Protein networks and pathway analysis / edited by Yuri Nikolsky, Julie Bryant. — New York : Humana Press ; London : Springer, c2009. – (58.17/M592/v.563)

Contents

    Contents
    
    SECTION I: INTERACTIONS
    1. Mining Protein-Protein Interactions from Published Literature Using Linguamatics I2E
    2. Relative Avidity， Specificity， and Sensitivity of Transcription Factor-DNA Binding in Genome-Scale Experiments
    3. Curation of Inhibitor-Target Data: Process and Impact on Pathway Analysis
    4. Profiling Protein Interaction Networks with Functional Protein Microarrays
    5. Manual Annotation of Protein Interactions
    SECTION II: AYALYSIS
    6. Gene Set Enrichment Analysis
    7. PANTHER Pathway: An Ontology-Based Pathway Database Coupled with Data Analysis Tools
    8. Prioritizing Genes for Pathway Impact Using Network Analysis 141
    9. Discovering Biological Networks from Diverse Functional Genomic Data 157
    10. Functional Analysis of OMICs Data and Small Molecule Compounds in an Integrated "Knowledge-Based" Platform 177
    11. Kinetic Modeling as a Tool to Integrate Multilevel Dynamic Experimental Data
    12. Cytoscape: A Community-Based Framework for Network Modeling 219
    13. Semantic Data Integration and Knowledge Management to Represent Biological Network Associations 241
    14. Solutions for Complex， Multi Data Type and Multi Tool Analysis: Principles and Applications of Using Workflow and Pipelining Methods 259
    SECTION III: APPLICATIONS
    15. High-Throughput siRNA Screening as a Method of Perturbation of Biological Systems and Identification of Targeted Pathways Coupled with Compound Screening 275
    16. Pathway and Network Analysis with High-Density Allelic Association Data 289
    17. miRNAs: From Biogenesis to Networks 303
    18. MetaMiner (CF): A Disease-Oriented Bioinformatics Analysis Environment 353
    19. Translational Research and Biomedical Informatics 369
    20. ArrayTrack: An FDA and Public Genomic Tool 379
    Index