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39. Sparkman L, Chandru H, Boggaram V: Ceramide decreases surfactant protein B gene expression via downregulation of TTF-1 DNA binding activity. Am J Physiol Lung Cell Mol Physiol 2006, 290(2):L351-358. 40. Wright JR: Immunoregulatory functions of surfactant proteins. Nat Rev Immunol 2005, 5(1):58-68. 41. Yang L, Yan D, Yan C, Du H: Peroxisome proliferator-activated receptor gamma and ligands inhibit surfactant protein B gene expression in the lung. J Biol Chem 2003, 278(38):36841-36847. 42. Kargi A, Gurel D, Tuna B: The diagnostic value of TTF-1, CK 5/6, and p63 immunostaining in classification of lung carcinomas. Appl Immunohistochem Mol Morphol 2007, 15(4):415-420. 43. Stefansson IM, Salvesen HB, Akslen LA: Loss of p63 and cytokeratin 5/6 expression is associated with more aggressive tumors in endometrial carcinoma patients. Int J Cancer 2006, 118(5):1227-1233. 44. Swarbrick A, Akerfeldt MC, Lee CS, Sergio CM, Caldon CE, Hunter LJ, Sutherland RL, Musgrove EA: Regulation of cyclin expression and cell cycle progression in breast epithelial cells by the helix-loop-helix protein Id1. Oncogene 2005, 24(3):381-389. 45. Zhang X, Ling MT, Wang Q, Lau CK, Leung SC, Lee TK, Cheung AL, Wong YC, Wang X: Identification of a novel inhibitor of differentiation-1 (ID-1) binding partner, caveolin-1, and its role in epithelial-mesenchymal transition and resistance to apoptosis in prostate cancer cells. J Biol Chem 2007, 282(46):33284-33294. 46. Korchynskyi O, ten Dijke P: Identification and functional characterization of distinct critically important bone morphogenetic protein-specific response elements in the Id1 promoter. J Biol Chem 2002, 277(7):4883-4891. 47. Pruneri G, Pignataro L, Valentini S, Fabris S, Maisonneuve P, Carboni N, Pece S, Capra M, Del Curto B, Neri A et al: Cyclin D3 immunoreactivity is an independent predictor of survival in laryngeal squamous cell carcinoma. Clin Cancer Res 2005, 11(1):242-248. 48. Zhao Y, Hamza MS, Leong HS, Lim CB, Pan YF, Cheung E, Soo KC, Iyer NG: Kruppel-like factor 5 modulates p53-independent apoptosis through Pim1 survival kinase in cancer cells. Oncogene 2008, 27(1):1-8. 49. Nandan MO, Chanchevalap S, Dalton WB, Yang VW: Kruppel-like factor 5 promotes mitosis by activating the cyclin B1/Cdc2 complex during oncogenic Ras-mediated transformation. FEBS Lett 2005, 579(21):4757-4762. 50. Li HH, Cai X, Shouse GP, Piluso LG, Liu X: A specific PP2A regulatory subunit, B56gamma, mediates DNA damage-induced dephosphorylation of p53 at Thr55. Embo J 2007, 26(2):402-411. 170
51. Shouse GP, Cai X, Liu X: Serine 15 phosphorylation of p53 directs its interaction with B56gamma and the tumor suppressor activity of B56gamma-specific protein phosphatase 2A. Mol Cell Biol 2008, 28(1):448-456. 171
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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
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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 and 180: 30. Delaval B, Ferrand A, Conte N,
Page 181: 27. Bai J, Cederbaum AI: Catalase p
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