AffyMiner: mining differentially expressed genes and biological knowledge in GeneChip microarray data

Background: DNA microarrays are a powerful tool for monitoring the expression of tens of thousands of genes simultaneously. With the advance of microarray technology, the challenge issue becomes how to analyze a large amount of microarray data and make biological sense of them. Affymetrix GeneChips are widely used microarrays, where a variety of statistical algorithms have been explored and used for detecting significant genes in the experiment. These methods rely solely on the quantitative data, i.e., signal intensity; however, qualitative data are also important parameters in detecting differentially expressed genes. Results: AffyMiner is a tool developed for detecting differentially expressed genes in Affymetrix GeneChip microarray data and for associating gene annotation and gene ontology information with the genes detected. AffyMiner consists of the functional modules, GeneFinder for detecting significant genes in a treatment versus control experiment and GOTree for mapping genes...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Guoqing Lu, The V. Nguyen, Yuannan Xia, Michael Fromm
• Keywords: Affymetrix Genechips, BMCBI 2006, Microarray Data, Significant Genes