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 Valérie de Crécy-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 Antónia 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, 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 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