Development and application of bioinformatics tools for discovery disease markers and disease targeting antibodies

DEVELOPMENT AND APPLICATION OF BIOINFORMATICS TOOLS FOR DISCOVERING DISEASE MARKERS AND DISEASE TARGETING ANTIBODIES TANG ZHIQUN (B. Eng & M.Med, HUST) A THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF PHARMACY NATIONAL UNIVERSITY OF SINGAPORE 2007 Acknowledgements ACKNOWLEDGMENTS The realization of this thesis was achieved due to the support of a large number of people, all of which contributed in various ways; without them this research would not have been possible. First and foremost, I would like to express my sincere and deep gratitude to my supervisor, Professor Chen Yuzong, who provides me with the excellent guidance and invaluable advices and suggestions throughout my PhD study in National University of Singapore. I have tremendously benefited from his profound knowledge, expertise in scientific research, as well as his enormous support, which will inspire and motivate me to go further in my future professional career. I am grateful to our BIDD group members for their insight suggestions and collaborations in my research work: Dr. Yap Chunwei, Dr Han Lianyi, Dr. Lin Honghuang, Dr Zheng Chanjuan, Ms Cui Juan, Mr Ung Choong Yong, Mr Xie Bin, Ms Zhang Hailei, Dr Wang Rong and Ms Jia Jia. I thank them for their valuable support and encouragement in my work. Finally, I owe my gratitude to my parents, husband and daughter for their love, constant support, understanding and encouragement throughout my life. I Table of contents TABLE OF CONTENTS ACKNOWLEDGMENTS . I TABLE OF CONTENTS II SUMMARY . IIV LIST OF TABLES . VII LIST OF FIGURES . IIX LIST OF SYMBOLS X Introduction 1.1 Overview of disease markers and therapeutic molecules 1.2 Current progress in disease marker discovery .3 1.2.1 Introduction to disease differentiation .3 1.2.2 Approaches of disease marker discovery .4 1.2.3 Brief introduction to microarray technology .7 1.2.4 The problems of current marker selection methods .15 1.3 Current progress in disease targeting molecule prediction, antibody as a case study .17 1.3.1 Overview of disease-targeting molecule 17 1.3.2 Introduction to therapeutic antibody 23 1.3.3 The need for development of antibody-antigen interaction databases .27 1.3.4 Current progress in antibody-antigen interaction prediction .30 1.4 Scope and research objective .31 Methodology 34 2.1 Support Vector Machines .34 2.1.1 Theory and algorithm .34 2.1.2 Performance evaluation .40 2.2 Methodology for gene selection from microarray data 42 2.2.1 Preprocessing of microarray data .42 2.2.2 Gene selection procedure .44 2.2.3 The development of therapeutic target prediction system .49 2.3 Methodology for therapeutic molecule prediction .53 2.3.1 Database development .53 2.3.2 Predictive system development 60 Colon cancer marker selection from microarray data 63 3.1 Introduction 63 3.2 Materials and methods .67 3.2.1 Colon cancer microarray datasets 67 3.2.2 Colon cancer gene selection procedure 68 3.2.3 Performance evaluation of signatures 69 3.3 Results and discussion .70 3.3.1 System of the disease marker selection .70 3.3.2 Consistency analysis of the identified disease markers .71 3.3.3 The predictive performance of identified markers in disease II Table of contents differentiation 87 3.3.4 Hierarchical clustering analysis of samples .93 3.3.5 Evaluation of sample labels .94 3.3.6 The function of the identified colon cancer markers .97 3.3.7 Hierarchical clustering analysis of the identified markers .99 3.3.8 Therapeutic target prediction .101 3.4 Summary 104 Lung adenocarcinoma survival marker selection 106 4.1 Introduction 106 4.2 Materials and Methods .109 4.2.1 Lung adenocarcinoma microarray datasets and data preprocess .109 4.2.2 Survival marker selection procedure .110 4.2.3 Performance evaluation of survival marker signatures 111 4.3 Results and discussion .113 4.3.1 System of the lung adenocarcinoma survival marker selection .113 4.3.2 Consistency analysis of the identified markers 113 4.3.3 The predictive ability of identified markers .120 4.3.4 Patient survival analysis using survival markers .126 4.3.5 Hierarchical clustering analysis of the survival markers .132 4.3.6 Therapeutic target prediction of survival markers .135 4.4 Summary 138 The development of bioinformatics tools for disease targeting antibody prediction .140 5.1 Introduction 140 5.2 The development of antibody information database 142 5.2.1 The objective of the AAIR development .142 5.2.2 The collection of related information 143 5.2.3 The construction of AAIR database .144 5.2.4 The interface of the AAIR database .146 5.3 Statistic analysis of disease targeting antibody information database .152 5.3.1 Distribution pattern of antibody-antigen pairs .152 5.3.2 Statistical analysis of sequence specificity of antibody-antigen recognition 158 5.4 Prediction performance of disease targeting antibody prediction system161 5.4.1 Overview of the prediction system 161 5.4.2 Prediction performance 161 5.5 Conclusion .165 Conclusion and future works .167 BIOBLIOGRAPHY .170 APPENDICES .194 LIST OF PUBLICATIONS 214 III Summary SUMMARY Thanks to the rapid progress on the research of genomics and genetics, our knowledge on the molecular basis of