Fig. 7

Genome-wide identification of genes whose expression levels are affected following fuchi knockdown. A MA-plots of log₂ fold-change (FC) versus log₂ average expression level (CPM) showing DEGs between fuchi pRNAi and control (untreated) embryos at stage 2 (st2), stage 3 (st3), and early stage 5 (st5e). Genes with FDR < 0.01 are highlighted in red or purple, with the purple genes included in both stage-3 and early stage-5 DEG lists. B Venn diagram showing the numbers of the DEGs from the three sample types and their overlaps. Note that fuchi (g26874) itself is included in all the DEG lists. C Graphs showing developmental profiling of the transcript levels for the top 10 DEGs from the stage-3 samples in wild-type embryos and the effects of fuchi pRNAi on the transcript levels. Top-hit proteins that resulted from blastx searches against mouse and Drosophila RefSeq protein databases are shown, although with no hits obtained with seven of the ten genes (E-value < 1e − 5). Data on fuchi (g26874) and α-catenin (g13984) validated the experiments. D Heat maps showing developmental profiling of the transcript levels for all the DEGs from the stage-3 (upper) and early stage-5 (lower) samples in wild-type embryos (sorted by FDR values). The top 50 DEGs from stage-3 are listed, where the genes included in stage-5 DEGs are indicated by purple asterisks. Genomic regions differentially accessible between wild-type and fuchi pRNAi embryos at stage 3 were found to be located within or close to some of the DEGs marked by “#” (related to Fig. 8 and Additional file 10: Table S13)