Plant systems biology

List of contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . XI Preface Frank J. Bruggeman, Jorrit J. Hornberg, Fred C. Boogerd and Hans V. Westerhoff Introduction to systems biology . . . . . . . . . . . . . . . . . . . . . . . . 1 Christophe Rothan and Mathilde Causse Natural and artifi cially induced genetic variability in crop and model plant species for plant systems biology . . . . . . . . . . . . . . 21 Christine H. Foyer, Guy Kiddle and Paul Verrier Transcriptional profi ling approaches to understanding how plants regulate growth and defence: A case study illustrated by analysis of the role of vitamin C . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 Lars Hennig and Claudia Köhler Case studies for transcriptional profi ling . . . . . . . . . . . . . . . . . . . 87 Cameron Johnson and Venkatesan Sundaresan Regulatory small RNAs in plants . . . . . . . . . . . . . . . . . . . . . . . 99 Erich Brunner, Bertran Gerrits, Mike Scott and Bernd Roschitzki Differential display and protein quantifi cation . . . . . . . . . . . . . . . . 115 Sven Schuchardt and Albert Sickmann Protein identifi cation using mass spectrometry: A method overview . . . . . 141 Dirk Steinhauser and Joachim Kopka Methods, applications and concepts of metabolite profi ling: Primary metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171 X Lloyd W. Sumner, David V. Huhman, Ewa Urbanczyk-Wochniak and Zhentian Lei Methods, applications and concepts of metabolite profi ling: Secondary metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195 Martine Dieuaide-Noubhani, Ana-Paula Alonso, Dominique Rolin, Wolfgang Eisenreich and Philippe Raymond Metabolic fl ux analysis: Recent advances in carbon metabolism in plants . . 213 Victoria J. Nikiforova and Lothar Willmitzer Network visualization and network analysis . . . . . . . . . . . . . . . . . 245 Christian H. Ahrens, Ulrich Wagner, Hubert K. Rehrauer, Can Türker and Ralph Schlapbach Current challenges and approaches for the synergistic use of systems biology data in the scientifi c community . . . . . . . . . . . . . . . . . . . 277 Matthias Steinfath, Dirk Repsilber, Matthias Scholz, Dirk Walther and Joachim Selbig Integrated data analysis for genome-wide research . . . . . . . . . . . . . . 309 Daniel Schöner, Simon Barkow, Stefan Bleuler, Anja Wille, Philip Zimmermann, Peter Bühlmann, Wilhelm Gruissem and Eckart Zitzler Network analysis of systems elements . . . . . . . . . . . . . . . . . . . . 331 Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 353