Differential Display Methods and Protocols

Preface ..............................................................................................................v Contributors .....................................................................................................xi PART I. METHODOLOGIES 1 Global Analysis of Gene Expression by Differential Display: A Mathematical Model Shitao Yang and Peng Liang .................................................................. 3 2 Automation of Fluorescent Differential Display With Digital Readout Jonathan D. Meade, Yong-jig Cho, Jeffrey S. Fisher, Jamie C. Walden, Zhen Guo, and Peng Liang ................................ 23 3 Ordered Differential Display Mikhail V. Matz and Ella A. Meleshkevitch ........................................ 59 4 GeneCalling®: Transcript Profiling Coupled to a Gene Database Query Richard A. Shimkets ............................................................................ 75 5 High-Density Sampling Differential Display of Prokaryotic mRNAs With RAP-PCR Dana M. Walters and Pierre E. Rouvière ............................................ 85 6 Vertical Arrays: Microarrays of Complex Mixtures of Nucleic Acids Rosana Risques, Gaelle Rondeau, Martin Judex, Michael McClelland, and John Welsh ............................................ 99 7 Automated Pattern Ranking in Differential Display Data Analysis Tero Aittokallio, Pekka Ojala, Timo J. Nevalainen, and Olli S. Nevalainen .................................................................. 111 8 Linking cDNA-AFLP-Based Gene Expression Patterns and ESTs Ling Qin, Pjotr Prins, and Johannes Helder ..................................... 123 PART II. APPLICATIONS 9 Differentially Expressed Genes Associated With Hepatitis B Virus HBx and MHBs Protein Function in Hepatocellular Carcinoma Dae-Ghon Kim .................................................................................. 141 10 Identification of Disease Markers by Differential Display: Prion Disease Michael Clinton, Gino Miele, Sunil Nandi, and Derek McBride ...................................................................... 157 11 Saturation Screening for p53 Target Genes by Digital Fluorescent Differential Display Yong-Jig Cho, Susanne Stein, Roger S. Jackson II, and Peng Liang.............................................................................. 179 12 Identification of p53-Regulated Genes by the Method of Differential Display Yunping Lin, Roger P. Leng, and Samuel Benchimol........................ 193 13 Identification by Differential Display of IL-24 Autocrine Loop Activated by Ras Oncogenes Zhongjia Tan, Mai Wang, and Peng Liang ........................................ 207 14 Comprehensive Analysis of Ovarian Gene Expression During Ovulation Using Differential Display Lawrence L. Espey ............................................................................. 219 15 Functional Analysis of Nocturnin: A Circadian Clock-Regulated Gene Identified by Differential Display Julie E. Baggs and Carla B. Green ..................................................... 243 16 Isolation and Characterization of Anthocyanin 5-O-Glucosyltransferase in Perilla frutescens var. crispa by Differential Display Mami Yamazaki and Kazuki Saito .................................................... 255 17 Identification of Target Genes of a Yeast Transcriptional Repressor Bernard Mai and Linda L. Breeden ................................................... 267 18 Detection of an mRNA Polymorphism by Differential Display Shan Liang, S. Paul Rossby, Peng Liang, Richard C. Shelton, D. Hal Manier, Amitabha Chakrabarti, and Fridolin Sulser ................ 279 19 Silencing in Yeast: Identification of Clr4 Targets Sergey V. Ivanov and Alla V. Ivanova .............................................. 287 20 Identification of mRNA Bound to RNA Binding Proteins by Differential Display Anne Carr-Schmid, Xinfu Jiao, and Megerditch Kiledjian ................ 299 Index ............................................................................................................ 315