Fig. 4

A linear component in the propagation of silencing over chromosome X outwards from the XIC. a K-means clustering during XCI identifies four groups (present in the four rows) of genes with different inactivation kinetics on the Xi: early inactivated genes (top row), genes that show inactivation at intermediate time points (second row), late inactivated genes (third row) and genes that are not inactivated (bottom row). The first three columns show the inactivation dynamics within the four clusters over the time course as an average (left) of the individual genes within the clusters, as a lineplot (middle) or as a heatmap (right). b Examples of genes within the clusters as shown in (a). Total expression levels in black, the contribution from the 129-derived or Cast-derived alleles in green and blue, respectively. See Additional file 1: Figure S6 for the genome browser views of the genes. c Location of the genes within the clusters as obtained in (a) over the linear X chromosome. On the right, the first column shows the clusters and the number of genes within each cluster. The second column shows the average distance of the genes within a cluster to the XIC. The last column shows the p value calculated using the gene set enrichment analysis (GSEA) rank test corrected for multiple testing (using FDR (false discovery rate); *significant). The running sum statistics for each cluster for the GSEA is shown in Additional file 1: Figure S9. d Early silencing of genes on the Xi plotting the Xi/Xa ratio per gene at day 2 after the onset of EB differentiation over the linear X chromosome. The trend line (polynomial order 3) of the Xi/Xa ratio is plotted in red