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. 2021 Nov 18;17(11):e1009908. doi: 10.1371/journal.pgen.1009908

Fig 3. A four-way comparison identifies DEGs that distinguish normal embryo development from Ehmt2 zygotic mutant embryo development.

Fig 3

(A) Four-way comparison. The four questions are depicted by arrows: “what it takes to develop” from 6- to 12-somite stage in the normal or in the mutant embryo (green arrows indicate the WT12-WT6 and HOMO12-HOMO6 comparisons), and “what it takes to be normal” at 6-somites or at the 12-somite stage (orange arrows mark the WT6-HOMO6 and WT12-HOMO12 comparisons). (B) Identifying what it takes to be normal. Venn diagrams show the number of the downregulated (left) and upregulated (right) DEGs between the Ehmt2+/+ (WT) and the Ehmt2−/− (HOMO) embryos at the 6-somite stage and at the 12-somite stage. (C) Identifying what it takes to develop from 6- to 12-somite stage. Venn diagrams show the number of downregulated (left) and upregulated (right) DEGs between the 12-somite and 6-somite stages, during normal Ehmt2+/+ (WT), or mutant Ehmt2−/− (HOMO) development. (D-E) Venn diagrams merge all of the downregulated (D), or all of the upregulated (E) DEGs from the two-way comparisons as described above. (F) Gene ontology analysis of the DEGs. Bubble plots depict the GO terms enriched in the segments of the 4-way Venn diagrams as indicated to the left and marked by arrows as above. (G-H) Understanding what it takes to be normal between WT6 vs. HOMO6, but not between WT12 vs. HOMO12 embryos. The Venn diagram segment is displayed in a heatmap (G) and as IGV browser examples (H). (I-L) Understanding what it takes to develop. Downregulation of 75 genes (I) or upregulation of 191 genes (K) only occurs between the 6-and 12- somite stages only in normal development (WT12 vs. WT6), but not in mutant development (HOMO12 vs. HOMO6); therefore, these developmental-specific changes require EHMT2. These are false negatives of the conventional WT12-HOMO6 comparison. Heatmaps (I and K) are shown for the Venn-diagram sections and IGV browser examples (J and L) are shown for the DEGs that drive the GO term in those sections.