The determination of protein function has been a major goal of molecular biology since the founding of the discipline. However, as we learn more about gene function, we discover that the context within which a gene is expressed controls the specific function of that gene. It has become critical to establish the background in which gene function is determined and to perform experiments in multiple applicable backgrounds. In Gene Function Analysis, Second Edition, a number of computational and experimental techniques are presented for identifying not only the function of an individual gene, but also the partners that work with that gene. The theme of data integration runs strongly through the computational techniques, with many focusing on gathering data from different sources and different biomolecular types. Experimental techniques have evolved to determine function in specific tissues and at specific times during development. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls.Authoritative and easily accessible, Gene Function Analysis, Second Edition seeks to serve both professionals and novices with a growing understanding of the complexity of gene function.

InhaltsangabePart I. Reviews 1. The Present State and Future Direction of Integrated Gene Function AnalysisMichael F. Ochs  Part II. Computational Methods 2. Performing Integrative Functional Genomics Analysis in GeneWeaver.orgJeremy J. Jay and Elissa J. Chesler 3. Functional Annotation of Differentially Regulated Geneset Using WebGestalt: A Geneset Predictive of Response to Ipilimumab in Tumor BiopsiesStefan Kirov, R. Ji R., J. Wang, and B. Zhang  4. ­Integrative Data-Mining Tools to Link Fene and FunctionBasma El Yacoubi and Valérie de Crécy-Lagard 5. Detection of Driver Protein Complexes in Breast Cancer Metastasis by Large Scale Transcriptome-Interactome IntegrationMaxime Garcia, Pascal Finetti, Francois Bertucci, Daniel Birnbaum, and Ghislain Bidaut 6. Pattern Identification in Time Course Gene Expression Data with the CoGAPS Matrix FactorizationElana J. Fertig, Genevieve Stein-O'Brien, Andrew Jaffe, and Carlo Colantuoni 7. Statistical Tools and R Software for Cancer Driver ProbabilitiesGiovanni Parmigiani, Simina Boca, Jie Ding, and Lorenzo Trippa 8. Predicting the Functional Consequences of Somatic Missense Mutations Found in TumorsHannah Carter and Rachel Karchin 9. Determining the Effect of DNA Methylation on Gene Expression in Cancer CellsChai-Jin Lee, Jared Evans, Kwangsoo Kim, Heejoon Chae, and Sun Kim 10. Reverse Engineering Transcriptional Gene NetworkVincenzo Belcastro and Diego di Bernardo 11. Integrating In Silico Resources to Map a Signaling NetworkHanqing Liu, Tim N. Beck, Erica A. Golemis, and Ilya G. Serebriiskii  Part III. Experimental Methods 12. A Method for Inducible Gene Over-Expression and Down-Regulation in Emerging Model Species Using PogostickBin Chen and Antónia Monteiro 13. Construction and Application of Site-specific Artificial Nucleases for Targeted Gene EditingFatma O. Kok, Ankit Gupta, Nathan D. Lawson, and Scot A. Wolfe 14. Selection of Recombinant Antibodies from Antibody Gene LibrariesMichael Hust, André Frenzel, Thomas Schirrmann, and Stefan Dübel 15. Construction of Simple and Efficient siRNA Validation Systems for Screening and Identification of Effective RNAi-Targeted Sequences from Mammalian GenesWen-Hui Tsai and Wen-Tsan Chang  16. Rapid Genetic Modification of Mouse Embryonic Stem Cells by Inducible Cassette Exchange RecombinationMichelina Iacovino, Megan E. Roth, and Michael Kyba 17. In Ovo Electroporation of miRNA-Based Plasmids to Investigate Gene Function in the Developing Neural TubeIrwin Andermatt, Nicole Wilson, and Esther T. Stoeckli 18. Proteomic Strategies: SILAC and 2D-DIGE - Powerful Tool to Investigate Cellular AlterationsArundhathi Sriharshan, Omid Azimzadeh, Randolph B. Caldwell, and Soile Tapio 19. Conditional Gene-Trap Mutagenesis in ZebrafishLisette A. Maddison, Mingyu Li, and Wenbiao Chen