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14. Everson Richard M. JF: Multi-class ROC analysis from a multi-objective optimisation perspective. Pattern Recognition Letters 2006, 27(8):22. 15. Delaval B, Ferrand A, Conte N, Larroque C, Hernandez-Verdun D, Prigent C, Birnbaum D: Aurora B -TACC1 protein complex in cytokinesis. Oncogene 2004, 23(26):4516- 4522. 16. Conte N, Delaval B, Ginestier C, Ferrand A, Isnardon D, Larroque C, Prigent C, Seraphin B, Jacquemier J, Birnbaum D: TACC1-chTOG-Aurora A protein complex in breast cancer. Oncogene 2003, 22(50):8102-8116. 17. Conte N, Charafe-Jauffret E, Delaval B, Adelaide J, Ginestier C, Geneix J, Isnardon D, Jacquemier J, Birnbaum D: Carcinogenesis and translational controls: TACC1 is down-regulated in human cancers and associates with mRNA regulators. Oncogene 2002, 21(36):5619-5630. 18. Gergely F, Karlsson C, Still I, Cowell J, Kilmartin J, Raff JW: The TACC domain identifies a family of centrosomal proteins that can interact with microtubules. Proc Natl Acad Sci U S A 2000, 97(26):14352-14357. 19. Gergely F: Centrosomal TACCtics. Bioessays 2002, 24(10):915-925. 20. Forbes A, Wadehra M, Mareninov S, Morales S, Shimazaki K, Gordon LK, Braun J: The tetraspan protein EMP2 regulates expression of caveolin-1. J Biol Chem 2007, 282(36):26542-26551. 21. Ho CC, Huang PH, Huang HY, Chen YH, Yang PC, Hsu SM: Up-regulated caveolin-1 accentuates the metastasis capability of lung adenocarcinoma by inducing filopodia formation. Am J Pathol 2002, 161(5):1647-1656. 22. Govers R, van der Sluijs P, van Donselaar E, Slot JW, Rabelink TJ: Endothelial nitric oxide synthase and its negative regulator caveolin-1 localize to distinct perinuclear organelles. J Histochem Cytochem 2002, 50(6):779-788. 23. Mundy DI, Machleidt T, Ying YS, Anderson RG, Bloom GS: Dual control of caveolar membrane traffic by microtubules and the actin cytoskeleton. J Cell Sci 2002, 115(Pt 22):4327-4339. 24. Thomas CM, Smart EJ: Caveolae structure and function. J Cell Mol Med 2008, 12(3):796-809. 25. Goligorsky MS, Li H, Brodsky S, Chen J: Relationships between caveolae and eNOS: everything in proximity and the proximity of everything. Am J Physiol Renal Physiol 2002, 283(1):F1-10. 26. Yano S, Yano N: Regulation of catalase enzyme activity by cell signaling molecules. Mol Cell Biochem 2002, 240(1-2):119-130. 168
27. Bai J, Cederbaum AI: Catalase protects HepG2 cells from apoptosis induced by DNA-damaging agents by accelerating the degradation of p53. J Biol Chem 2003, 278(7):4660-4667. 28. Kondo T, Kitano T, Iwai K, Watanabe M, Taguchi Y, Yabu T, Umehara H, Domae N, Uchiyama T, Okazaki T: Control of ceramide-induced apoptosis by IGF-1: involvement of PI-3 kinase, caspase-3 and catalase. Cell Death Differ 2002, 9(6):682- 692. 29. Oshiro MM, Futscher BW, Lisberg A, Wozniak RJ, Klimecki WT, Domann FE, Cress AE: Epigenetic regulation of the cell type-specific gene 14-3-3sigma. Neoplasia 2005, 7(9):799-808. 30. Yang HY, Wen YY, Chen CH, Lozano G, Lee MH: 14-3-3 sigma positively regulates p53 and suppresses tumor growth. Mol Cell Biol 2003, 23(20):7096-7107. 31. Zhang Y, Karas M, Zhao H, Yakar S, LeRoith D: 14-3-3sigma mediation of cell cycle progression is p53-independent in response to insulin-like growth factor-I receptor activation. J Biol Chem 2004, 279(33):34353-34360. 32. Dubois T, Paleotti O, Mironov AA, Fraisier V, Stradal TE, De Matteis MA, Franco M, Chavrier P: Golgi-localized GAP for Cdc42 functions downstream of ARF1 to control Arp2/3 complex and F-actin dynamics. Nat Cell Biol 2005, 7(4):353-364. 33. Kaneda A, Kaminishi M, Sugimura T, Ushijima T: Decreased expression of the seven ARP2/3 complex genes in human gastric cancers. Cancer Lett 2004, 212(2):203-210. 34. Taira K, Umikawa M, Takei K, Myagmar BE, Shinzato M, Machida N, Uezato H, Nonaka S, Kariya K: The Traf2- and Nck-interacting kinase as a putative effector of Rap2 to regulate actin cytoskeleton. J Biol Chem 2004, 279(47):49488-49496. 35. Heale JT, Ball AR, Jr., Schmiesing JA, Kim JS, Kong X, Zhou S, Hudson DF, Earnshaw WC, Yokomori K: Condensin I interacts with the PARP-1-XRCC1 complex and functions in DNA single-strand break repair. Mol Cell 2006, 21(6):837-848. 36. Maeda Y, Hunter TC, Loudy DE, Dave V, Schreiber V, Whitsett JA: PARP-2 interacts with TTF-1 and regulates expression of surfactant protein-B. J Biol Chem 2006, 281(14):9600-9606. 37. Brasch F, Johnen G, Winn-Brasch A, Guttentag SH, Schmiedl A, Kapp N, Suzuki Y, Muller KM, Richter J, Hawgood S et al: Surfactant protein B in type II pneumocytes and intra-alveolar surfactant forms of human lungs. Am J Respir Cell Mol Biol 2004, 30(4):449-458. 38. Das A, Boggaram V: Proteasome dysfunction inhibits surfactant protein gene expression in lung epithelial cells: mechanism of inhibition of SP-B gene expression. Am J Physiol Lung Cell Mol Physiol 2007, 292(1):L74-84. 169
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An Adenocarcinoma Case Study of the
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DEDICATION The work presented in th
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TABLE OF CONTENTS LIST OF TABLES ..