diseases has been significantly enhanced, which has greatly contributed to the discovery of disease markers for disease differentiation, and to the design of disease-targeting molecules like small-molecule agents or antibodies for disease treatment. The key disease markers determine the characteristics of disease, therefore could be further analyzed the possibility of these markers severing as targets for disease targeting molecule design. The main objective of this dissertation is to develop a disease marker discovery system from microarray data and a bioinformatics tool for disease-targeting molecule prediction. It is of crucial essence to find the marker genes responsible for disease initiation and progress. The marker genes may benefit early disease diagnosis and correct prediction of prognosis. The expression level of such markers presents potential therapeutic drug targets and may give suggestions to proper treatment regime. Microarray can measure the expression level of thousand of genes at one time, presenting the most important platform for disease diagnosis, disease prognosis and disease marker discovery. Current microarray data analysis tools provided good predictive performance. However, the markers produced by those tools have been found to be highly unstable with the variation of patient sample size and combination. The patient-dependent nature of the markers diminishes their application potential for diagnosis and prognosis. To solve this problem, we developed a novel gene selection method based on Support Vector Machines, IV Summary recursive feature elimination, multiple random sampling strategies and multi-step evaluation of gene-ranking consistency. The as-developed program can be utilized to derive disease markers which present both good prediction performance and high levels of consistency with different microarray dataset combinations. After program implementation, two different cases were tested: colon cancer marker discovery by using a well-studied 62-sample colon-cancer dataset and lung adenocarcinoma survival marker discovery by using an 86-sample lung adenocarcinoma dataset. In the first case, the derived 20 colon cancer marker signatures are found to be fairly stable with 80% of top-50 and 69%~93% of all markers shared by all 20 signatures. The shared 104 markers include 48 cancer-related genes, 16 cancer-implicated genes and 52 previously-derived colon cancer markers. The derived signatures outperform all previously-derived signatures in predicting colon cancer outcomes from an independent dataset. The possibility of the markers as therapeutic target was exploited by a therapeutic target prediction system. Six known targets and 18 potential targets were identified by this system. In the second case, 21 lung adenocarcinoma survival markers were shared by 10 marker signatures. known and novel targets were predicted as therapeutic targets. These results suggested the effectiveness of our system on deriving stable disease markers and discovering therapeutic target. One major application of marker discovery is the finding of disease targeting molecules for disease prevention and treatment. For this purpose, therapeutic antibodies, a class of effective disease-targeting molecules, were employed to develop a therapeutic antibody prediction system based on antibody-antigen V Summary sequence recognition information. Eventually, an antibody antigen information resource (AAIR) database, which provides information of sequence-specific antibody-antigen recognition and their immunological relevance, was developed. Three classes of information are included in the database. The first class is antigen information consisting of antigen name, sequence, function and source organism. The second class is antibody information containing antibody isotype, source organism, molecular and structural type of antibody. The third one is disease and therapeutic information composed of disease class, targeted disease, diagnosis and therapeutic indication. Currently, AAIR contains 2,777 antibody-antigen pairs covering 159 disease conditions, 2,035 antibody heavy chain sequences, 1,701 antibody light chain sequences, 619 distinct antigen sequences (584 proteins/peptides and 35 other molecules), 254 antigen epitope sequences, and 157 binding affinity constants for antigen-antibody pairs from various viruses, bacteria, tumor types, and autoimmune responses. The potential application of the data in AAIR for the study of antibody-antigen recognition was demonstrated by applying machine learning models to predict antibody from antigen sequence. It can be concluded from the performance of machine learning models that the information in AAIR is capable of producing comparable and reasonable preliminary results to characterize pair-wise interaction between antibody and antigen, and would be useful for antibody and antigen design. VI List of tables LIST OF TABLES Table 1-1 Table 1-2 Table 1-3 Table 1-4 A list of public microarray databases 10 US FDA-approved molecule targeting drugs (small molecules) 19 US FDA-approved therapeutic antibody drugs .25 Public antibody and antigen databases. 