Fig. 4

Expression profiles of clusters of probes affected by larval diet across adult diets and age classes in females (a) and males (b). In females (a), Clusters 1 and 4 were not associated with any significant enrichment of gene ontology (GO) terms or tissue-specific genes. Cluster 1 had variable expression in 0.25SY, low expression in 1SY, and high expression in 2.5SY-raised flies, while cluster 4 had roughly the opposite expression pattern. Expression of Cluster 2 and Cluster 3 in particular increases with increasing larval diet. Both clusters were enriched for genes annotated with GO terms relating to ribosomes. In males (b), clusters can be roughly classified into three different groups showing similar expression profiles. Clusters in the first group (Group 1) are most highly expressed in 0.25SY-raised flies and least expressed in 1SY-raised flies, while 2.5SY-raised flies fall in between. They differ primarily in the tightness of co-expression, with 2.5SY-raised flies showing the most variation. Clusters 1, 3 and 5 in Group 1 are very significantly enriched for genes with testes-specific expression, and for testes-specific GO terms and contain nearly half of all probes affected by larval diet in males. The second group (Group 2) shows the inverse expression profile of Group 1 and clusters also differ primarily in the tightness of co-expression, especially in 2.5SY-raised flies. The last group (Group 3) consists of one cluster whose expression is positively correlated with increasing larval diet. This cluster significantly overlaps in cluster composition with female cluster 3 (a) as well as sharing a similar expression profile and GO enrichment for terms related to ribosomes and transcription and translation. Clusters of probes with similar expression profiles were identified using K-means clustering. * indicates number of GO terms with Benjamin-corrected p-value <0.05 associated with a cluster *:1 term, **: 2 to 9 terms,***: 10 or more terms