mRNA-sequencing and ChIA-PET analyses.

<p><i>Sim2</i> (<b>a</b>) and <i>Arnt</i> (<b>b</b>) mRNA levels (RPKM) in A6, B8, C4 SIM2 clones and three EB3 replicates. <b>c.</b> Comparison of the gene expression level (mean log2 RPKM between the 3 replicates) between <i>Sim2</i> expressing cells (y-axis) and EB3 control cells (x-axis). Each blue dot represents a gene; differentially expressed genes (EdgeR FDR<0.05) are shown in red. The diagonal line represents the expected distribution of genes equally expressed between <i>Sim2</i> expressing and non-expressing cells. <b>d.</b> Enrichment of Sim2 targets among the genes upregulated in <i>Sim2</i> expressing clones as revealed by the GSEA analysis. Genes were sorted according to their expression fold change between <i>Sim2</i> expressing and non-expressing cells (x-axis, 0 showing the most upregulated gene). Black vertical bars show the position of the SIM2 targets in the ranked list. The enrichment score (ES in green) significantly deviates from zero at the beginning of the distribution showing that the SIM2 targets are not randomly distributed in the ranked list but enriched among the most upregulated genes. p: FDR corrected p-value <b>e.</b> ChIA-PET interactions occurring between SIM2 DNA binding sites and promoters of genes differentially expressed in <i>Sim2</i> expressing cells compared to EB3 cells (FDR<0.05). Blue lines show inter-chromosomal interactions and red lines intra-chromosomal interactions.