29 Table 2-1 Table 2-2 Table 2-3 Table 2-4 Table 2-5 Table 2-6 Table 2-7 List of some popular used support vector machines softwares .40 Relationships among terms of performance evaluation 41 Entry ID list table 57 Main information table .57 Data type table 57 Reference information table 57 Logical view of the database .58 Table 3-1 Statistics of the colon cancer gene signatures for differentiating colon cancer patients from normal people by 10 different studies that used the same microarray dataset 65 Distribution of the selected colon cancer genes of the 10 studies in Table 3-1 with respect to different cancer-related classes 66 Gene information for colon cancer genes shared by all of the 20 signatures 74 Statistics of the selected colon cancer genes from a colon cancer microarray dataset by class-differentiation systems .85 Overall accuracies of 500 training-test sets on the optimal SVM parameters .86 Average colon cancer prediction accuracy and standard deviation of 500 SVM class-differentiation systems constructed by 42 samples collected from Stanford Microarray Database 87 Average colon cancer prediction accuracy and standard deviation of 500 SVM class-differentiation systems constructed by using Alon’s colon cancer microarray dataset 90 List of colon cancer genes shared by all 20 signatures .99 Prediction results from therapeutic target prediction system 102 Table 3-2 Table 3-3 Table 3-4 Table 3-5 Table 3-6 Table 3-7 Table 3-8 Table 3-9 Table 4-1 Table 4-2 Table 4-3 Table 4-4 Table 4-5 Statistics of lung adenocarcinoma survival marker signatures from references 109 Statistics of the lung adenocarcinoma survival markers by class-differentiation systems .115 Gene information for lung adenocarcinoma survival markers shared by all of 10 signatures. 116 Average survivability prediction accuracy of 500 SVM class-differentiation systems on the optimal SVM parameters for lung adenocarcinoma prediction .120 Average survivability prediction accuracy of the 500 SVM class-differentiation systems constructed by 84 samples from independent .122 VII List of tables Table 4-6 Table 4-7 Table 4-8 Table 4-9 Table 5-1 Table 5-2 Table 5-3 Table 5-4 Table 5-5 Table 5-6 Table 5-7 Table 5-8 Table 5-9 Table 5-10 Table 5-11 Table 5-12 Table 5-13 Average survivability prediction accuracies of the 500 PNN class-differentiation systems constructed by 84 samples from independent .123 Average survivability prediction accuracy of 500 SVM class-differentiation systems constructed by 86 samples from Beer’s lung adenocarcinoma dataset 125 Average survivability prediction accuracies of the 500 PNN class-differentiation systems constructed by 86 samples from Beer’s lung adenocarcinoma dataset 126 Comparison of the survival rate in clusters with other groups, by using different signatures and Beer’s microarray dataset .128 Antibody-antigen pair ID table .145 Antibody-antigen pair main information table .145 Antibody-antigen pair data type table .145 Protein information table 145 Protein data type table .146 Reference information table 146 Distribution pattern of antibody-antigen pairs involved in different disease classes .153 Distribution pattern of antibody-antigen pairs involved in different disease types 154 Distribution pattern of antigen in different Pfam 157 Distribution of antigens of different sequence variations that can be selectively recognized by antibodies in which the VH-VL differ by one to 208 amino acids .160 Performance evaluation of SVM prediction system of antibody-antigen pairs involved in cancer, influenza, HIV infection and allergy by using five-fold cross validation .162 Performance evaluation of SVM prediction system of antibody-antigen pairs for antigens from four different protein domain families, Keratin high sulfur B2 protein, Adenovirus E3 region protein CR1, Hemagglutinin and Transglycosylase SLT domain by using five-fold cross validation .164 Performance evaluation of SVM prediction system of antibody-antigen pairs .165 VIII List of figures LIST OF FIGURES Figure 1-1 Figure 1-2 Procedure of microarray experiment Filter method versus wrapper method for feature selection 14 Figure 2-1 Figure 2-2 Figure 2-3 Figure 2-4 Figure 2-5 Figure 2-8 Margins and hyperplanes 36 Architecture of support vector machines 40 Overview of the gene selection procedure 45 Architecture of therapeutic target prediction system 50 Flowchart of database design 53 Architecture of disease targeting antibody prediction system 61 Figure 3-1 The system of colon cancer genes derivation and colon cancer differentiation 71 Hierarchical clustering analysis of 62 samples from the gene expression profile of 104 selected genes. .95 Hierarchical clustering analysis of 56 samples and 104 genes on colon cancer microarray 96 Classes of genes involved in oncogenic transformation .98 Figure 3-2 Figure 3-3 Figure 3-4 Figure 4-1 Figure 4-2 Figure 4-3 Figure 4-4 Figure 4-5 Figure 4-6 Figure 5-1 Figure 5-2 Figure 5-3 Figure 5-4 Architecture of neural networks 112 System for lung adenocarcinoma survival marker derivation and survivability prediction .114 Hierarchical clustering analysis of the 21 lung adenocarcinoma survival markers from Beer’s microarray dataset (350). The tumor samples were aggregated into three clusters. Substantially elevated (red) and decreased (green) expression of the genes is observed in individual tumors. .129 Kaplan-Meier survival analysis of the three clusters