Transcriptomic analysis of gene regulation by nanoparticles. A) Hierarchical clustering of significantly effected (compared to time matched controls) transcripts shows a higher preponderance of down regulation (green) by SPIO nanoparticle exposures. Up-regulation (red) was more prominent during earlier time points where the most highly induced mRNAs encoded inflammatory cytokines. B) Highest ranking biological processes associated with transcripts up-regulated by in vivo exposure to SPIO nanoparticles. Cellular processes associated with inflammation and clearance of foreign bodies (cytokine production, cell migration, chemotaxis) were significantly upregulated.