Fig. 3

Characteristics of differentially expressed genes. a Heatmap showing enrichment for genes expressed in tissues (rows) of wild-type flies from FlyAtlas among genes in the Fig. 2 clusters or among all genes expressed in our study (columns). The proportion of genes in a column enriched in each tissue (see key) is shown in hierarchical order. Tissues are written out except: ta ganglion = thoracicoabdominal ganglion; CNS = central nervous system; acc gland = male accessory gland; V = virgin, and M = mated. The carcass is the thorax and abdomen without gut and reproductive tract. b Heatmap showing GO biological process terms (rows) enriched in any cluster (see key). GO terms are also presented in hierarchical clustering order. c-d Browser views showing expression of two sets of related genes that are genomic neighbors and are positively regulated by lilli and Su(Tpl) (female, one day after induction). c The lysosomal α-mannosidase (LMan) genes. d The Jonah (Jon) chymotrypsin genes. Chromosome arm and genome coordinates are shown (top). The longest annotated transcript of each gene is shown. In the gene models, untranslated (gray boxes) and coding (yellow boxes) regions, and introns (gray lines) are shown. Transcription direction is shown (bent arrows). Base-level read density per million reads (RPM) (see Methods; arbitrary scale) is shown for RNAi (light green) and sham (dark green) as are test genes or sham abbreviations (right). Instances of significant induction-dependent differential expression are indicated (asterisks). e Boxplot of primary transcript length (in base pairs) by cluster (blue) or among all expressed genes (green). Clusters with significantly shorter (Wilcoxon rank test, p < 0.05) primary transcript than all expressed genes are indicated (asterisks)