of patients from Figure 4-3 130 Hierarchical clustering analysis of the 21 lung adenocarcinoma markers from Bhattacharjee’s microarray dataset .131 Kaplan-Meier survival analysis of the three clusters of patients from Figure 4-5 132 Structure of AAIR .144 The interface displaying a research result on AAIR .149 Interface displaying the detailed information of an antibody-antigen pair in the AAIR 150 Interface displaying the detailed information of an antibody entry in AAIR .151 IX Appendices MGC22793 (H87135) PMP22 (T94350) TPM1 (Z24727) POSTN (D13665) PTPRH (D15049) PRPSAP1(T65380) CDX1 (U15212) CCL14 (Z49269) COX8A (T51250) KIF5A (U06698) DTWD2 (R98842) CBX3 (U26312) FXYD1 (T67077) IFITM2 (X57351) CPSF1 (U37012) CNOT1 (T64885) MORF4L2(D14812) GSTM4 (M96233) ATP2A2 (M23115) FBL (X56597) CALM2 (D45887) PCCB (X73424) ITPR3 (H25136) IL1R2 (H78386) HSP90AA1(X15183) SFRS9 (U30825) THBS2 (L12350) CALM2 (M19311) 20 86 84 77 82 85 86 82 100 90 89 85 90 86 85 84 84 79 75 75 88 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 19 19 19 18 87 88 89 90 91 92 93 94 95 96 97 99 100 101 103 108 109 110 111 112 116 119 130 83 107 125 113 90 75 82 76 95 81 123 104 73 96 79 135 110 112 88 99 70 106 101 109 100 113 94 86 116 102 111 93 95 106 88 104 91 78 103 121 87 99 76 94 101 98 89 108 109 112 107 116 114 110 96 113 119 120 86 78 108 81 120 93 114 88 96 103 92 105 85 106 97 95 102 116 99 118 110 113 117 100 101 111 125 87 89 95 79 90 91 76 107 80 114 73 103 93 111 83 99 101 115 104 105 108 113 96 94 112 116 92 105 90 94 85 98 84 80 93 83 99 88 92 95 107 89 97 108 111 100 101 106 104 91 103 96 89 76 94 81 110 83 95 104 111 85 93 112 107 108 92 86 96 97 99 101 98 109 84 107 92 99 80 98 85 105 110 111 81 84 90 114 115 88 79 106 113 89 95 94 109 78 102 103 101 108 99 77 89 74 97 84 122 109 71 103 82 87 101 114 92 88 110 118 94 113 105 108 98 91 115 119 95 98 93 92 88 86 82 87 75 70 108 81 97 119 112 90 102 74 109 118 95 99 107 115 91 106 105 100 90 100 97 83 109 86 104 103 80 95 82 105 94 107 96 93 92 123 117 106 98 102 88 101 91 131 125 93 80 82 78 79 81 101 74 71 108 102 77 104 106 87 95 67 112 86 96 97 107 91 99 94 81 107 85 99 89 77 117 91 106 82 87 78 110 96 98 100 143 103 97 109 111 95 116 104 115 130 92 91 90 78 93 88 104 114 73 98 77 100 96 107 81 79 71 126 106 95 111 103 94 89 108 133 101 85 83 103 75 110 81 97 121 74 98 99 100 92 95 93 88 91 125 105 108 104 101 90 96 109 106 135 86 96 113 92 100 82 107 99 101 85 102 109 110 105 90 94 89 121 74 97 103 106 83 78 111 88 104 103 91 88 78 92 81 117 101 76 95 80 93 110 104 86 97 102 114 89 99 108 105 136 69 111 109 116 106 95 98 81 91 82 89 94 76 90 83 105 108 109 93 86 70 124 107 96 100 103 88 115 110 101 114 99 94 110 84 85 93 74 95 109 104 105 98 112 106 96 107 103 145 92 100 117 121 97 83 101 111 119 83 68 109 71 118 98 85 101 114 94 96 103 67 106 95 99 77 121 91 105 110 112 89 72 107 104 116 119 102 109 105 199 Appendices PCK1 (L05144) 18 115 105 123 104 ALDH1A1 (M31994) H05803 HDGF (D16431) MAPK3 (M84490) NXPH3 (H40699) ZNRF1 (H11460) CANX (L10284) MYH9 (T57882) MSTP9 (T51539) CD46 (T83368) FGFR2 (T94993) CCDC106 (T47424) CD44 (M59040) PRPS1 (D00860) AVPI1 (R60883) ATP5A1 (T74556) FAS (M67454) IARS (U04953) PFN1 (T61661) PSMC2 (H72965) ITGA7 (X74295) ZNF3 (X07290) PTPRO (Z48541) DPT (R48303) RIMS2 (R75843) T47383 AMPD3 (M84721) SULT1E1 (H67764) 17 17 17 17 17 16 16 16 15 15 15 15 14 14 14 13 13 13 13 12 12 12 11 11 11 10 9 56 65 102 117 123 131 134 141 98 105 122 126 137 138 145 106 118 120 149 121 128 132 127 129 151 46 124 135 47 46 68 97 126 125 124 128 134 140 111 133 150 132 145 138 127 148 139 45 73 83 139 138 145 94 126 63 109 123 112 122 129 143 141 103 120 114 126 98 122 83 107 119 97 118 125 115 108 132 129 133 127 124 117 131 122 146 129 100 130 48 117 105 47 64 88 45 72 97 106 115 67 106 117 102 110 131 123 121 48 70 97 126 119 118 104 116 93 46 107 102 112 106 125 96 46 45 66 113 116 110 130 108 112 124 122 120 132 117 124 114 100 98 128 140 121 135 130 127 115 48 146 113 103 118 112 91 120 100 129 121 117 123 126 123 111 127 51 109 43 50 127 103 117 116 131 120 142 96 104 110 101 124 130 122 149 111 128 133 129 137 140 121 125 135 133 151 111 98 115 114 113 63 115 137 126 135 122 128 127 124 129 103 110 120 134 138 118 133 50 111 114 113 117 50 72 105 136 129 128 112 132 121 108 144 131 127 142 135 138 48 66 113 132 130 118 121 127 110 105 140 102 124 125 122 151 112 129 120 138 123 131 154 139 116 119 137 125 122 118 120 140 41 114 133 117 67 114 119 133 118 94 113 59 140 112 136 131 132 123 120 124 107 129 130 148 122 111 145 112 127 112 115 108 46 66 98 122 129 128 117 123 60 114 108 116 127 120 124 46 98 106 122 121 120 100 130 64 107 129 49 66 49 78 108 139 138 137 114 51 115 133 130 134 126 128 118 123 115 119 120 127 126 117 116 125 102 113 123 122 121 126 132 113 133 104 76 136 116 120 129 131 135 113 118 122 140 127 128 124 123 134 48 149 115 118 112 132 200 100 117 111 102 97 120 116 119 115 113 43 Appendices MXD1 (L06895) 142 135 T47342 IGFBP3 (M35878) CYP2A7 (K03192) IMPDH2 (R42501) DNAJA1 (L08069) CEACAM1(X16354) RPS19 (T52185) PLP2 (L09604) PTPRD (L38929) TNIP1 (D30755) RNASE3 (M28128) POLD4 (R44418) COL1A1 (T51558) EIF1 (T61599) GCN5L2 (R52081) MUC1 (X52228) RBMY2BP(U36621) ACTA2 (T60155) SLC2A4 (M91463) KCNH2 (X86779) HIVEP2 (R39209) CDK4 (T86749) GYPC (X12496) COX5B (T71049) NPM1 (M26697) TUBB (T56604) C1R (T53889) NME1 (T86473) 8 7 6 6 5 5 4 4 4 3 3 3 144 104 155 136 105 155 142 128 130 133 121 104 107 132 136 134 32 133 139 143 54 141 144 114 146 131 147 148 150 143 102 115 152 137 154 116 68 137 132 115 138 102 141 119 90 147 126 153 145 113 139 139 119 60 132 136 101 24 123 134 157 134 134 131 144 143 156 138 148 94 136 131 125 142 125 97 111 134 146 146 135 149 144 141 134 135 141 150 147 143 135 124 136 84 102 126 146 142 145 147 125 144 155 92 127 126 116 126 137 142 133 130 144 24 137 132 134 155 154 118 119 97 141 152 141 136 156 109 131 119 156 147 149 153 128 114 96 109 121 140 153 154 128 130 136 27 127 124 201 Appendices GTF2A2 (R01221) 150 153 ITGB1 (H65425) CD55 (M31516) ATP6V1E1(X76228) FTL (H87344) PI3 (Z18538) WEE1 (X62048) H61410 FLNA (R78934) SELENBP1(T59162) AURKB (R97912) AP3B2 (U37673) ANXA13 (Z11502) PPIB (T59878) NPTN (R61359) SEMG2 (M81651) 2 1 1 1 1 1 1 146 148 58 63 139 143 152 118 152 142 151 144 124 79 128 143 139 202 Appendices Table S3 The clinical information of 86 lung adenocarcinoma samples from Beer et al (350) Sample ID cluster ID1 AD2 AD5 L01 L06 L26 L33 L43 L56 L62 L83 L91 L92 AD10 L04 L13 L19 L34 L36 L37 L41 L54 Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Age Sex 65.6 62 76.7 57.9 61.4 53.5 50.6 60.2 52.3 62 63.7 55.4 65 51.7 67.1 56.5 77.2 69.7 64.4 73.1 45.8 F F M F M F F M F F M M M M M M M M M F F Tumor stage. either or 1 1 1 3 1 3 3 T (tumor size) N (nodal status) Survival times (month)2 Patient's survival status 2 2 1 0 0 0 0 2 0 0 2 2 91.8 108.2 47 91.9 17.7 29.4 78.5 61.8 52.4 30.6 6.1 8.5 84.1 45.8 79.5 9.6 14.9 7.2 2.6 8.4 alive alive alive alive alive alive alive alive alive alive alive alive death death death death death death death death death classification (tumor histological type)3 BD BA BD/CC BD BD BD BD BD/CC BD BA/mucinous BD/mucinous BD BD BD BD BD BD BD/PA BD BD/CC BD Tumor differentiation p53 nuclear accumulation status 12/13th codon K-ras mutation status Smoking Poor Well Poor Poor Poor Moderate Moderate Moderate Moderate Well Poor Poor Moderate Poor Moderate Moderate Moderate Moderate Poor Poor Poor + + + + + + + + NA + + + + + + 48 positive 100 NA 90 23 57 90 none none 30 50 60 50 25 40 45 25 84 26 75 These clusters are obtained from hierarchical cluster analysis of the 86 samples and 21 survival marker genes share by 10 signatures This is patient's survival time from operation date to death or last follow up as of May 2001 BD: bronchial derived; BA: bronchial alveolar; CC: clear cell; PA: papillary; Note that some tumors contained a mixture of two histological types Patient smoking history in packs per year 203 Appendices L40 L80 L61 L95 L96 AD7 L02 L09 L101 L103 L104 L105 L108 L111 L12 L18 L23 L25 L27 L38 L42 L46 L47 L48 L52 L57 L65 L78 Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster 54.9 68.2 63.1 72 64 56 63.2 48.2 46.3 84.6 68.5 74.2 61 54.9 44.6 82.5 62.2 62.6 70 78.5 76 60.4 60 42.8 67.3 73.6 59.6 75.6 F F F F F M M F F F F F F F F F M F M F F M M M M F M F 1 3 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 2 2 1 1 0 0 0 0 0 0 0 0 0 0 0 20.1 10.1 20.6 5.4 21.2 68.1 39.1 98.7 40 30.8 24.4 28.3 19.5 1.5 85.2 48.2 15.1 14.5 21.1 10 63.4 82.4 60.5 77.8 65.4 54.8 52.9 36.5 death death death death death alive alive alive alive alive alive alive alive alive alive alive alive alive alive alive alive alive alive alive alive alive alive alive BD BD/mucinous BD BD BD BD BD BD B/A/mucinous B/A B/A B/A with PA B/A B/A BD BD BD/PA BD BD BD BD BD BD BD BA BD/PA BD BD Moderate Moderate Moderate Poor Moderate Moderate Poor Moderate Well Well Well Well Well Well Moderate Well Moderate Well Poor Poor Well Poor Moderate Moderate Well Moderate Moderate Moderate + + + + - + + + + + + + + + + + + + + 7.5 50 30 50 50 80 27 none NA none 75 100 40 15 none 20 50 60 40 160 27 60 30 50 60 108 204 Appendices L82 L85 L97 L50 AD3 AD8 L05 L08 L102 L106 L107 L17 L22 L30 L31 L49 L59 L64 L76 L81 L84 L86 L87 L88 L89 L99 L100 L24 AD6 Cluster 69.2 F 34.1 alive BA/BD Well - - 40 Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster 60.2 63.6 72.1 59.5 75 54.6 59.9 74.6 82.8 59.4 40.9 65.6 51.8 62.1 65.8 71.5 65.4 46.2 58.4 66.8 62.7 66.3 52.9 58.8 73.8 72.9 84.5 66.2 M F M F M F F F F F F M F F F F M M M F F M F M M F F M 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 2 1 1 2 1 0 0 0 0 0 0 0 0 0 0 0 0 26.8 4.9 19 93.7 34.2 110.6 107.9 40 25.3 13 83.7 12.5 20.2 25.2 70.7 54.6 48.1 87.7 36 32.2 10.1 10.4 8.3 12.2 4.5 43.8 1.6 34.6 alive alive death alive alive alive alive alive alive alive alive alive alive alive alive alive alive alive alive alive alive alive alive alive alive censored censored death BD/mucinous B/A BD/PA BD BD BD/CC BD BD B/A BD BD/PA BD BD BA/mucinous BD BD/PA BD BD BA BD B/A BD BD BD B/A/mucinous B/A BD BA Moderate Well Moderate Moderate Moderate Moderate Moderate Moderate Well well/mod. Moderate Moderate Moderate Well Moderate Moderate Moderate Poor Well Poor Well Moderate Poor Moderate Well Well Poor Well + + + + + + NA - + + + + + + + + + + + + + 60 34 100 positive 14 29 80 50 none none 15 90 20 20 20 25 12 50 90 15 45 18 60 48 55 2.5 75 NA 205 Appendices L11 L20 L35 L45 L53 L79 L90 L94 Cluster 68.2 F 34.7 death BA Well - + none Cluster