InhaltsangabeMethods 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 YenYi 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 TsungLin Cheng a and WenTsan 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 CellBased TwoHybrid Selection System Stacey Thibodeau-Beganny and J. Keith Joung