Gene expression profiles and functional annotations for the eight largest clusters of co-expressed genes. On the left-hand side the average expression levels for the genes in the eight clusters are shown (log2-transformed expression values, divided by the median for that gene across all time points and treatments). Dashed lines represent parasitized and unbroken lines represent unparasitized larvae, and the bars indicate standard errors. Functional annotations associated with clusters are shown along the top, and colors in the matrix indicate the strength of association (yellow = Ease scores (see text) <0.05; red = after Bonferroni correction at P < 0.05; grey = at least one gene with this annotation). The full annotation for all probe sets is provided in Additional data file 1.