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Conclusion.........................
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LIST OF FIGURES Figure Page Figure
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violate the linear correlation rela
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Chapter 1: An Introduction to Micro
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previously stated, rigorous reagent
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Factors influencing Signal Interpre
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likelihood that no such structural
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hybridization and multiple dye stra
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classical reaction equations, modif
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prevent the hybridization of probes
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platforms are used to deposit them
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and chip layout [64]. In particular
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whether analyses based upon individ
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The process of determining a candid
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implemented in order to demonstrate
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affecting probe-target duplex forma
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It has long been known that the var
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probes can thus be reincorporated i
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(Carr, ms in review). This ProbeFAT
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have specific attributes which can
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elow saturation. The investigator m
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a. A filter based on how many probe
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means. The remaining sets possess s
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for the 24 samples in the Lu, et al
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Table 2.1: Probe Numbers per filter
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the effect can be. Both the type of
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described above. In Figure 2.3, the
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various data processing stages are
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position of the probe on the transc
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Figure 2.5: BaFL consistency. Demon
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Figure 2.6: Probe-Transcript region
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Table 2.3: ProbeSet behavior predic
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cleansing process. This is demonstr
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Table 2.4: ProbeSet behavior of pro
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A Priori Prediction We demonstrated
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Conclusion We have presented a comp
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mind that they are most aware of th
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Probe Cleansing Methods The BaFL pr
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are significant assume such a data
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cleansing process and were assessed
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sample selection, with replacement,
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Figure 3.1: P value distributions.
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Figure 3.2: Down selection models-
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cleansing methods were used to gene
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Discussion A striking result from t
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Figure 3.6: Concordance summary. Th
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whole model analysis without permut
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change, apparently the greater vari
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though in Chapter 2 we showed that
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Although a list of 325 candidate ge
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was determined to consist of 30 Pro
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Figure 4.1: Non-traditional PCA ana
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for the RMA and dCHIP interpretatio
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was one of them: it is counted as p
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Figure 4.5: Kaplan-Meyer survival c
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Figure 4.7: Low grade tumor surviva
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The candidate gene list values were
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ejecting the null hypothesis [8], a
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Figure 4.9: GO connectivity of cand
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under linear and non-linear dimensi
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sample cleansing process and these
Page 129 and 130: averaged to give a final approximat
Page 131 and 132: 119 Table 5.1: : NSCLC candidate ge
Page 133 and 134: Figure 5.1: NSCLC ProbeSet gain sel
Page 135 and 136: Figure 5.3: NSCLC refined average p
Page 137 and 138: statistical criterion, but it appea
Page 139 and 140: lacking p53 mutations [30]. While,
Page 141 and 142: Kruppel-like factor 5 (KLF5) has al
Page 143 and 144: Appendix A # This is the main drive
Page 145 and 146: def Driver(usr, pswd, db, logfile,
Page 147 and 148: def DriverXH(usr, pswd, db, logfile
Page 149 and 150: fp.write('\tTable '), fp.write(msk[
Page 151 and 152: #determine outliers lowrs1=nonzero(
Page 153 and 154: tmp="update sample_mask set exclude
Page 155 and 156: fp.write('\n'+msk[ptr[j]]+' exclude
Page 157 and 158: cur, conn=UpdateWorkReg(cur, conn,
Page 159 and 160: Appendix E # The result of permutin
Page 161 and 162: BIBLIOGRAPHY 149
Page 163 and 164: 13. Bowtell DD: Options available--
Page 165 and 166: method addressing dye, intensity-de
Page 167 and 168: 73. Alter O, Brown PO, Botstein D:
Page 169 and 170: 11. Kumari S, Verma LK, Weller JW:
Page 171 and 172: 38. Michael Stonebraker LAR, Michae
Page 173 and 174: 64. Cropp CS, Lidereau R, Leone A,
Page 175 and 176: 15. Irizarry RA: affy. In.: Biocond
Page 177 and 178: Chapter 4: 1. Minna JD, Roth JA, Ga
Page 179: 30. Delaval B, Ferrand A, Conte N,
Page 183 and 184: 51. Shouse GP, Cai X, Liu X: Serine
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