High frequency of B-catenin mutations in mouse HCCs induced by a non-genotoxic CAR agonist

Microarray data analysis
For the gene expression profile, 150 ng of RNA were amplified (Illumina TotalPrep RNA Amplification Kit), labeled and hybridized on Illumina microarray (RatRef-12 V1 BeadChips, Illumina Inc., San Diego, CA, USA), including 21,791 genes.The intensity files were loaded into the Illumina BeadStudio 3.0.19.0 software (Illumina Inc, San Diego, CA, USA) and BRB Array Tools (Version 4.2.0) for quality control and gene expression analysis. First, the quantile normalization algorithm was applied on the dataset. Only genes whose expression differed by at least 1.5 fold from the median in at least 20% of the arrays and characterized by a 50th percentile of intensities greater than 300 were retained. The FDR-adjusted p-values were calculated using the Benjamini-Hochberg procedure [39]. According to these criteria, 2,281 expressed transcripts out of 21,791 showed reproducible up- or down-regulation. To identify the differentially expressed genes, we applied the Random-Variance Model and Multivariate Permutation Test. Following this analysis, 1,784 genes showed reproducible up- or down-regulation in at least one comparison