Description
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. Part I. Reviews 1. The Present State and Future Direction of Integrated Gene Function Analysis Michael F. Ochs Part II. Computational Methods 2. Performing Integrative Functional Genomics Analysis in GeneWeaver.org Jeremy J. Jay and Elissa J. Chesler 3. Functional Annotation of Differentially Regulated Geneset Using WebGestalt: A Geneset Predictive of Response to Ipilimumab in Tumor Biopsies Stefan Kirov, R. Ji R., J. Wang , and B. Zhang 4. Integrative Data-Mining Tools to Link Fene and Function Basma El Yacoubi and Valrie de Crcy-Lagard 5. Detection of Driver Protein Complexes in Breast Cancer Metastasis by Large Scale Transcriptome-Interactome Integration Maxime Garcia, Pascal Finetti, Francois Bertucci, Daniel Birnbaum, and Ghislain Bidaut 6. Pattern Identification in Time Course Gene Expression Data with the CoGAPS Matrix Factorization Elana J. Fertig, Genevieve Stein-O’Brien, Andrew Jaffe, and Carlo Colantuoni 7. Statistical Tools and R Software for Cancer Driver Probabilities Giovanni Parmigiani, Simina Boca, Jie Ding, and Lorenzo Trippa 8. Predicting the Functional Consequences of Somatic Missense Mutations Found in Tumors Hannah Carter and Rachel Karchin 9. Determining the Effect of DNA Methylation on Gene Expression in Cancer Cells Chai-Jin Lee, Jared Evans, Kwangsoo Kim, Heejoon Chae, and Sun Kim 10. Reverse Engineering Transcriptional Gene Network Vincenzo Belcastro and Diego di Bernardo 11. Integrating In Silico Resources to Map a Signaling Network Hanqing 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 Pogostick Bin Chen and Antnia Monteiro 13. Construction and Application of Site-specific Artificial Nucleases for Targeted Gene Editing Fatma O. Kok, Ankit Gupta, Nathan D. Lawson, and Scot A. Wolfe 14. Selection of Recombinant Antibodies from Antibody Gene Libraries Michael Hust, Andr Frenzel, Thomas Schirrmann, and Stefan Dbel 15. Construction of Simple and Efficient siRNA Validation Systems for Screening and Identification of Effective RNAi-Targeted Sequences from Mammalian Genes Wen-Hui Tsai and Wen-Tsan Chang 16. Rapid Genetic Modification of Mouse Embryonic Stem Cells by Inducible Cassette Exchange Recombination Michelina Iacovino, Megan E. Roth, and Michael Kyba 17. In Ovo Electroporation of miRNA-Based Plasmids to Investigate Gene Function in the Developing Neural Tube Irwin Andermatt, Nicole Wilson, and Esther T. Stoeckli 18. Proteomic Strategies: SILAC and 2D-DIGE – Powerful Tool to Investigate Cellular Alterations Arundhathi Sriharshan, Omid Azimzadeh, Randolph B. Caldwell, and Soile Tapio 19. Conditional Gene-Trap Mutagenesis in Zebrafish Lisette A. Maddison, Mingyu Li, and Wenbiao Chen
