Figure 4

Manual SNP selection to study Insig1 → Dhrc7 and Insig1 → Fdft1 in mouse liver. Using female liver gene expression data and SNP markers from the BxH mouse intercross, NEO retrieves known causal relationships in the cholesterol biosynthesis pathway: Insig1 → Dhrc7 and Insig1 → Fdft1. The single marker LOD score curves in (a) motivate our choice of manually selected SNPs (one SNP on chromosome 16 and another on chromosome 8). These SNP markers can also be used to screen for genes that are reactive to Insig1, see Table 2. Figures (b) and (c) show the causal models used to compute the model p-values in favor of edge orientations Insig 1 → Dhcr 7 and Insig 1 → Fdft 1, respectively. More details on the individual edges are presented in Table 1.