Fig. 2

Illustration of the grouping scheme for target genes of a transcription factor. a The co-expression matrix of MYB target genes in shRNA knockdown of MYB lymphoma cells by hierarchical clustering analysis (Pearson correlation and complete linkage). b, c The poor clustering results from the co-expression of randomly selected 100 (b) and 200 genes (c). In panels a–c, the left subplots show the outcomes of all tested genes, and the right subplots show the outcomes of genes after the filtering step. Compared to the random cases, MYB target genes have a clear pattern of red and blue diagonal blocks from their co-expression. d, e The percentage of differentially expressed genes remained after the filtering step in the case of FOXM1 and MYB knockdown, respectively. f, g The proportion of genes from the activation group that are positively correlated with the TF expression (red bars) and the proportion of genes from the inhibition group that are negatively correlated with the TF expression (blue bars). h Spearman correlation (average and standard deviation) between TF activity and target expression (red) and between TF expression and target expression (blue)