Protein Interaction Networks

The analysis of protein-protein interactions is fundamental to the understanding of cellular organization, processes, and functions. Proteins seldom act as single isolated species; rather, proteins involved in the same cellular processes often interact with each other. Functions of uncharacterized proteins can be predicted through comparison with the interactions of similar known proteins. Recent large-scale investigations of protein-protein interactions using such techniques as two-hybrid systems, mass spectrometry, and protein microarrays have enriched the available protein interaction data and facilitated the construction of integrated protein-protein interaction networks. The resulting large volume of protein-protein interaction data has posed a challenge to experimental investigation. This book provides a comprehensive understanding of the computational methods available for the analysis of protein-protein interaction networks. It offers an in-depth survey of a range of approaches, including statistical, topological, data-mining, and ontology-based methods. The author discusses the fundamental principles underlying each of these approaches and their respective benefits and drawbacks, and she offers suggestions for future research.

Spis treści:
1. Introduction
2. Experimental approaches to generation of protein-protein interaction data
3. Computational methods for the prediction of protein-protein interactions
4. Basic properties and measurements of protein interaction networks
5. Modularity analysis of protein interaction networks
6. Topological analysis of protein interaction networks Woo-chang Hwang
7. Distance-based modularity analysis
8. Graph-theoretic approaches to modularity analysis
9. Flow-based analysis of protein interaction networks
10. Statistics and machine learning based analysis of protein interaction networks Pritam Chanda and Lei Shi
11. Integration of gene ontology into the analysis of protein interaction networks Young-rae Cho
12. Data fusion in the analysis of protein interaction networks
13. Conclusion.