Genome wide analysis of transcript levels following EGFR pathway perturbation

in the Drosophila ovary

We have used microarray analysis of Drosophila stage 9-10 egg chambers to study crosstalk among the 4 main signaling pathways known to be active in the dorsal anterior follicle cells. These are the ecdysone, TGF-b, EGF, and Notch receptor pathways. Hypomorphic loss-of-function (LOF) mutants for components of the Drosophila EGF receptor (DER) pathway as well as Gal4/UAS targeted overexpression of constitutively active (ca) mutant components were used to perturb the pathways. Labeled cDNA probes were prepared from purified ovarian RNA and hybridized to spotted DNA microarrays. The data from the microarrays was analyzed by: 1) removing data from damaged spots; 2) normalization by a [0,1] transformation; 3 discarding individual points that constitute statistical outliers among repeated experiments; and 4) clustering of averaged data values for the different genetic backgrounds. Viewing the clustered data in a hierarchical scheme enabled identification of groups of genes for which the transcriptional response in the LOF and gain-of-function (GOF) backgrounds complemented one another. These groups were searched for components of other signaling pathways.