Genome-wide transcriptional profiling showed that reducing gravity levels in the International Space Station (ISS) causes important alterations in Drosophila gene expression intimately linked to imposed spaceflight-related environmental constrains during Drosophila metamorphosis. However simulation experiments on ground testing space-related environmental constraints show differential responses. Curiously although particular genes are not common in the different experiments the same GO groups including a large multigene family related with behavior stress response and organogenesis are over represented in them. A global and integrative analysis using the gene expression dynamics inspector (GEDI) self-organizing maps reveals different degrees in the responses of the transcriptome when using different environmental conditions or microgravity/hypergravity simulation devices. These results suggest that the transcriptome is finely tuned to normal gravity. In regular environmental conditions the alteration of this constant parameter on Earth can have mild effects on gene expression but when environmental conditions are far from optimal the gene expression is much more intense and consistent effects.