Protein Networks and Pathway Analysis

In this book, 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 book is authoritative and cutting-edge.

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.

A broad overview of experimental and analytical methods of functional data analysis written by the leaders in the field Details multiple aspects of biological networks, from collecting binary interactions to building algorithms and modeling Provides a guide to real life and research applications of current methods of systems biology Covers a wide range of cell-based assay formats and systems Presents a modular approach to experimental design, covering model biological systems, screening modalities, detection technologies, and approaches to data analysis Comprehensive guide to developing, running, and analyzing cell-based assays in high-throughput screening Includes supplementary material: sn.pub/extras

Inhalt
I: Interactions.- Mining ProteinProtein Interactions from Published Literature Using Linguamatics I2E.- Relative Avidity, Specificity, and Sensitivity of Transcription FactorDNA Binding in Genome-Scale Experiments.- Curation of Inhibitor-Target Data: Process and Impact on Pathway Analysis.- Profiling Protein Interaction Networks with Functional Protein Microarrays.- Manual Annotation of Protein Interactions.- II: Analysis.- Gene Set Enrichment Analysis.- PANTHER Pathway: An Ontology-Based Pathway Database Coupled with Data Analysis Tools.- Prioritizing Genes for Pathway Impact Using Network Analysis.- Discovering Biological Networks from Diverse Functional Genomic Data.- Functional Analysis of OMICs Data and Small Molecule Compounds in an Integrated Knowledge-Based Platform.- Kinetic Modeling as a Tool to Integrate Multilevel Dynamic Experimental Data.- Cytoscape: A Community-Based Framework for Network Modeling.- Semantic Data Integration and Knowledge Management to Represent Biological Network Associations.- Solutions for Complex, Multi Data Type and Multi Tool Analysis: Principles and Applications of Using Workflow and Pipelining Methods.- III: Applications.- High-Throughput siRNA Screening as a Method of Perturbation of Biological Systems and Identification of Targeted Pathways Coupled with Compound Screening.- Pathway and Network Analysis with High-Density Allelic Association Data.- miRNAs: From Biogenesis to Networks.- MetaMiner (CF): A Disease-Oriented Bioinformatics Analysis Environment.- Translational Research and Biomedical Informatics.- ArrayTrack: An FDA and Public Genomic Tool.