Computational Methods I -- Gene Function Inference From Gene Expression of Deletion Mutants -- Association Analysis for Large-Scale Gene Set Data -- Estimating Gene Function With Least Squares Nonnegative Matrix Factorization -- From Promoter Analysis to Transcriptional Regulatory Network Prediction Using PAINT -- Prediction of Intrinsic Disorder and Its Use in Functional Proteomics -- Computational Methods II -- Sybil: Methods and Software for Multiple Genome Comparison and Visualization -- Estimating Protein Function Using Protein-Protein Relationships -- Bioinformatics Tools for Modeling Transcription Factor Target Genes and Epigenetic Changes -- Mining Biomedical Data Using MetaMap Transfer (MMTx) and the Unified Medical Language System (UMLS) -- Statistical Methods for Identifying Differentially Expressed Gene Combinations -- Experimental Methods -- Gene Function Analysis Using the Chicken B-Cell Line DT40 -- Design and Application of a shRNA-Based Gene Replacement Retrovirus -- Construction of Simple and Efficient DNA Vector-Based Short Hairpin RNA Expression Systems for Specific Gene Silencing in Mammalian Cells -- Selection of Recombinant Antibodies From Antibody Gene Libraries -- A Bacterial/Yeast Merged Two-Hybrid System -- A Bacterial/Yeast Merged Two-Hybrid System -- Engineering Cys2His2 Zinc Finger Domains Using a Bacterial Cell-Based Two-Hybrid Selection System.

With the advent of high-throughput technologies, the number of genes of interest has expanded and the traditional methods for gene function analysis cannot achieve the throughput necessary for large-scale exploration. In Gene Function Analysis, a select team of experts bring together a number of recently developed techniques for studying gene function. The volume begins with a variety of computational techniques, which provide an excellent point of departure for the cutting-edge experimental methods that follow. Written in the highly successful Methods in Molecular Biology™ series format, each chapter surveys its subject with readily reproducible laboratory protocols, a list of the necessary materials, and the popular Notes section, which contains tips for troubleshooting and avoiding known pitfalls. Comprehensive and timely, Gene Function Analysis offers researchers a clear guide and the important tools they need to further study the intricate human genome.