About this book
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.
Table of contents
Methods in Molecular Biology: Gene Function Analysis
Table of Contents
Computational Methods I
1 Gene function inference from gene expression of deletion mutants
Ghislain Bidaut
2 Association analysis for large scale gene set data
Stefan Kirov, Bing Zhang, Jay Snoddy
3 Estimating Gene Function with Least Squares Nonnegative Matrix
Factorization
Guoli Wang and Michael F. Ochs
4 From Promoter Analysis to Transcriptional Regulatory Network
Prediction Using PAINT
Gregory E. Gonye, Praveen Chakravarthula, James S. Schwaber,
Rajanikanth Vadigepalli
5 Prediction of Intrinsic Disorder and its Use in Functional Proteomics
Vladimir N. Uversky, Predrag Radivojac, Lilia M. Iakoucheva, Zoran
Obradovic, A. Keith Dunker
Computational Methods II
6 Sybil: Methods and Software for Multiple Genome Comparison and
Visualization
Jonathan Crabtree, Samuel V. Angiuoli, Jennifer R. Wortman, Owen White
7 Estimating protein function using protein-protein relationships
Shailesh V. Date
8 Bioinformatics tools for modeling transcription factor target genes
and epigenetic changes
Ramana V. Davuluri
9 Mining Biomedical Data Using MetaMap Transfer (MMTx) and the Unified
Medical Language System (UMLS)
John D. Osborne, Simon Lin, Lihua (Julie) Zhu, Warren A. Kibbe
10 Statistical Methods for Identifying Differentially Expressed Gene
Combinations
Yen-Yi Ho, Leslie Cope, Marcel Dettling, Giovanni Parmigiani
Experimental Methods
11 Gene Function Analysis using the chicken B-cell Line DT40
Randolph B Caldwell, Petra Fiedler, Ulrike Schoetz and Jean-Marie
Buerstedde
12 Design and application of an shRNA-based gene replacement retrovirus.
Rugang Zhang, Peter D. Adams and Xiaofen Ye
13 Construction of simple and efficient DNA vector-based short hairpin
RNA
expression systems for specific gene silencing in mammalian cells
Tsung-Lin Cheng a and Wen-Tsan Chang
14 Selection of recombinant antibodies from antibody gene libraries
Michael Hust, Stefan Dübel and Thomas Schirrmann
15 A bacterial/yeast merged two-hybrid system: protocol for yeast
screening with single or parallel baits.
Nadezhda Tikhmyanova, Eugene Izumchenko, Ilya G. Serebriiskii, Erica A.
Golemis
16 A bacterial/yeast merged two-hybrid system: protocol for bacterial
screening
Ilya G. Serebriiskii, Nadia Milech, Erica A. Golemis
17 Engineering Cys2His2 Zinc Finger Domains using a Bacterial
Cell-Based Two-Hybrid Selection System
Stacey Thibodeau-Beganny and J. Keith Joung