Fig. 2

Transcriptome analysis of let-418; chd-3 double mutants identifies a gene population redundantly regulated by the two Mi2 homologues. a, b Venn Euler diagrams showing the total number of deregulated genes in each mutant genotype (wild-type on let-418(RNAi); chd-3(eh4) on control(RNAi); chd-3(eh4) on let-418(RNAi)) at the 24-cell (a) and 100-cell (b) stages, relative to control(RNAi)-treated wild-type embryos. List of genes deregulated more than 1.5 fold (log2 fold change) with a p value <0.1 were used. Common genes p value <0.01. c Dot plots of common deregulated genes between the indicated genotypes at 1 h (24-cell) or 3 h (100-cell) stages. Genes deregulated below the threshold Log2FC of 1.5 are displayed in gray shaded areas. d Proportion of up- and down-regulated genes in each RNA-Seq sample. e, f Venn Euler diagrams of commonly down-regulated genes in chd-3(eh4) mutants treated with control or let-418(RNAi) at the 24-cell (e) or 100-cell (f) stage. p values of common genes <0.01. g Cumulative enrichment of RNA-Seq up- or down-regulated genes in tissue- and stage-specific genes of the Spencer lists. Only enrichments with significant p value (<0.01) were scored. All enrichments were combined in one column per sample, but a same gene can be present in multiple lists. EE early embryo, LE late embryo, YA Young adults