Extract‐SAGE: An integrated platform for cross­analysis and GA­based selection of SAGE data

Serial analysis of gene expression (SAGE) is a powerful quantification technique for gene expression data. The huge amount of tag data in SAGE libraries of samples is difficult to analyze with current SAGE analysis tools. Data is often not provided in a biologically significant way for cross‐analysis and ‐comparison, thus limiting its application. Hence, an integrated software platform that can perform such a complex task is required. Here, we implement set theory for cross‐analyzing gene expression data among different SAGE libraries of tissue sources; up‐ or down‐regulated tissue‐specific tags can be identified computationally. Extract‐SAGE employs a genetic algorithm (GA) to reduce the number of genes among the SAGE libraries. Its representative tag mining will facilitate the discovery of the candidate genes with discriminating gene expression. AVAILABILITY: This software and user manual are freely available at ftp://sage@bio.kuas.edu.tw/Extract-SAGE.zip.