Cluster Cluster Cluster Cluster Cluster Cluster 79.8 64.4 74.9 58.5 49 63.8 72 M M F F F F M 3 1 2 2 2 0 19.9 28.2 29.6 16.6 8.7 5.8 2.4 death death death death death death death BA BD BD BD/PA BD BD/PA BD/mucinous Well Moderate Poor Moderate Poor Moderate Moderate + - + + - 30 30 none 60 100 50 206 Appendices Table S4 The clinical information of 84 lung adenocarcinoma samples from Bhattacharjee et al (351) Sample ID Cluster ID1 Age Sex Stage:AJCC TNM Stage Summary AD111 AD115 AD118 AD120 AD122 AD123 AD127 AD130 AD136 AD159 AD162 AD164 Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster 76 70 69 68 73 60 65 75 66 71 75 68 F F M M F M F M F M F M T1NxMx T2N1M0 T1N0Mx T2N0Mx T2N1Mx T3N0Mx T1N2Mx T2N1Mx T2N0Mx T2N1Mx T2N0Mx T3N0Mx IA IIB IA IB IIB IIB IIIA IIB IB IIB IB IIB Survival time (month)2 72.4 21.9 49.6 38.9 33.9 74 8.2 7.1 31.4 19.7 41.7 15 AD167 Cluster 77 M T2N0Mx IB AD169 Cluster 47 F T2N0Mx AD170 Cluster 61 F AD173 AD179 AD187 Cluster Cluster Cluster 57 85 69 F M M Patient's status* Clinical Path (type diameter features) 3 3 d d ad 2.0 m-p ad 6.5 m ad 2.5 m ad 8.0 m ad 5.0 m ad 5.0 m ad 1.8 p ad 15.0 BAC ad 4.0 m ad 5.5 m-p ad 3.5 m ad 4.5 p 41.7 ad 2.5 w w/BAC IB 20 ad 2.5 m T1N0M0 IA 78.4 ad 2.5 w w/pap T2N1Mx T2N0Mx T1N0Mx IIB IB IA 22.3 24.3 86.3 d 3 ad 5.0 m-p ad 5.6 m w/BAC ad 1.8 p Path II4 adm/adw adm adm adm adm,pap adp BAC adm adw,acinar admod,acinar adpoor, acinar adw,acinar/adm bac adw/pap or BAC,mucinous w/pap BAC & pap,well admod,acinar adw//adw,acinar adp Site of elapse/ metastasis lung, LN lung, LN bone lung LN LN Smoking5 40 75 25 54 126 69 100 100 80 60 80 bone, myocardium 21.6 60 lung, bone lung 27 24.75 120 These clusters are obtained from hierarchical cluster analysis of the 84 samples and 21 survival marker genes we selected. Patient status at last followup or death (1= alive; 2=alive with recurrence; 3= dead with recurrence; 4= dead without evidence of recurrence; d= dead, disease status unknown) 3,4 diameter (cm) subtype (BAC = bronchioloalveolar carcinoma). type (ad = adenocarcinoma ) differentiation (p, m-p, m, m-w, w) /w= with Smoking: patient smoking history (self-reported) in pack/year 207 Appendices AD183 AD188 AD201 AD203 AD207 AD212 AD213 AD225 AD226 AD228 AD230 Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster 75 74 46 60 64 55 69 88 56 60 56 F F M F F F M M F F M T1N0Mx T2NxMx T1N2 T1N0Mx T2 T2N0M0 T1Nx T2NxMx T1N0Mx T2N0 T1N0 IA IB IIIA IA IB IB IA IB IA IB IA 42.2 21.6 12.3 106.1 66.8 59 48.8 2.6 60.5 41.2 56.7 d d ad 2.0 m BAC ad 2.7 BAC ad 1.5 m ad 2.2 m-p ad 3.5 w BAC ad 3.0 m-p ad 2.5 m ad 3.5 m ad 2.0 m ad 3.0 m ad 2.5 p adw//adw,acinar adw,acinar AD232 Cluster 73 M T1Nx IA 56.3 a ad 2.4 w BAC AD236 AD239 AD240 Cluster Cluster Cluster 53 60 77 F M F T2N0Mx T2N0M0 T1N0M0 IB IB IA 14.2 58.5 43.5 1 ad 5.5 m-p ad 2.9 m w/BAC ad 2.0 m-w BAC 40 40 AD243 Cluster 64 F T1N0M0 IA 50.1 ad 1.5 w w/BAC adw resemblance to BAC 30 AD247 AD249 AD250 AD252 AD255 AD258 AD259 Cluster Cluster Cluster Cluster Cluster Cluster Cluster 49 67 61 66 79 67 58 M M F F M M M T1N0 T1Nx T1Nx T1N0 T2N0 T2Nx T3N0 IA IA IA IA IB IB IIB 71.1 31 91 16.5 44.8 12.3 20.5 3 d ad 2.0 m ad 1.2 m ad 2.0 w w/BAC ad 1.4 ad 3.5 m ad 4.5 p ad 5.0 AD260 Cluster 61 M T2Nx IB 21 d ad 3.0 m AD261 Cluster 66 F T1N0 IA 57.6 ad 2.7 w w/BAC lung, bone ad m brain adp adm (BAC cluster) 25 lung, brain adm lung LN, CSF, brain bone adm some BACpattern 22.5 116 90 0 54 111 72 18 75 60 32 45 10 50 50 54 45 50 75 208 Appendices AD262 Cluster 63 F T4N1Mx IIIB 16.6 ad 2.0 m-p AD266 AD267 AD268 AD276 AD277 AD283 AD287 AD296 AD299 AD301 AD302 AD304 AD308 AD309 AD311 AD313 AD317 AD318 AD323 AD327 AD330 AD331 Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster 65 61 50 68 72 78 36 63 78 59 65 71 62 77 63 74 41 54 56 50 50 59 F M F M F M F M F F F F M F F F F M F F F M T1N0 T2N0M0 T2N0M0 T2N2 T1Nx T1N0 T4Nx T1N1 T1N0M0 T2N0M0 T2N3Mx T2N0 T2N0 T2N0 T2N0 T1N0 T2Nx T2N0M0 T2N1 T2N0 T1N1 T1N0M0 IA IB IB IIIA IA IA IIIB IIA IA IB IIIB IB IB IB IB IA IB IB IIB IB IIA IA 41.9 56 50.1 4.5 8.2 47.2 7.4 9.3 37.9 7.8 57.8 8.2 79 37.6 50.5 25.3 99.1 83 6.8 81.9 7.3 52.9 1 3 d 3 3 3 1 d ad 2.5 w w/BAC ad 2.8 m-p ad 3.5 p ad 2.1 m-p ad 3.0 m ad 2.5 m w/pap ad 4.0 p ad 2.4 m-p w/pap ad 2.2 m-p ad 4.0 p ad 3.7 w BAC ad 5.0 p ad 4.0 m ad 3.4 w ad 5.0 m ad 1.5 m-p ad 3.5 m pap ad 4.0 muc ad 4.0 p ad 6.5 m ad 2.4 m ad 2.0 m AD332 Cluster 52 M TxN0 I ad m AD335 AD336 Cluster Cluster 40 71 F M T3N0 T2N0Mx IIB IB 46.9 21.1 ad 4.5 m ad 1.7 m AD338 Cluster 55 F T2NxMx IB 75.4 ad 5.0 w BAC AD346 Cluster 65 F T1N0 IA 17.3 ad 2.5 m 10 adm lung, bone, liver pleura, brain liver, ?bone lung, LN, bone, groin adp adm w/BAC adw ok 50% adp liver lung brain lung lung, liver, spleen brain lung LN adm brain pleura, liver, colon, ?adrenal, ?pancreas 120 10 140 27 20 10 88 50 40 35 66 13 90 100 39 27 40 45 75 20 (1) ad w/BAC or ( 2)BAC 15 50 209 Appendices AD347 Cluster 65 F T2N0Mx IB 0.5 ad 3.5 m BAC AD351 AD353 AD356 AD361 AD362 AD366 AD367 AD368 Cluster Cluster Cluster Cluster Cluster Cluster Cluster Cluster 43 69 72 54 56 71 55 33 F M M F M M F F T2N1 T2N0Mx T2N0 T2N T2N0 T2N2 T2N0 T2N0 IIA IB IB IB IB IIIA IB IB 24.3 13.7 49.2 6.4 71.5 9.4 76.1 62.6 1 d ad 5.5 m ad 3.5 m BAC ad 4.0 w BAC ad 4.5 p ad 6.5 BAC ad 6.2 m-p w/pap ad 6.5 m-p ad 6.0 