All microarray data are MIAME compliant. Raw data has been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE25988. RNA was isolated from 3 groups of 200 fly heads from each genotype and hybridized to Affymetrix Drosophila 2.0 oligonucleotide microarray chips at the Partners HealthCare Center for Personalized Genetic Medicine Microarray Facility (Harvard University). Microarray data was processed and analyzed as described in Kong et al. [45]. Genes were selected as differentially expressed by pairwise t-tests between the w;iso control, the BxJ, and the EP1306 mutants with a cutoff of P<0.05 following normalization and subtraction of the averaged w;iso control. The 555 genes that were chosen for clustering were then further selected by ANOVA with a P<0.05. Clustering was performed using the HOPACH (Hierarchical Ordered Partitioning and Collapsing Hybrid) algorithm [25].
