Transcript clustering identifies that genotype is the major driver of variation in the 4 months samples. (A) Singular value decomposition stratifies the 4 months samples into two groups based on genotype. (B). In addition, hierarchical clustering, suggests that two samples (shown in red) are outliers compared to the other samples, and so are not included in comparisons to identify differentially expressed (DE) genes. (C) DE genes were identified by comparing the three 4 months B6.APBTg (AD) samples with the three B6 control samples (WT) using Cuffdiff. A total of 151 DE genes were identified (90 upregulated, 61 downregulated, see Additional file 2: Table S2). (D) Pathway analysis identified axon guidance, vascular smooth muscle contraction (VSM cont.) and calcium signaling (Calc sign.) as over-represented pathways (P < 0.05). (E) Analysis of the DE genes with the greatest fold changes identified genes commonly associated with the hypothalamus as down regulated including oxytocin (Oxt), glycoprotein hormones, alpha polypeptide (Cga), pro-opiomelanocortin-alpha (Pomc) and growth hormone (Gh).