Gene Regulatory Networks Methods and Protocols
Gene regulatory networks play a vital role in organismal development and function by controlling gene expression. With the availability of complete genome sequences, several novel experimental and computational approaches have recently been developed whic
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MOLECULAR BIOLOGY™
Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK
For further volumes: http://www.springer.com/series/7651
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Gene Regulatory Networks Methods and Protocols Edited by
Bart Deplancke Inst. Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
Nele Gheldof Faculté de Biologie det Médecine, Centre Intégratif de Génomique, Université de Lausanne, Bâtiment Génopode, Lausanne, Switzerland
Editors Bart Deplancke, Ph.D Inst. Bioengineering École Polytechnique Fédérale de Lausanne Lausanne 1015, Switzerland bart.deplancke@epfl.ch
Nele Gheldof Faculté de Biologie det Médecine Centre Intégratif de Génomique Université de Lausanne Bâtiment Génopode Lausanne 1015, Switzerland [email protected]
ISSN 1064-3745 e-ISSN 1940-6029 ISBN 978-1-61779-291-5 e-ISBN 978-1-61779-292-2 DOI 10.1007/978-1-61779-292-2 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2011936383 © Springer Science+Business Media, LLC 2012 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Humana Press, c/o Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. Printed on acid-free paper Humana Press is part of Springer Science+Business Media (www.springer.com)
Preface Gene regulatory networks (GRNs) play a vital role in organismal development and function by controlling gene expression, and deregulation of these networks is often implicated in disease because of inappropriate gene expression or silencing. GRNs depict the dynamic interactions between genomic and regulatory state components. The genomic components comprise genes and their associated cis-regulatory elements. The regulatory state components consist primarily of transcriptional complexes that bind the latter elements as well as noncoding RNAs such as microRNAs that control gene expression via posttranscriptional mechanisms. With the availability of complete genome sequences, several novel approaches have recently been developed which promise to significantly enhance our ability to identify either the genomic or regulatory state components, or the interactions between these two. In this volume, we briefly detail how each of these approaches contributes to a more comprehensive understanding of the composition and function of GRNs, and provide a comprehensive protocol on how to implement them in the laboratory. In a
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