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Genomics and Proteomics Engineering in Medicine and Biology - Metin Akay

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GENOMICS AND PROTEOMICS ENGINEERING IN MEDICINE AND BIOLOGY

IEEE Press

445 Hoes Lane

Piscataway, NJ 08854

IEEE Press Editorial Board

Mohamed E. El-Hawary, Editor in Chief

J. B. Anderson

S. V. Kartalopoulos

N. Schulz

R. J. Baker

M. Montrose

C. Singh

T. G. Croda

M. S. Newman

G. Zobrist

R. J. Herrick

F. M. B. Periera

 

Kenneth Moore, Director of IEEE Book and Information Services (BIS)

Catherine Faduska, Senior Acquisitions Editor

Steve Welch, Acquisitions Editor

Jeanne Audino, Project Editor

IEEE Engineering in Medicine and Biology Society, Sponsor EMB-S Liaison to IEEE Press, Metin Akay

GENOMICS AND

PROTEOMICS

ENGINEERING

IN MEDICINE

AND BIOLOGY

Edited by

Metin Akay

IEEE Engineering in Medicine and Biology Society, Sponsor

Copyright # 2007 by the Institute of Electrical and Electronics Engineers, Inc. All rights reserved.

Published by John Wiley & Sons, Inc. Published simultaneously in Canada.

No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning, or otherwise, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, (978) 750-8400, fax (978) 750-4470, or on the Web at www.copyright.com. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, (201) 748-6011, fax (201) 748-6008, or online at http://www.wiley.com/go/permission.

Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose. No warranty may be created or extended by sales representatives or written sales materials. The advice and strategies contained herein may not be suitable for your situation. You should consult with a professional where appropriate. Neither the publisher nor author shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages.

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Library of Congress Cataloging-in-Publication Data is available

ISBN-13 978-0-471-63181-1

ISBN-10 0-471-63181-7

Printed in the United States of America

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To the memory of my late brother, C¸ etin Akay, who dedicated his short but meaningful life to the well-being and happiness of others as well as a democratic and secular Turkey.

May God bless his soul.

&CONTENTS

Preface

xi

Contributors

xiii

1. Qualitative Knowledge Models in Functional Genomics

 

and Proteomics

1

Mor Peleg, Irene S. Gabashvili, and Russ B. Altman

 

1.1. Introduction

1

1.2. Methods and Tools

3

1.3. Modeling Approach and Results

6

1.4. Discussion

19

1.5. Conclusion

20

References

21

2. Interpreting Microarray Data and Related Applications

 

Using Nonlinear System Identification

25

Michael Korenberg

 

2.1. Introduction

25

2.2. Background

25

2.3. Parallel Cascade Identification

30

2.4. Constructing Class Predictors

34

2.5. Prediction Based on Gene Expression Profiling

35

2.6. Comparing Different Predictors Over the Same Data Set

46

2.7. Concluding Remarks

48

References

49

3. Gene Regulation Bioinformatics of Microarray Data

55

Gert Thijs, Frank De Smet, Yves Moreau, Kathleen Marchal,

 

and Bart De Moor

 

3.1. Introduction

55

3.2. Introduction to Transcriptional Regulation

57

3.3. Measuring Gene Expression Profiles

59

3.4. Preprocessing of Data

61

3.5. Clustering of Gene Expression Profiles

63

vii

viii

CONTENTS

 

 

3.6.

Cluster Validation

70

 

3.7.

Searching for Common Binding Sites of Coregulated Genes

76

 

3.8.

Inclusive: Online Integrated Analysis of Microarray Data

87

 

3.9.

Further Integrative Steps

89

 

3.10. Conclusion

90

 

References

91

4. Robust Methods for Microarray Analysis

99

 

George S. Davidson, Shawn Martin, Kevin W. Boyack, Brian N. Wylie,

 

 

Juanita Martinez, Anthony Aragon, Margaret Werner-Washburne,

 

 

Mo´nica Mosquera-Caro, and Cheryl Willman

 

 

4.1. Introduction

99

 

4.2. Microarray Experiments and Analysis Methods

100

 

4.3. Unsupervised Methods

103

 

4.4. Supervised Methods

117

 

4.5. Conclusion

127

 

References

128

5. In Silico Radiation Oncology: A Platform for Understanding

 

 

Cancer Behavior and Optimizing Radiation Therapy Treatment

131

 

G. Stamatakos, D. Dionysiou, and N. Uzunoglu

 

 

5.1. Philosophiae Tumoralis Principia Algorithmica: Algorithmic

 

 

 

Principles of Simulating Cancer on Computer

131

 

5.2. Brief Literature Review

133

 

5.3. Paradigm of Four-Dimensional Simulation of Tumor Growth

 

 

 

and Response to Radiation Therapy In Vivo

135

 

5.4. Discussion

148

 

5.5. Future Trends

150

 

References

150

6. Genomewide Motif Identification Using a Dictionary Model

157

 

Chiara Sabatti and Kenneth Lange

 

 

6.1. Introduction

157

 

6.2. Unified Model

160

 

6.3. Algorithms for Likelihood Evaluation

164

 

6.4. Parameter Estimation via Minorization–Maximization Algorithm

167

 

6.5. Examples

170

 

6.6. Discussion and Conclusion

171

 

References

172

7. Error Control Codes and the Genome

173

 

Elebeoba E. May

 

7.1. Error Control and Communication: A Review

173

CONTENTS

ix

7.2. Central Dogma as Communication System

180

7.3. Reverse Engineering the Genetic Error Control System

184

7.4. Applications of Biological Coding Theory

203

References

205

8. Complex Life Science Multidatabase Queries

209

Zina Ben Miled, Nianhua Li, Yue He, Malika Mahoui, and Omran Bukhres

 

8.1. Introduction

209

8.2. Architecture

212

8.3. Query Execution Plans

214

8.4. Related Work

219

8.5. Future Trends

222

References

223

9. Computational Analysis of Proteins

227

Dimitrios I. Fotiadis, Yorgos Goletsis, Christos Lampros,

 

and Costas Papaloukas

 

9.1. Introduction: Definitions

227

9.2. Databases

229

9.3. Sequence Motifs and Domains

232

9.4. Sequence Alignment

235

9.5. Modeling

241

9.6. Classification and Prediction

242

9.7. Natural Language Processing

248

9.8. Future Trends

252

References

252

10. Computational Analysis of Interactions Between Tumor and

 

Tumor Suppressor Proteins

257

E. Pirogova, M. Akay, and I. Cosic

 

10.1. Introduction

257

10.2. Methodology: Resonant Recognition Model

261

10.3. Results and Discussions

265

10.4. Conclusion

284

References

285

Index

289

About the Editor

299