieuwerts2006 ER - TY - JOUR AU - Chan, C. -. H. AU - Morrow, J. AU - Li, C. -. F. AU - Gao, Y. AU - Jin, G. AU - Moten, A. PY - 2013 DA - 2013// TI - Pharmacological Inactivation of Skp2 SCF Ubiquitin Ligase Restricts Cancer Stem Cell Traits and Cancer Progression JO - Cell VL - 154 UR - https://doi.org/10.1016/j.cell.2013.06.048 DO - 10.1016/j.cell.2013.06.048 ID - Chan2013 ER - TY - JOUR AU - Siegel, R. L. AU - Miller, K. D. AU - Jemal, A. PY - 2015 DA - 2015// TI - Cancer statistics, 2015 JO - CA: Cancer J Clinicians VL - 65 ID - Siegel2015 ER - TY - JOUR AU - Zhao, F. AU - Siu, M. K. Y. AU - Jiang, L. AU - Tam, K. F. AU - Ngan, H. Y. S. AU - Le, X. F. PY - 2014 DA - 2014// TI - Overexpression of forkhead box protein M1 (FOXM1) in ovarian cancer correlates with poor patient survival and contributes to paclitaxel resistance JO - PloS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0113478 DO - 10.1371/journal.pone.0113478 ID - Zhao2014 ER - TY - JOUR AU - Washio, T. AU - Motoda, H. PY - 2003 DA - 2003// TI - State of the Art of Graph-based Data Mining JO - SIGKDD Explor Newsl VL - 5 UR - https://doi.org/10.1145/959242.959249 DO - 10.1145/959242.959249 ID - Washio2003 ER -