Table 1

Putative direct LXR target genesa

Gene type and KEGG pathway (KEGG pathway identifier)No. of genesP value% of genes with the adjacent LXR-RXR peak
LXR-induced genes (59 genes, 63% with peaks)
    PPAR signaling pathway (mmu03320)73.32E−05100
    Polyunsaturated fatty acid biosynthesis (mmu01040)48.82E−05100
    Limonene and pinene degradation (mmu00903)30.008100
    Benzoate degradation via CoA ligation (mmu00632)30.010100
    Bile acid biosynthesis (mmu00120)30.013100
    Glycerolipid metabolism (mmu00561)30.019100
     Valine, leucine, and isoleucine degradation (mmu00280)30.021100
    Fatty acid metabolism (mmu00071)30.022100
    Fatty acid biosynthesis (mmu00061)20.032100
    Glycerophospholipid metabolism (mmu00564)30.042100
LXR-repressed genes (102 genes, 70% with peaks)
    Complement and coagulation cascades (mmu04610)83.21E−06100
    PPAR signaling pathway (mmu03320)50.005100
  • a Putative direct LXR target genes were identified by selecting genes with an adjacent LXR-RXR binding site(s) and counting the recovered RNA polymerase II ChIP-seq tags within gene bodies (position plus 250 to the end of the gene) in wild-type (WT) and LXRα/β double knockout (LXRdKO) mice treated with vehicle (Veh) or T0901317 (T09), respectively. LXR-regulated genes were defined as induced genes if the following condition was met: no. of tags for T09-treated WT mice/no. of tags for Veh-treated WT mice > mean plus 1.5SD, where no. is number and 1.5SD is the standard deviation multiplied by 1.5. They were defined as repressed genes if the following condition was met: no. of tags for Veh-treated WT mice/no. of tags for T09-treated WT mice > mean plus 1.5SD. T09-regulated genes were considered LXR dependent if following condition was met: [(no. of tags for Veh-treated WT mice/no. of tags for T09-treated WT mice)/(no. of tags for Veh-treated LXRdKO mice/no. of tags for T09-treated LXRdKO mice)] > mean plus 1.5SD.