We have developed an application called HAPI (High-Density Array Pattern Interpreter), which facilitates the analysis of microarray data by selecting subsets of genes with specific characteristics and displaying them with dynamic links to web-based databases. This allows comparison of subsets of selected genes by determining similarities and common properties of a selected set of genes using a lexical algorithm based on Mesh keywords associated with each gene. We tested the software's potential by analysing the transcriptional changes induced by the infection of CD 4+ T cells with the human immunodeficiency virus type 1 (HIV-1). Aliquots of either infected or uninfected control cells were obtained at 30 minutes, 2, 4, 8, 16, 24, 48 and 72 hours after infection or mock-infection (control) and analysed with the Hu6800 GeneChip. HIV infection of a CD4+ T cell modulated a large number of genes at the transcriptional level. Genes were repressed, induced or modulated significantly very early after inoculation of the virus. Some expected outcomes such as the activation of NFkB, p68 kinase and Rnase L were confirmed by the GeneChip analysis and further corroborated by using real-time quantitative PCR. The modulation of genes and gene families not previously considered associated with HIV infection was also uncovered. Functional genomic approaches represent powerful tools to dissect the relationship between infectious agents and their host cells.
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