Fig. 4

a The 100 probes most upregulated (red) or downregulated (green) with shRNA #1 to Wapal were identified and the Log2 fold change (Log2 FC) calculated for Wapal shRNA #2, Smc3 shRNAs, and from published studies in which the pluripotency-associated TFs Nanog or Oct4 were depleted by siRNAs. Log2 FC is displayed, with the color scheme indicated. b GSEA was used (see “Methods” section for details) to identify pathways globally dysregulated by Wapal depletion. Six gene sets from pluripotent cells which all exhibited substantial enrichment in Wapal-depleted samples are shown. Positive normalized enrichment score (NES) indicates that the gene set is enriched in Wapal-depleted samples as compared to samples infected with the empty vector. False discovery rate (FDR < 25 %) and p value <0.01 were used to determine statistically significant changes in gene set expression. c ChIP-seq datasets were used to generate a list of high-confidence targets of Polycomb-mediated gene silencing by the presence of both H3K27me3 and H2Aub1 in their promoters (1455 genes). For each gene, the expression changes after Wapal or Smc3 depletion were measured by microarray. For genes with multiple probes, maximal probe deviation was used. Genes that showed minimal change in their expression after Wapal depletion or the two shRNAs did not demonstrate similar changes were eliminated because of possible off-target effects. Log₂ fold change is displayed, with a color scheme shown below