Methods of Microarray Data Analysis IV

Contributing Authors ix Preface xiii Acknowledgments xv Introduction 1 CANCER: CLINICAL CHALLENGES AND OPPORTUNITIES DAVID G. BEER 9 GENE EXPRESSION DATA AND SURVIVAL ANALYSIS PETER J. PARK 21 THE NEEDED REPLICATES OF ARRAYS IN MICROARRAY EXPERIMENTS FOR RELIABLE STATISTICAL EVALUATION SUE-JANEWANG, JAMES J. CHEN 35 POOLING INFORMATION ACROSS DIFFERENT STUDIES AND OLIGONUCLEOTIDE CHIP TYPES TO IDENTIFY PROGNOSTIC GENES FOR LUNG CANCER JEFFREY S.MORRIS, GUOSHENG YIN, KEITH BAGGERLY, CHUNLEI WU, AND LI ZHANG 51 vi Contents APPLICATION OF SURVIVAL AND META-ANALYSIS TO GENE EXPRESSION DATA COMBINED FROM TWO STUDIES LINDAWARNOCK, RICHARD STEPHENS, JOANN COLEMAN 67 MAKING SENSE OF HUMAN LUNG CARCINOMAS GENE EXPRESSION DATA: INTEGRATION AND ANALYSIS OF TWO AFFYMETRIX PLATFORM EXPERIMENTS XIWU LIN, DANIEL PARK, SERGIO ESLAVA, KWAN R. LEE, RAYMOND L.H. LAM, AND LEI A. ZHU 81 ENTROPY AND SURVIVAL-BASED WEIGHTS TO COMBINE AFFYMETRIX ARRAY TYPES AND ANALYZE DIFFERENTIAL EXPRESSION AND SURVIVAL JIANHUA HU, GUOSHENG YIN, JEFFREY S. MORRIS, LI ZHANG, FRED A. WRIGHT 95 ASSOCIATING MICROARRAY DATA WITH A SURVIVAL ENDPOINT SIN-HO JUNG, KOUROS OWZAR, STEPHEN GEORGE 109 DIFFERENTIAL CORRELATION DETECTS COMPLEX ASSOCIATIONS BETWEEN GENE EXPRESSION AND CLINICAL OUTCOMES IN LUNG ADENOCARCINOMAS KERBY SHEDDEN AND JEREMY TAYLOR 121 PROBABILISTIC LUNG CANCER MODELS CONDITIONED ON GENE EXPRESSION MICROARRAY DATA CRAIG FRIEDMAN, WENBO CAO, AND CHENG FAN 133 INTEGRATION OF MICROARRAY DATA FOR A COMPARATIVE STUDY OF CLASSIFIERS AND IDENTIFICATION OF MARKER GENES 147 DANIEL BERRAR, BRIAN STURGEON, IAN BRADBURY, C. STEPHEN DOWNES, AND WERNER DUBITZKY USE OF MICROARRAY DATA VIA MODEL-BASED CLASSIFICATION IN THE STUDY AND PREDICTION OF SURVIVAL FROM LUNG CANCER LIAT BEN-TOVIM JONES, SHU-KAY NG, CHRISTOPHE AMBROISE, KATRINAMONICO, NAZIM KHAN AND GEOFFMCLACHLAN 163 Methods of microarray data analysis IV vii MICROARRAY DATA ANALYSIS OF SURVIVAL TIMES OF PATIENTS WITH LUNG ADENOCARCINOMAS USING ADC AND K-MEDIANS CLUSTERING WENTING ZHOU, WEICHENWU, NATHAN PALMER, EMILYMOWER, NOAH DANIELS, LENORE COWEN, AND ANSELM BLUMER 175 HIGHER DIMENSIONAL APPROACH FOR CLASSIFICATION OF LUNG CANCER MICROARRAY DATA F. CRIMINS, R. DIMITRI, T. KLEIN, N. PALMER AND L. COWEN 191 MICROARRAY DATA ANALYSIS USING NEURAL NETWORK CLASSIFIERS AND GENE SELECTION METHODS GAOLIN ZHENG, E. OLUSEGUN GEORGE, GIRI NARASIMHAN 207 A COMBINATORIAL APPROACH TO THE ANALYSIS OF DIFFERENTIAL GENE EXPRESSION DATA MICHAEL A. LANGSTON, LAN LIN, XINXIA PENG, NICOLE E. BALDWIN, CHRISTOPHER T. SYMONS, BING ZHANG AND JAY R. SNODDY 223 GENES ASSOCIATED WITH PROGNOSIS IN ADENOCARCINOMA ACROSS STUDIES AT MULTIPLE INSTITUTIONS ANDREW V. KOSSENKOV, GHISLAIN BIDAUT, AND MICHAEL F. OCHS 239 Index 255