Analysis of gene expression in HIV transgenic mice (TG26) with lymphoma in comparison to asymptomatic TG26 mice, and background control (FVBN).Tg26 carries a pNL4-3 HIV-1 provirus lacking part of the gag-pol region, rendering the virus non-infectious.. Mus musculus

About 15% of the TG26 mice develop lymphoma. HIV protein expression is observed, particularly the protein p17/Matrix. Total cellular RNA from spleen and lymph nodes from 3 groups of animals: FVB/N controls (n=3), Tg26 asymptomatic (n=6), and Tg26 with lymphoma (n=6). Results provide insights into the gene expression program in animals with lymphoma. Overall design: Gene expression analysis was performed using Affymetrix GeneChip Mouse Gene 1.0 ST to identify genes and pathways associated wirh B Cell Lymphoma in HIV-1 Transgenic Mice. Raw data pre-processing was monitored using standard diagnostic plots (i.e., 2-D image plots, RNA degradation plots, MA-plots, and box plots). Affymetrix microarray data were normalized at probe-level by using the Frozen Robust Multiarray Analysis (fRMA) method. A generalized linear model approach, coupled with empirical Bayes standard errors shrinkage, and including coefficients for data heterogeneity as derived from surrogate variable analysis (SVA), was used for identifying differentially expressed genes between animal groups. Correction for multiple testing was performed using the Benjamini–Hochberg method.