Differential Display Methods and Protocols

1. Front Matter

   Pages i-xiii

   PDF

2. Methodologies

   1. Front Matter

      Pages 1-1

      PDF

   2. Global Analysis of Gene Expression by Differential Display

      • Shitao Yang, Peng Liang

      Pages 3-21

   3. Automation of Fluorescent Differential Display With Digital Readout

      • Jonathan D. Meade, Yong-jig Cho, Jeffrey S. Fisher, Jamie C. Walden, Zhen Guo, Peng Liang

      Pages 23-57

   4. Ordered Differential Display

      • Mikhail V. Matz, Ella A. Meleshkevitch

      Pages 59-74

   5. GeneCalling®

      • Richard A. Shimkets

      Pages 75-83

   6. High-Density Sampling Differential Display of Prokaryotic mRNAs With RAP-PCR

      • Dana M. Walters, Pierre E. Rouvière

      Pages 85-97

   7. Vertical Arrays

      • Rosana Risques, Gaelle Rondeau, Martin Judex, Michael McClelland, John Welsh

      Pages 99-109

   8. Automated Pattern Ranking in Differential Display Data Analysis

      • Tero Aittokallio, Pekka Ojala, Timo J. Nevalainen, Olli S. Nevalainen

      Pages 111-122

   9. Linking cDNA-AFLP-Based Gene Expression Patterns and ESTs

      • Ling Qin, Pjotr Prins, Johannes Helder

      Pages 123-138

3. Applications

   1. Front Matter

      Pages 139-139

      PDF

   2. Differentially Expressed Genes Associated With Hepatitis B Virus HBx and MHBs Protein Function in Hepatocellular Carcinoma

      • Dae-Ghon Kim

      Pages 141-155

   3. Identification of Disease Markers by Differential Display

      • Michael Clinton, Gino Miele, Sunil Nandi, Derek McBride

      Pages 157-178

   4. Saturation Screening for p53 Target Genes by Digital Fluorescent Differential Display

      • Yong-jig Cho, Susanne Stein, Roger S. Jackson, Peng Liang

      Pages 179-192

   5. Identification of p53-Regulated Genes by the Method of Differential Display

      • Yunping Lin, Roger P. Leng, Samuel Benchimol

      Pages 193-206

   6. Identification by Differential Display of IL-24 Autocrine Loop Activated by Ras Oncogenes

      • Zhongjia Tan, Mai Wang, Peng Liang

      Pages 207-218

   7. Comprehensive Analysis of Ovarian Gene Expression During Ovulation Using Differential Display

      • Lawrence L. Espey

      Pages 219-241

   8. Functional Analysis of Nocturnin

      • Julie E. Baggs, Carla B. Green

      Pages 243-254

   9. Isolation and Characterization of Anthocyanin 5-O-Glucosyltransferase in Perilla frutescens var. crispa by Differential Display

      • Mami Yamazaki, Kazuki Saito

      Pages 255-266

   10. Identification of Target Genes of a Yeast Transcriptional Repressor

       • Bernard Mai, Linda L. Breeden

       Pages 267-277

Since the first edition of this book dedicated to differential display (DD) technology was published in 1997, we have witnessed an explosive interest in studying differential gene expression. The gene-hunting euphoria was initially powered by the invention of DD, which was gradually overtaken by DNA microarray technology in recent years. Then why is there still the need for second edition of this DD book? First of all, DD still enjoys a substantial lead over DNA microarrays in the ISI citation data (see Table 1), despite the h- dreds of millions of dollars spent each year on arrays. This may come as a surprise to many, but to us it implies that many of the DNA microarray studies went unpublished owing to their unfulfilled promises (1). Second, unlike DNA microarrays, DD is an “open”-ended gene discovery method that does not depend on prior genome sequence information of the organism being studied. As such, DD is applicable to the study of all living organisms—from bacteria, fungi, insects, fish, plants, to mammals—even when their genomes are not sequenced. Second, DD is more accessible technically and financially to most cost-conscious “cottage-industry” academic laboratories. So clearly DD still has its unique place in the modern molecular biological toolbox for gene expression analysis.

• DNA
• Microarray
• PCR
• fungi
• gene expression
• genes
• transcription

"The variety of applications...is so broad that almost every newcomer...can use these protocols as a starting point for a specific study...highly recommended for purchase by everyone interested in the comparative gene expression, and especially to newcomers to the field." -Trends in Biotechnology

From Reviews of the First Edition...
"...really helpful for all geneticists and cellular and molecular biologists...a precious book which should be in all hands!" -Cellular and Molecular Biology

"...For any would-be gene hunter thinking of or already practicing differential display, this book will provide an invaluable and long overdue guide to the technique." -Molecular Medicine

"....an ideal resource for any research group interested in using DD." -Microbiology Today

"...highly recommend[ed]...for purchase by everyone interested in the comparative gene expression,, and especially to newcomers to the field." -Trends in Biotechnology

• Department of Cancer Biology, The Vanderbilt-Ingram Cancer Center, Nashville

  Peng Liang

• GenHunter Corporation, Nashville

  Jonathan D. Meade

• Dana Farber Cancer Institute, Boston

  Arthur B. Pardee

Policies and ethics