Representative genes differentially expressed in TRAF3−/−mouse B lymphomas identified by the transcriptome microarray analysis. (A) Heatmap of representative microarray data. The mRNA expression profiles of splenocytes from 3 pairs of LMC and tumor-bearing B-TRAF3−/− mice were analyzed by microarray analysis. cRNA was hybridized to the Illumina Sentrix MouseRef-8 24 K Array (Illumina). Genes shown in the heatmap are selected from 160 up-regulated and 244 down-regulated genes: red indicates overexpression, blue indicates underexpression, and black indicates median expression. Values under the color key indicates Log2 (fold of change). Dendrogram on top of the heatmap shows the relatedness between samples as determined by hierarchical clustering. (B) Verification of transcript up-regulation of genes identified by the microarray analysis using quantitative real time PCR. Total cellular RNA was prepared from splenocytes of LMC mice, or splenic B lymphomas (spl) and ascites (asc) of diseased B-TRAF3−/− mice, and cDNA was synthesized by reverse transcription. Real time PCR was performed using TaqMan primers and probes (FAM-labeled) specific for mouse Diras2, MCC, Tbc1d9, Ccbp2, Btbd14a, Sema7a, Twsg1, Ppap2b, TCF4, Tnfrsf19, Zcwpw1, and Abca3. Each reaction also included the probe (VIC-labeled) and primers for mouse β-actin mRNA, which served as endogenous control. Relative mRNA expression levels of each gene were analyzed using the Sequencing Detection Software (Applied Biosystems) and the comparative Ct (ΔΔCt) method. Graphs depict the results of two experiments with duplicate reactions in each experiment (mean ± S.D.), and mouse ID of each sample is indicated in the graphs.