Principal mechanisms of lysosomal gene regulation by IL-4 and Stat6. Analyses of gene expression data from wild-type and Stat6-deficient mouse macrophages (Additional file 9 and Figure 5) support a model in which lysosomal genes are regulated through three main mechanisms. The expression of lysosomal genes in category I (n = 42) is induced by IL-4 in a pathway that depends on Stat6. Category II genes (n = 82) are suppressed by IL-4 in Stat6-deficient cells, but are induced or remain unchanged in wild-type cells, which points to IL-4 triggering at least two opposing regulatory signals. Lysosomal genes in catergory III (n = 44) are suppressed by IL-4 in a Stat6-independent manner. The mechanisms by which IL-4 suppresses lysosomal gene expression in this system are currently unknown.