m-p w/muc AD374 Cluster 51 M T2N0 IB 8.8 ad 11.0 p AD375 AD379 AD382 Cluster Cluster Cluster 47 65 51 F M F T2N0 T2N1 T2N2Mx IB IIB IIIA 23.4 35.4 30.1 d ad 7.2 p ad 5.5 w/clear ad 5.0 p adm 20 lung, LN adw w/bac BAC muc lung brain lung, pleura, pericardium, diaphragm adm lung, adrenal, brain brain 30 50 40 23 25 32 100 13 80 31 210 Appendices Table S5 Gene Name (EST number) List of 10 derived lung adenocarcinoma prognosis marker gene signatures selected by SVM class-differentiation systems Number of signatures which included this gene Gene rank in each signature (Number of selected gene in each signaure) (51) (54) (42) (34) (46) (54) (57) (50) (53) 10 (47) ADFP(X97324) 10 46 35 28 19 22 15 18 13 CXCL3(X53800) 10 37 24 23 14 19 PLD1(U38545) 10 31 41 17 11 SLC2A1(K03195) 10 12 13 12 11 10 10 29 11 10 10 12 10 23 25 27 11 32 25 14 28 LDHB(X13794) 10 10 11 15 16 11 15 FXYD3(U28249) 10 11 29 14 52 18 42 22 REG1A(J05412) 10 13 23 15 16 45 14 10 14 24 26 30 46 28 40 27 27 10 18 30 16 22 12 31 15 FUT3(U27326) 10 19 14 19 21 28 10 15 30 21 PRKACB (M34181) 10 20 15 33 TUBA4A(X06956) 10 21 14 25 13 53 49 29 26 14 VEGF(M27281) 10 22 33 26 30 14 26 19 23 32 RPS3(X55715) 10 25 10 39 55 13 17 36 ANXA8(X16662) 10 28 32 18 12 21 20 22 18 26 VDR(J03258) 10 32 39 33 30 11 16 37 CXCR7(U67784) 10 33 47 30 24 43 41 37 27 39 29 POLD3(D26018) 10 35 25 15 18 11 50 31 BSG(X64364) 10 36 38 39 17 33 48 27 20 33 CYP24(L13286) 23 13 34 20 22 23 41 19 25 30 27 11 25 19 34 32 24 31 39 35 28 39 36 29 25 38 41 GARS(U09510) 41 26 31 31 26 19 46 44 20 SPRR2A(M21302) 21 13 34 40 21 21 34 47 18 49 37 44 34 56 35 53 16 12 14 17 20 34 25 12 23 12 20 33 22 48 35 51 17 22 46 SPRR1B (M19888) GALNT4 (Y08564) CHRNA2 (U62431) SERPINE1 (J03764) HLA-G (HG273-HT273) WNT10B (U81787) NULL (HG2175-HT2245) CD58(Y00636) KRT14(J00124) E48(X82693) 16 15 44 34 FADD(X84709) 12 STX1A(L37792) 15 18 ENO2(X51956) 24 32 38 32 SPRR2A(L05188) 29 41 45 44 48 28 FEZ2(U69140) 38 KRT18(X12876) 43 ALDH2(X05409) UCN(U43177) SCYB5(L37036) 31 23 42 19 36 16 24 45 42 30 26 26 44 43 10 45 20 21 13 18 33 42 31 41 22 47 17 23 10 29 211 Appendices AIP-1(U23435) 37 42 NULL(U92014) 42 17 NULL(L43579) 47 54 CEBPA(U34070) KIAA0138 (D50928) 34 29 TFF1(X52003) 40 34 KRT19(Y00503) 49 RPS26(X69654) 17 28 S100A2(Y07755) 26 51 GS3686 (AB000115) 46 36 EMP1(Y07909) HPCAL1(D16227) 43 LCN2(S75256) 38 PEX7(U88871) EFNB2(U81262) 44 ALDH8(U37519) 45 EPS8(U12535) 20 NDRG1(D87953) 22 CSTB(U46692) 40 PSPH(Y10275) 44 CYBA(M21186) CNN3(S80562) 28 18 27 39 35 17 24 19 12 32 36 42 24 37 47 25 30 37 37 24 40 43 54 20 49 21 40 34 49 38 27 41 38 33 36 41 37 29 44 40 43 30 52 50 NULL(U49020) ALDH7(U10868) 45 AXL (HG162-HT3165) 53 TYRO3(U02566) P2RX5(U49395) GRO1(X54489) ERBB3(M34309) BM-002(Z70222) LAMB3(U17760) INHA(X04445) TAX1BP2 (U25801) IGHM(V00563) 27 SPRR2A(X53065) 48 NP(K02574) 50 P63(X69910) 51 48 46 45 27 10 23 29 VIPR1(X77777) 40 17 57 39 40 49 50 51 35 16 10 35 32 36 32 16 28 51 16 42 13 21 39 38 46 31 AP3B1(U91931) 48 C6(X72177) 50 HFL1(M65292) PRKCN (HG2707-HT2803) SHB(X75342) EIF5A(S72024) FCGR3B(J04162) 38 24 13 33 47 212 Appendices GRIN1 (HG4188-HT4458) SLC2A3(M20681) CA9(X66839) FLJ20746 (U61836) PPBP(M54995) TUBA4A (HG2259-HT2348) 47 45 42 43 52 54 EMS1(M98343) 53 IGF2(M17863) 36 CHAT (HG4051-HT4321) 31 LAMC2(U31201) BMP2(M22489) KIAA0111 (D21853) TNFAIP6 (M31165) NULL (HG415-HT415) 50 43 52 35 46 213 List of publications LIST OF PUBLICATIONS 1. Tang Zhiqun, Han Lianyi, Xie Bin, Cui Juan, Ung Choong Yong, Jiang Li, Wang Rong, Cao Zhiwei, Chen Yuzong, “Antibody Antigen Information Resource Database and Its Potential Application to Antibody Discovery and Studies of Antigen Recognition”, (Under review) 2. Tang Zhiqun, Han Lianyi, Lin Honghuang, Cui Juan, Jia Jia, Low Boon Chuan, Li Baowen, Chen Yuzong, “Derivation of Stable Microarray Cancer-differentiating Signatures by a Feature-selection Method Incorporating Consensus Scoring of Multiple Random Sampling and Gene-Ranking Consistency Evaluation”, Cancer Research 67: 9996-100003, 2007 3. Tang Zhiqun, Han Lianyi, Xie Bin, Ung Choong Yong, Jiang Li, Chen Yuzong, “AAIR: Antibody Antigen Information Resource”, J Immunol 178(8): 4705, 2007 4. Tang Zhiqun, Lin Honghuang, Zhang Hailei, Han Lianyi, Chen Xin, Chen Yuzong, “Prediction of Functional Class of Proteins and Peptides Irrespective of Sequence Homology by Support Vector Machines”, Bioinformatics and Biology Insights. 1: 19-47, 2007 5. Cui Juan, Han Lianyi, Lin Honghuang, Tang Zhiqun, Ji Zhiliang, Cao Zhiwei, Li Yixue and Chen Yuzong, “Advances in exploration of machine learning methods for predicting functional class and interaction profiles of proteins and peptides irrespective of sequence homology”, Curr. Bioinformatics 2(2): 95-112, 2007 6. Cui Juan, Han Lianyi, Lin Honghuang, Tang Zhiqun, Zheng Chanjuan, Cao Zhiwei, Chen Yuzong, “Prediction of MHC-Binding Peptides of Flexible Lengths from Sequence-Derived Structural and Physicochemical Properties”, Mol. Immunol. 44: 866-877, 2007 7. Cui Juan, Han Lianyi, Lin Honghuang, Tang Zhiqun, Zheng Chanjuan, Cao Zhiwei, Chen Yuzong, “Computer Prediction of Allergen Proteins from Sequence-Derived Protein Structural and Physicochemical Properties”, Mol. Immunol. 