Protein Networks and Pathway Analysis

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