Protein Networks and Pathway Analysis

I: Interactions.- Mining Protein–Protein Interactions from Published Literature Using Linguamatics I2E.- Relative Avidity, Specificity, and Sensitivity of Transcription Factor–DNA 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.