Gene Function Analysis

by Ochs, Michael F.

• ISBN13: 9781588297341
• ISBN10: 1588297349
• Edition: 1st
• Format: Hardcover
• Copyright: 2007-09-19
• Publisher: Humana Pr Inc

Summary

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[Trademark] 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.

Table of Contents

Preface	p. vii
Contributors	p. xiii
Computational Methods I
Gene Function Inference From Gene Expression of Deletion Mutants	p. 1
Association Analysis for Large-Scale Gene Set Data	p. 19
Estimating Gene Function With Least Squares Nonnegative Matrix Factorization	p. 35
From Promoter Analysis to Transcriptional Regulatory Network Prediction Using PAINT	p. 49
Prediction of Intrinsic Disorder and Its Use in Functional Proteomics	p. 69
Computational Methods II
Sybil: Methods and Software for Multiple Genome Comparison and Visualization	p. 93
Estimating Protein Function Using Protein-Protein Relationships	p. 109
Bioinformatics Tools for Modeling Transcription Factor Target Genes and Epigenetic Changes	p. 129
Mining Biomedical Data Using MetaMap Transfer (MMTx) and the Unified Medical Language System (UMLS)	p. 153
Statistical Methods for Identifying Differentially Expressed Gene Combinations	p. 171
Experimental Methods
Gene Function Analysis Using the Chicken B-Cell Line DT40	p. 193
Design and Application of a shRNA-Based Gene Replacement Retrovirus	p. 211
Construction of Simple and Efficient DNA Vector-Based Short Hairpin RNA Expression Systems for Specific Gene Silencing in Mammalian Cells	p. 223
Selection of Recombinant Antibodies From Antibody Gene Libraries	p. 243
A Bacterial/Yeast Merged Two-Hybrid System: Protocol for Yeast Screening With Single or Parallel Baits	p. 257
A Bacterial/Yeast Merged Two-Hybrid System: Protocol for Bacterial Screening	p. 291
Engineering Cys2His2 Zinc Finger Domains Using a Bacterial Cell-Based Two-Hybrid Selection System	p. 317
Index	p. 335
Table of Contents provided by Ingram. All Rights Reserved.