44(4): 514-520, 2007 8. Zheng Chanjuan, Han Lianyi, Xie Bin, Liew CY, Ong Serene, Cui Juan, Zhang Hailei, Tang Zhiqun, Gan Shoo Hui, Jiang Li, Chen Yuzong, “PharmGED: Pharmacogenetic Effect Database”, Nucleic Acids Res. 35:D794-D799, 2007 9. Cui Juan, Han Lianyi, Lin Honghuang, Tang Zhiqun, Zheng Chanjuan, Cao Zhiwei, Chen Yuzong, “MHC-BPS: MHC-Binder Prediction Server for Identifying Peptides of Flexible Lengths from Sequence-Derived Physicochemical Properties”, Immunogenetics 58(8):607-13, 2006 10. Han Lianyi, Zheng Chanjuan, Lin Honghuang, Cui Juan, Li Hu, Zhang Hailei, Tang Zhiqun, Chen Yuzong, “Prediction of Functional Class of Novel Plant Proteins by a Statistical Learning Method”, New Phytologist. 168:109-121, 2005 214 [...]... overview of disease markers and therapeutic molecules The following two sections of this chapter introduce the current progress in disease marker discovery (Section 1.2) and therapeutic molecules prediction (Section 1.3) The motivation of this work and outline of the structure of this document are presented in Section 1.4 1.1 Overview of disease markers and therapeutic molecules Knowing the origin of a disease. .. database for gene expression profile from 91 normal human and mouse samples across a diverse array of tissues, organs, and cell lines An extensive and easily searchable database of gene expression information about the mouse Microarray database containing tens of millions of expression profiles Information and microarray expression data for genes involved in mitosis and meiosis, gamete formation and germ... (7, 8), cardiovascular disorders (9, 10) and obesity (11) For accurate disease diagnosis and proper treatment selection, it is very important to identify the gene markers responsible for disease initiation Moreover, the discovery of the markers responsible for disease progress is critical because such markers can be used to identify disease stages, subtypes and prognosis effect in an accurate manner... pathology reports offer little information about the potential treatment regime which a disease will respond to Therefore, new disease differentiation method is needed for accurate diagnosis and treatment Fortunately, disease differentiation based on molecular profile of diseases can overcome those limitations (6, 21-24) Microarray technology, which is capable of providing the expression profile information... source of gene expression data, microarray data is used in this study for gene selection Microarray measures the expression profiles of thousands of genes at the same time and have been explored for deriving disease genes or disease markers (5, 26, 55-62), elucidating pathogenesis of disease (55, 60, 63-66), deciphering mechanism of drug action (67-69), determining treatment-strategies (70, 71), and characterizing... critical for disease diagnosis, prognosis, treatment and disease- targeting molecule design, can be a difficult task since human genome contains approximately 25,000 genes (1), which are expressed at different time and are cooperated as an integrated team The discovery of the disease markers can facilitate disease target identification and disease targeting molecule design The first section (Section 1.1) of. .. progress in disease targeting molecule prediction, antibody as a case study 1.3.1 Overview of disease- targeting molecule As introduced in the previous section, Microarray data can be employed to discover markers closely related to disease initiation and progression and can provide candidate disease targets The interaction between disease targets and therapeutic molecules is crucial for drug discovery. .. understanding the entire abnormal course of the disease and helping the treatment of the disease Sometimes it is very easy to determine the cause of certain diseases, such as infectious diseases which are generally caused by virus, bacteria or parasites However, the sources of some diseases may not be easily identified, especially some genetic diseases resulting from an accumulation of inherited and 1... cancer research for the identification of cancer markers, and provide new insights into tumorigenesis, tumor progression and invasiveness (5, 6, 26-29) 1.2.2 Approaches of disease marker discovery 1.2.2.1 Traditional gene discovery method Two approaches, the candidate gene approach and positional cloning approach, have traditionally been used to discover genes underlying human diseases Candidate gene... interaction (17) Disease targeting molecule design aims to identify small molecules or antibodies that bind strongly to the disease targets (15, 16) The understanding of the interaction of targets and therapeutic molecules are crucial for disease targeting molecule design The rapid progress in human genome project and functional 2 Chapter 1 Introduction genomics provides an ever-increasing number of potential . discovery of disease markers for disease differentiation, and to the design of disease- targeting molecules like small-molecule agents or antibodies for disease treatment. The key disease markers. DEVELOPMENT AND APPLICATION OF BIOINFORMATICS TOOLS FOR DISCOVERING DISEASE MARKERS AND DISEASE TARGETING ANTIBODIES TANG ZHIQUN (B. Eng. The development of bioinformatics tools for disease targeting antibody prediction 140 5.1 Introduction 140 5.2 The development of antibody information database 142 5.2.1 The objective of the