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The Interactions of Differentially Expressed Genes

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The Interactions of Differentially Expressed Genes THE INTERACTIONS OF DIFFERENTIALLY EXPRESSED GENES DIRECTLY TARGETED BY WNT\β-CATENIN SIGNALING: IMPLICATIONS FOR COLORECTAL CARCINOGENESIS By Charles F. Murchison A thesis presented to the Department of Medical Informatics and Clinical Epidemiology and the Oregon Health & Science University School of Medicine in partial fulfillment of the requirements for the degree of Masters of Science December 2010 School of Medicine Oregon Health & Science University Certificate of Approval This is to certify that the Master’s Thesis of Charles F. Murchison “The Interactions of Differentially Expressed Genes Directly Targeted by Wnt\β-catenin Signaling: Implications for Colorectal Carcinogenesis” Has been approved _________________________________________ Thesis Advisor _________________________________________ Committee Member _________________________________________ Committee Member TABLE OF CONTENTS LIST OF TABLES ..................................................................................................................... v LIST OF FIGURES .................................................................................................................. vi ACKNOWLEDGEMENTS ...................................................................................................... vii ABSTRACT .......................................................................................................................... viii CHAPTER 1 – INTRODUCTION 1.1 COLON CANCER .................................................................................................... 1 1.2 ADENOMA DEVELOPMENT AND THE WNT SIGNALING PATHWAY...................... 4 1.3 MICROARRAYS AND POOLED ANALYSES .............................................................. 6 1.4 OTHER HIGH-THROUGHPUT TECHNIQUES ........................................................... 9 1.5 A MULTI-METHOD APPROACH ........................................................................... 12 CHAPTER 2 – METHODS 2.1 LITERATURE SEARCH FOR EXPRESSION STUDIES .............................................. 14 2.2 NORMALIZATION OF CEL FILES TO ABSOLUTE INTENSITY ................................ 15 2.3 DIFFERENTIAL EXPRESSION ............................................................................... 18 2.4 CO-EXPRESSION................................................................................................. 19 i 2.5 MODULE COMPARISON: PATIENT VS CELL-LINE ................................................ 19 2.6 WNT TRANSCRIPTION FACTOR BINDING DATA .................................................. 20 2.7 EXPRESSION PATTERNS AND β-CATENIN BINDING ............................................ 21 2.8 THE PROTEIN-PROTEIN INTERACTION NETWORKS ............................................ 22 2.9 CODINGS FOR THE NETWORK ............................................................................ 24 2.10 EVALUATION OF THE DISCOVERY NETWORK ................................................... 26 2.11 NULL NETWORK MODEL – COMPARING OBSERVED AND PERMUTED PROPORTIONS OF METRICS ............................................................................. 28 CHAPTER 3 – RESULTS 3.1 LITERATURE SEARCH OF mRNA EXPRESSION STUDIES ...................................... 32 3.2 NORMALIZATION ASSESSMENT FOR POOLING .................................................. 33 3.3 AGGREGATE STUDY OF MRNA EXPRESSION ...................................................... 33 3.4 FILTERING OF SACO DATA OF β-CATENIN BINDING ........................................... 36 3.5 THE PROTEIN PRODUCT INTERACTION NETWORK............................................. 36 3.6 NETWORK NODES WITH SINGLE METRICS OF INTEREST ................................... 37 3.7 NODES MATCHING MULTIPLE CRITERIA AND A FINAL NETWORK ..................... 38 3.8 ASSESSMENT OF THE NULL MODEL ................................................................... 40 3.9 ANNOTATION OF FUNCTION FOR IDENTIFIED GENES/NODES .......................... 41 ii CHAPTER 4 – DISCUSSION 4.1 INITIAL ANALYSIS – DIFFERENTIAL EXPRESSION PROFILES AND DIRECT β-CATENIN TARGETING ...................................................................................... 44 4.2 BIOLOGICAL ANNOTATION – THE 8 FUNCTIONAL ACTIVITY CATEGORIES FOR THE REFINED NETWORK ............................................................................. 47 4.3 CELL GROWTH, PROLIFERATION AND REGULATION OF THE CELL CYCLE .......... 48 4.4 PHOSPHORYLATION AND UBIQUITINATION ...................................................... 49 4.5 CELL FATE AND DIFFERENTIATION, AND EPITHELIAL CELL POLARITY ................ 50 4.6 EPIGENETICS AND HISTONE MODIFICATION ...................................................... 