Transcript clustering of 5 months samples identified insulin signaling as a critical pathway activated in early stages of AD. (A) Hierarchical clustering clustered three of the 5 months AD samples with the 4 months samples (now termed Stage 1), and the remaining four with the 6 months samples (now termed Stage 2). The 5 months AD samples are shown in red. (B) The 5 months samples in Stage 1 were compared with the 5 months samples in Stage 2 using Cuffdiff. A total of 187 genes were differentially expressed (47 upregulated, 187 downregulated, see Additional file 3). (C) Pathway analysis showed that both the ribosome (Rib.) and insulin signaling pathway (Ins. Sign.) were overrepresented in the DE genes (P < 0.05). (D) Comparing Stage 1 with Stage 2, six genes in the insulin signaling pathway were differentially expressed (3 upregulated, 3 downregulated).