Gene Function Analysis

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 Valerie de Crecy-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 Antonia 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, Andre Frenzel, Thomas Schirrmann, and Stefan Dubel 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