51 4.7 CELL-CELL INTERACTIONS, MOLECULAR TRANSPORT, INTER-CELLULAR SIGNALING .......................................................................................................... 52 4.8 PARTICIPANTS IN THE CANONICAL WNT PATHWAY – COFACTORS AND RECEPTORS ................................................................................................. 54 4.9 UBIQUITOUSLY EXPRESSED GENES – GENERALIZED FUNCTIONALITY AND MULTIPLE BIOLOGICAL CIRCUMSTANCES .................................................. 56 4.10 EXPRESSION LOCALIZED OUTSIDE THE COLON ................................................ 57 4.11 OBSERVATIONS ON NODES IN THE CANONICAL WNT PATHWAY.................... 59 4.12 FINAL TRENDS ................................................................................................... 60 CHAPTER 5 – CONCLUSIONS 5.1 LIMITATIONS OF THE CURRENT STUDY .............................................................. 64 5.2 FUTURE DIRECTIONS .......................................................................................... 65 iii 5.3 CONTRIBUTIONS TO THE FIELD .......................................................................... 66 REFERENCE LIST ................................................................................................................ 69 TABLES ............................................................................................................................... 83 FIGURES ........................................................................................................................... 111 iv LIST OF TABLES TABLE 1 – STUDIES USED FOR mRNA ANALYSIS ............................................................... 83 TABLE 2 – SIGNIFICANCE COUNTS OF PROBES FROM mRNA ANALYSIS .......................... 84 TABLE 3 – CONCORDANT GENES BY DIRECTION OF DIFFERENTIAL EXPRESSION ............ 85 TABLE 4 – TOP 5 CONCORDANTLY UPREGULATED AND DOWNREGULATED GENES ....... 86 TABLE 5 – DIRECT TARGETS OF β-CATENIN SHOWING UPREGULATION AND DOWNREGULATION ................................................................................. 88 TABLE 6 – METRICS OF THE INITIAL PROTEIN INTERACTION NETWORK .......................... 95 TABLE 7 – GENES WITH MRNA OVEREXPRESSION FOUND IN ADENOMAS AND CELL LINES ................................................................................................ 96 TABLE 8 – GENES WITH MRNA UNDEREXPRESSION FOUND IN ADENOMAS AND CELL LINES ................................................................................................ 97 TABLE 9 – METRICS OF NODES WITH ALTERED CO-EXPRESSION UNDER ADENOMATOUS CONDITIONS ........................................................................ 98 TABLE 10 – METRICS FOR β-CATENIN DIRECT TARGETS AND NEIGHBORS ...................... 99 TABLE 11 – METRICS FOR INTERACTION NETWORK HUBS AND HUB NEIGHBORS ........ 101 TABLE 12 – METRICS FOR KNOWN WNT PARTICIPANTS AND NEIGHBORS ................... 105 TABLE 13 – FULL METRICS LISTING FOR THE FINAL 65 NETWORK NODES ..................... 107 TABLE 14 – STATISTICAL ASSESSMENT OF NULL NETWORK MODEL .............................. 110 v LIST OF FIGURES FIGURE 1 – COLONIC CRYPT AND ADENOCARCINOMA DEVELOPMENT ........................ 111 FIGURE 2 – WNT ACTIVATION OF β-CATENIN DEPENDENT TRANSCRIPTION ................ 113 FIGURE 3 – SERIAL ANALYSIS OF CHROMATIN OCCUPANCY .......................................... 115 FIGURE 4 – DENSITY GRAPH OF SPOT INTENSITIES FROM mRNA AGGREGATION ANALYSIS ............................................................................. 117 FIGURE 5 – BOX PLOTS OF INDIVIDUAL ARRAYS COMPARING NORMALIZATIONS ........ 119 FIGURE 6 – VENN DIAGRAM FOR DIFFERENTIALLY EXPRESSED GENES BY MODULE GROUPING ............................................................................... 123 FIGURE 7 – OVERVIEW OF THE BASE PROTEIN INTERACTION NETWORK ...................... 125 FIGURE 8 – COLOR CODED LEGEND FOR TABLES 7-12 ................................................... 127 FIGURE 9 – REFINED INTERACTION NETWORK USED FOR VISUALIZATION ................... 129 vi ACKNOWLEDGEMENTS This thesis would not have been possible without the guidance and support of my advisor Dr. Shannon McWeeney. Her tireless devotion and formidable intellect are matched only by her enthusiasm for the study of Bioinformatics and the entire discipline benefits from her involvement. Words do little justice to the generosity and insight she has given over the years but thank you, Shannon, for everything. Equally central in the development and implementation of this project were the members of my thesis advisory committee, Drs. Greg Yochum and Motomi Mori. Such a broad and inter-disciplinary study required a great deal of understanding of numerous disparate fields. Their advice in molecular biology and microarray analysis were indispensible in bringing this
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