Analyzing the basic principles of tissue microarray data measuring the cooperative phenomena of marker proteins in invasive breast cancer

References

• Botstein D, Fink GR. Yeast: an experimental organism for 21st century biology. Genetics. 2011;189(3):695–704.
   PubMed Web of Science ®Google Scholar
• Vidal M, Cusick ME, Barabasi AL. Interactome networks and human disease. Cell. 2011;144(6):986–998.
   PubMed Web of Science ®Google Scholar
• Reverter A, Chan EK. Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks. Bioinformatics. 2008;24(21):2491–2497.
   Web of Science ®Google Scholar
• Gunsalus KC, Rhrissorrakrai K. Networks in Caenorhabditis elegans. Curr Opin Genet Dev. 2011;21(6):787–798.
   Web of Science ®Google Scholar
• Costanzo M, Baryshnikova A, Bellay J, et al. The genetic landscape of a cell. Science. 2010;327(5964):425–431.
   PubMed Web of Science ®Google Scholar
• Baba K, Shibata R, Sibuya M. Partial correlation and conditional correlation as measures of conditional independence. Aust N Z J Stat. 2004;46(4):657–664.
   Web of Science ®Google Scholar
• Peng X, Li Y, Walters KA, et al. Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers. BMC Genomics. 2009;10:373.
   PubMed Web of Science ®Google Scholar
• Szederkenyi G, Banga JR, Alonso AA. Inference of complex biological networks: distinguishability issues and optimization-based solutions. BMCSystBiol. 2011;5:177.
   Google Scholar
• Kononen J, Bubendorf L, Kallioniemi A, et al. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat Med. 1998;4(7):844–847.
   PubMed Web of Science ®Google Scholar
• Moch H, Kononen T, Kallioniemi OP, Sauter G. Tissue microarrays: what will they bring to molecular and anatomic pathology? Adv Anat Pathol. 2001;8(1):14–20.
   PubMed Web of Science ®Google Scholar
• Packeisen J, Korsching E, Herbst H, Boecker W, Buerger H. Demystified ... tissue microarray technology. Mol Pathol. 2003;56(4):198–204.
   PubMedGoogle Scholar
• Chrysovergis A, Gorgoulis VG, Giotakis I, et al. Simultaneous over activation of EGFR, telomerase (h TERT), and cyclin D1 correlates with advanced disease in larynx squamous cell carcinoma: a tissue microarray analysis. Med Oncol. 2011;28(3):871–877.
   Web of Science ®Google Scholar
• Chatterjee SK, Zetter BR. Cancer biomarkers: knowing the present and predicting the future. Future Oncol. 2005;1(1):37–50.
   Google Scholar
• West RB, van de Rijn M. The role of microarray technologies in the study of soft tissue tumours. Histopathology. 2006;48(1):22–31.
   Web of Science ®Google Scholar
• Hewitt SM. The application of tissue microarrays in the validation of microarray results. Methods Enzymol. 2006;410:400–415.
   PubMed Web of Science ®Google Scholar
• Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559.
   PubMed Web of Science ®Google Scholar
• Abd El-Rehim DM, Pinder SE, Paish CE, et al. Expression of luminal and basal cytokeratins in human breast carcinoma. J Pathol. 2004;203(2):661–671.
   PubMed Web of Science ®Google Scholar
• Korsching E, Jeffrey SS, Meinerz W, Decker T, Boecker W, Buerger H. Basal carcinoma of the breast revisited: an old entity with new interpretations. J Clin Pathol. 2008;61(5):553–560.
   PubMed Web of Science ®Google Scholar
• Kononen J, Bubendorf L, Kallioniemi A, et al. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat Med. 1998;4(7):844–847.
   PubMed Web of Science ®Google Scholar
• Packeisen J, Buerger H, Krech R, Boecker W. Tissue microarrays: a new approach for quality control in immunohistochemistry. J Clin Pathol. 2002;55(8):613–615.
   PubMed Web of Science ®Google Scholar
• Korsching E, Packeisen J, Agelopoulos K, et al. Cytogenetic alterations and cytokeratin expression patterns in breast cancer: integrating a new model of breast differentiation into cytogenetic pathways of breast carcinogenesis. Lab Invest. 2002;82(11):1525–1533.
   PubMed Web of Science ®Google Scholar
• Korsching E, Packeisen J, Liedtke C, et al. The origin of vimentin expression in invasive breast cancer: epithelial-mesenchymal transition, myoepithelial histogenesis or histogenesis from progenitor cells with bilinear differentiation potential? J Pathol. 2005;206(4):451–457.
   Web of Science ®Google Scholar
• Pearson K. Determination of the coefficient of correlation. Science. 1909;30(757):23–25.
   PubMedGoogle Scholar
• Efron B, Tibshirani RJ. An Introduction to the Bootstrap. New York: Chapman and Hall; 1993.
   Google Scholar
• Manly BFJ. Randomization, Bootstrap and Monte Carlo Methods in Biology. London: Chapman and Hall; 1997.
   Google Scholar
• Myrvold WC. Probabilities in statistical mechanics: what are they? 2012. Available from: http://philsci-archive.pitt.edu/9236/47Stat MechProbsPhilSciRevised.pdf. Accessed November 22, 2012.
   Google Scholar
• Shao MM, Chan SK, Yu AM, et al. Keratin expression in breast cancers. Virchows Arch. 2012;461(3):313–322.
   PubMed Web of Science ®Google Scholar
• Abd El-Rehim DM, Ball G, Pinder SE, et al. High-throughput protein expression analysis using tissue microarray technology of a large well- characterised series identifies biologically distinct classes of breast cancer confirming recent cDNA expression analyses. Int J Cancer. 2005;116(3):340–350.
   Web of Science ®Google Scholar
• Chen MH, Yip GW, Tse GM, et al. Expression of basal keratins and vimentin in breast cancers of young women correlates with adverse pathologic parameters. Mod Pathol. 2008;21(10):1183–1191.
   Web of Science ®Google Scholar
• Choo JR, Nielsen TO. Biomarkers for basal-like breast cancer. Cancers. 2010;2(2):1040–1065.
   PubMedGoogle Scholar
• Sarrio D, Rodriguez-Pinilla SM, Hardisson D, Cano A, Moreno-Bueno G, Palacios J. Epithelial-mesenchymal transition in breast cancer relates to the basal-like phenotype. Cancer Res. 2008;68(4):989–997.
   PubMed Web of Science ®Google Scholar
• van de Rijn M, Perou CM, Tibshirani R, et al. Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome. Am J Pathol. 2002;161(6):1991–1996.
   PubMed Web of Science ®Google Scholar
• Schymik B, Buerger H, Krämer A, et al. Is there “progression through grade” in ductal invasive breast cancer? Breast Cancer Res Treat. 2012;135(3):693–703.
   Web of Science ®Google Scholar
• Shen MK. Algorithm 202: generation of permutations in lexicographical order. Commun ACM. 1963;6(9):517.
   Google Scholar