Pathway Analysis for Drug Discovery

This book introduces drug researchers to the novel computational approaches of pathway analysis and explains the existing applications that can save time and money in the drug discovery process. It covers traditional computational methods and software for pathway analysis microarray, proteomics, and metabolomics. It explains pathway reconstruction of diseases and toxic states, pathway analysis in various phases, dynamic modeling of drug responses, and more. This is a core resource for drug discovery and pharmaceutical industry researchers, chemists, and biologists and for professionals in related fields.

Preface vii Contributors ix 1 Introduction to Pathway Analysis 1 Anton Yuryev 2 Software Infrastructure and Data Model for Pathway Analysis 27 Fedor Bokov and Anton Yuryev 3 Automatic Pathway Inference in Heterogeneous Biological Association Networks 47 Anton Yuryev, Andrey Kalinin, and Nikolai Daraselia 4 Algorithmic Basis for Pathway Visualization 67 Sergey Simakov, Iaroslav Ispolatov, Sergei Maslov, and Alexander Nikitin 5 Pathway Analysis of High-Throughput Experimental Data 103 Andrey Y. Sivachenko 6 Integrative Pathway Analysis of Disease Molecular Data 121 Andrej Bugrim, Zoltan Dezso, Yuri Nikolsky, and Tatiana Nikolskaya 7 Whole-Genome Expression Profiling of Papillary Serous Ovarian Cancer: Activated Pathways,Potential Targets, and Noise 149 John Farley, Laurent L. Ozbun, and Michael J. Birrer 8 Mammalian Proteome and Toxicant Network Analysis 165 Sean Ekins and Craig N. Giroux 9 Unraveling Mechanisms of Toxicity with the Power of Pathways: ToxWiz Tool as an IllustrativeExample 195 Mark P. Kühnel, Bojana Cosovic, Goran Medic, Robert B. Russell, and Gordana Apic 10 Impact of Chemistry Information on Pathway Analysis 219 Sreenivas Devidas 11 Propagation of Concentration Perturbations in Equilibrium Protein Binding Networks 237 Sergei Maslov and Iaroslav Ispolatov 12 An Adaptive System Model of the Yeast Glucose Sensor System 263 Todor Vujasinovic and André Siniša Žampera 13 Present and Future of Pathway Analysis in Drug Discovery 285 Anton Yuryev Index 297