Figure 3

Gene expression profile of lymphoproliferative disease of BCL2⁺IL6⁺AID⁻ mice. (a) Heat map of differentially expressed genes in AID-deficient tissues (open square) compared with AID-proficient tissues (closed square). Up and downregulated genes are indicated in red and blue, respectively. Illumina microarray data were processed using GenomeStudio v1.9.0 (Illumina). Raw expression values were normalized using the quantile method and assessed for genes with differential expression based on analysis of variance (ANOVA). Probe set values were normalized to a mean of zero (mean centered) and a standard deviation of one. The false discovery rate (FDR) was then applied to adjust P-values for Multiple test correction. Differentially expressed genes were selected with thresholds based on FDR-adjusted P-values smaller than 0.01 and fold changes larger than 2 or smaller than −2. (b) Shown on the right is a heat map of the top-50 ANOVA-selected genes found to be differentially expressed in the AID⁺ and AID⁻ samples included in panel a. Shown on the left is a bar graph of fold expression changes of the top 10 up or downregulated genes (labeled below and above the x-axis, respectively). (c) Presented to the left is a gene set enrichment analysis-generated enrichment plot of a genetic pathway, GNF2_LYN, that distinguished AID⁺ and AID⁻ samples and contained Myd88 as a core enrichment gene up-regulated in the AID⁻ sample. Depicted to the right is a heat map of the expression of GNF2_LYN enrichment genes in AID⁺ and AID⁻ tissues. The enrichment core (12 genes) is indicated by a green vertical line that is labeled with gene symbols. The location of Myd88 (4th gene from the top) is marked by a left-pointing black arrow. (d) Table of pathway regulators (column 1) identified as activated or inhibited in AID⁻ samples (column 2) using IPA’s upstream analysis module (Ingenuity Systems, Redwood City, CA, USA). The WebGestalt gene set analysis tool (http://bioinfo.vanderbilt.edu/webgestalt) confirmed the activation of NFκB in AID⁻ vs AID⁺ tumors, as NFκB was the only pathway represented twice among the top 10 pathways (not shown). The enrichment ratios were 3.61 (P=7.3 × 10⁻⁵) and 3.55 (P=2 × 10⁻³), respectively.