Fig. 3

Differential gene expression. Differential gene expression analysis was performed with the limma R package, version 3.38.3. Samples were grouped according to AFP status, and fold changes calculated between “high AFP” and “normal AFP” samples. Absolute fold changes of 2 with FDR = 0.05 are marked as blue lines. Significant genes are highlighted in red. The AFP gene is labeled. As expected, it shows the largest fold change of 3.97 (adjusted p = 1.72 × 10^–9). Differential expression according to AFP status and additional covariates ‘vascular invasion’ and ‘gender’ are summarized in Additional file 3: Table S2