ABSTRACT
ABSTRACT 190 SECTION 1 SAGE EXPERIMENTATION 190
1. What Is SAGE? 190 2. Brief Introduction to SAGE Procedure 191
A. Generation of the Library 192 3. What is the Difference between SAGE and Microarray? 194 4. Application of SAGE to Medical Research 196
A. SAGE in Cancer 197 B. SAGE in Cardiovascular Diseases 198 C. New Gene Mapping and Karyotyping 198
SECTION 2 SAGE DATA ANALYSIS 199 1. SAGE Data Analysis Steps 199 2. What Online Programs Are Available? 200 3. Demo: How to Analyze Generated Raw SAGE Data 202
A. Data Input 202 B. Scatter Plot 202 C. Identification of Tag 202 D. Data Exportation 203
SECTION 3 RETRIEVE DATA FROM SAGE DATABASES 204
1. Brief Introduction to Available SAGE Databases 204 2. How to Retrieve Data from GEO 207 3. Demo of the Procedure Preceding Section: A Step-By-Step Tutorial 208
ABSTRACT SAGE is a powerful technology for measuring global gene expression, through rapid generation of large numbers of transcript tags. It rivals microarray analysis, with the advantage that it is affordable for standard laboratories. It provides a platform to define complete metabolic pathways and has been applied to study responses to drug treatment. The SAGE technique’s high sensitivity and its global assessment of the transcriptome suggest that it is a perfect tool for analytical studies on representative samples to find candidate genes, which can be assessed in larger clinical populations. Although technically quite distinct, SAGE has some of the same limitations associated with microarray studies. As with microarrays, comparisons between SAGE studies of hormone-regulated gene expression in different tissues or cell types will likely reveal relatively limited overlaps in gene expression profiles. Comparisons between different SAGE studies may be complicated by the number of different statistical methods used to analyze expression patterns in SAGE libraries, which, like microarrays, must deal with “noise” associated with stochastic variations in gene expression. Nevertheless, SAGE will continue to be significant in building a reference database for gene expression analysis. This chapter describes the SAGE method, differences between SAGE and microarrays, applications of this technology to medical research, steps for SAGE data analysis, and methods to retrieve data from SAGE databases.
