Fig. 6: Loss of Firre RNA affects gene expression.
From: Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome
a Upregulated genes in ΔFirreXa and Gene Ontology (GO) term enrichment. The Venn diagram shows the number of upregulated genes in ΔFirreXa versus WT, and in ΔFirreXa versus ΔFirreXa+mtransgene, with the overlapping gene set representing upregulated genes in ΔFirreXa that are rescued by transgene expression. The scatter plot shows dysregulated genes in ΔFirreXa versus WT (grey), with genes rescued by reduced expression in ΔFirreXa+mtransgene versus ΔFirreXa (more than 2-fold; p value < 0.05 by the Wald test) highlighted in orange. The top 20 GO terms of overlapping upregulated genes in ΔFirreXa versus WT, which are rescued in ΔFirreXa+mtransgene are listed. The X-axis indicates the FDR (−log10). b Downregulated genes in ΔFirreXa and Gene Ontology (GO) term enrichment. The Venn diagram shows the number of downregulated genes in ΔFirreXa versus WT, and in ΔFirreXa versus ΔFirreXa+mtransgene, the overlapping gene set representing downregulated genes in ΔFirreXa that are rescued by transgene expression. The scatter plot shows dysregulated genes in ΔFirreXa versus WT (gray), with genes rescued by increased expression in ΔFirreXa+mtransgene versus ΔFirreXa (more than 2-fold; p value <0.05 by the Wald test) highlighted in blue. The top 20 GO terms of overlapping downregulated genes in ΔFirreXa versus WT, which are rescued in ΔFirreXa+mtransgene are listed. The X-axis indicates the FDR (−log10). c Xi-expression fold changes for genes that are subject to or escape XCI between ΔFirreXa and WT. Upregulated genes are in red and downregulated genes in green. To note, one upregulated gene and one gene subject to XCI are in gray, as they showed more than 2-fold change in expression but with a p value >0.05 by the Wald test in ΔFirreXa versus WT. Genes are ordered from centromere to telomere along the Xi.
