Figure 3.

Gene set enrichment analysis of TCF-3 target genes. TCF-3-dependent genes were defined by gene expression profiling in three BL cell lines (BL41, Daudi, and Defauw) following TCF-3 knockdown (day 1 and day 2) or wild-type (wt) ID3 overexpression (day 1 and day 2) (Schmitz et al. 2012). To rank genes based on their TCF-3 dependency, a one-sample RVM t-test model (Wright and Simon 2003) was used to calculate p values against the null hypothesis that the average log-ratio was zero. Kolmogorov-Smirnov curves were generated for centroblast (A) and centrocyte (B) gene signatures (Victora et al. 2012), based on the ordering of BL gene expression data by their one-sided p values. Enrichment results were calculated by comparing the proportion of genes with one-sided p values < 0.01 inside and outside the centroblast and centrocytes signatures.