From the beginning of the OMICs biology era, science has been pursuing the reduction of the complex 'genome-wide' assays in order to understand the essential biology that lies beneath it.
In "Protein Networks and Pathway Analysis", expert practitioners present a compilation of methods of functional data analysis, often referred to as 'systems biology', and its applications in drug discovery, medicine and basic disease research. The volume is divided into three convenient sections, covering the elucidation of protein, compound and gene interactions, analytical tools, including networks, interactome and ontologies, and applications of functional analysis. As a volume in the highly successful "Methods in Molecular Biology" series, this work provides detailed descriptions and hands-on implementation advice.
Authoritative and cutting-edge, "Protein Networks and Pathway Analysis" presents both 'wet lab' experimental methods and computational tools in order to cover a broad spectrum of issues in this fascinating new field.
Part I: Interactions 1. Mining Protein-Protein Interactions from Published Literature Using Linguamatics I2E Judith Bandy, David Milward, and Sarah McQuay 2. Relative Avidity, Specificity, Sensitivity of Transcription Factor-DNA Binding in Genome-Scale Experiments Vladimir A. Kuznetsov 3. Curation of Inhibitor-Target Data: Process and Impact on Pathway Analysis Sreenivas Devidas 4. Profiling Protein Interaction Networks with Functional Protein Microarrays Dawn R. Mattoon and Barry Schweitzer 5. Manual Annotation of Protein Interactions Svetlana Bureeva, Svetlana Zvereva, Valentin Romanov, and Tatiana Serebryiskaya Part II: Analysis 6. Gene Set Enrichment Analysis Charles A. Tilford and Nathan O. Siemers 7. PANTHER Pathway: An Ontology-Based Pathway Database Coupled with Data Analysis Tools Huaiyu Mi and Paul Thomas 8. Prioritizing Genes for Pathway Impact Using Network Analysis Aaron N. Chang 9. Discovering Biological Networks from Diverse Functional Genomic Data Chad L. Myers, Camelia Chiriac, and Olga G. Troyanskaya 10. Functional Analysis of OMICs Data and Small Molecule Compounds in an Integrated "Knowledge-Based" Platform Yuri Nikolsky, Eugene Kirillov, Roman Zuev, Eugene Rakhmatulin, and Tatiana Nikolskaya 11. Kinetic Modeling as a Tool to Integrate Multilevel Dynamic Experimental Data Ekaterina Mogilevskaya, Natalia Bagrova, Tatiana Plyusnina, Nail Gizzatkulov, Eugeniy Metelkin, Ekaterina Goryacheva, Sergey Smirnov, Yuriy Kosinsky, Aleksander Dorodnov, Kirill Peskov, Tatiana Karelina, Igor Goryanin, and Oleg Demin 12. Cytoscape: A Community Based Framework for Network Modeling Sarah Killcoyne, Gregory W. Carter, Jennifer Smith, and John Boyle 13. Semantic Data Integration and Knowledge Management to Represent Biological Network Associations Sascha Losko and Klaus Heumann 14. Solutions for Complex, Multi Data Type and Multi Tool Analysis: Principles and Applications of Using Workflow and Pipelining Methods Robin E. J. Munro and Yike Guo Part III: Applications 15. High-Throughput siRNA Screening as a Method of Perturbation of Biological Systems and Identification of Targeted Pathways Coupled with Compound Screening Jeff Kiefer, Hongwei H. Yin, Qiang Q. Que, and Spyro Mousses 16. Pathway and Network Analysis with High-Density Allelic Association Data Ali Torkamani and Nicholas J. Schork 17. MiRNAs: From Biogenesis to Networks Giuseppe Russo and Antonio Giordano 18. MetaMiner (CF): A Disease-Oriented Bioinformatics Analysis Environment Jerry M. Wright, Yuri Nikolsky, Tatiana Serebryiskaya, and Diana R. Wetmore 19. Translational Research and Biomedical Informatics Michael Liebman 20. ArrayTrack: An FDA and Public Genomic Tool Hong Fang, Stephen C. Harris, Zhenjiang Su, Minjun Chen, Feng Qian, Leming Shi, Roger Perkins, and Weida Tong