Guide to ANALYSIS OF DNA MICROARRAY DATA Second Edition Steen Knudsen Center for Biological Sequence Analysis BioCentrum-DTU Technical University of Denmark @ WI LEY-LISS A JOHN WILEY & SONS, INC., PUBLlCATION Contents Preface Acknowledgments I Introduction to DNA Microarray Technology 1.1 Hybridization 1.2 Gold Rush? 1.3 The Technology Behind DNA Microarrays 1.3.1 Afimetrix GeneChip Technology 1.3.2 Spotted Arrays 1.3.3 Digital Micromirror Arrays 1.3.4 Inkjet Arrays 1.3.5 Bead Arrays 1.3.6 Parallel Sequencing on Microbead Arrays 1.4.1 Emerging Technologies Example: Afimetrix vs. Spotted Arrays Serial Analysis of Gene Expression (SAGE) I .4 1.5 1.6 Summary I . 7 Further Reading ... X l l l xv 1 1 2 3 4 7 9 10 12 12 14 14 15 17 19 2 Overview of Data Analysis 23 Vii This Page Intentionally Left Blank Guide to ANALYSIS OF DNA MICROARRAY DATA This Page Intentionally Left Blank Guide to ANALYSIS OF DNA MICROARRAY DATA Second Edition Steen Knudsen Center for Biological Sequence Analysis BioCentrum-DTU Technical University of Denmark @ WI LEY-LISS A JOHN WILEY & SONS, INC., PUBLlCATION Copyright %: 2004 by John Wiley & Sons, Inc. All rights reserved Published by John Wiley & Sons, Inc.. Hoboken. New Jersey. 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 I07 or I08 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) 646-8600, 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.. 1 I 1 River Street, Hoboken, NJ 07030. (201) 748-601 I . fax (201) 748-6008. Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this hook. they make no representation 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 he 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. For general information on our other products and services please contact our Customer Care Department within the U.S. at 877-762-2974. outside the U.S. at 317-572-3993 or fax 31 7-572-4002 Wiley also publishes its hooks in a variety of electronic formats. Some content that appears in print, however. rnav not he available in electronic format. Library of Congress Cataloging-in-Publication Data is available. ISBN 0-471-65604-6 Printed in the United States of America I 0 9 8 7 6 5 4 3 2 I TO Linnea This Page Intentionally Left Blank