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Practical Systems Biology
EXPERIMENTAL BIOLOGY REVIEWS Environmental Stress and Gene Regulation Sex Determination in Plants Plant Carbohydrate Biochemistry Programmed Cell Death in Animals and Plants Biomechanics in Animal Behaviour Cell and Molecular Biology of Wood Formation Molecular Mechanisms of Metabolic Arrest Environment and Animal Development: Genes, Life Histories and Plasticity Brain Stem Cells Endocrine Interactions of Insect Parasites and Pathogens Vertebrate Biomechanics and Evolution Osmoregulation and Drinking in Vertebrates Host–Parasite Interactions The Nuclear Envelope The Carbon Balance of Forest Biomes Comparative Genomics and Proteomics in Drug Discovery The Eukaryotic Cell Cycle Drosophila: A Toolbox for the Study of Neurodegenerative Disease
Practical Systems Biology Edited by CLAIRE GRIERSON School of Biological Sciences, University of Bristol, Bristol, UK
ALISTAIR HETHERINGTON School of Biological Sciences, University of Bristol, Bristol, UK
Published by: Taylor & Francis Group In US: 270 Madison Avenue, New York, NY 10016 In UK: 2 Park Square, Milton Park Abingdon, Oxon OX14 4RN This edition published in the Taylor & Francis e-Library, 2008. “To purchase your own copy of this or any of Taylor & Francis or Routledge’s collection of thousands of eBooks please go to www.eBookstore.tandf.co.uk.”
© 2008 by Taylor & Francis Group First published 2008 ISBN 0-203-96719-4 Master e-book ISBN
ISBN: 9780415407809 This book contains information obtained from authentic and highly regarded sources. Reprinted material is quoted with permission, and sources are indicated. A wide variety of references are listed. Reasonable efforts have been made to publish reliable data and information, but the author and the publisher cannot assume responsibility for the validity of all materials or for the consequences of their use. All rights reserved. No part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information storage or retrieval system, without written permission from the publishers. A catalog record for this book is available from the British Library. Library of Congress Cataloging-in-Publication Data Practical systems biology/edited by Claire Grierson, Alistair Hetherington. p. cm. – (Experimental biology reviews) Includes bibliographical references. ISBN 978-0-415-40780-9 (alk. paper) 1. Computational biology. 2. Genomics. 3. Bioinformatics. 4. Proteomics. 5. Metabolism. I. Grierson, Claire. II. Hetherington, A.M. QH324.2.P695 2008 572.80285–dc22 2008003914 Editor: Editorial Assistant: Production Editor: Indexed by:
Elizabeth Owen Sarah E. Holland Helen Powis Shirley May
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Contents Contributors Preface 1.
2.
3.
Bioinformatic approaches to biological systems David R. Westhead, Iain W. Manfield and Christopher J. Needham
ix xiii 1
1 Introduction 2 Getting systems information from public data sources 3 Using informatics methods to drive data generation 4 Conclusion References
1 2 11 15 15
Cell sampling and global nucleic acid amplification Vigdis Nygaard and Eivind Hovig
17
1 Introduction 2 Cellular characterization and assaying gene expression 3 Global analysis of the transcriptome – gene expression analysis at the RNA level 3.1 Cell sampling considerations: Effect of sample properties on the transcriptome/ transcript distribution to be assayed 4 Approaches to reduce RNA requirements in microarray experiments 4.1 Global mRNA amplification 5 Concluding remarks Protocol 1: Linear RNA amplification References