Relationship between 2-isoproplymalate and genes linked to eQTL hot spot 1 on Chromosome III.

<p>(A) 2-isopropylmalate is an intermediate metabolite in the leucine biosynthesis pathway and <i>LEU2</i> is a key enzyme in this pathway; (B) 2-isopropylmalate concentrations are linked to the <i>LEU2</i> locus and is reactive to <i>LEU2</i> expression; (C) 2-isopropylmalate is reactive to <i>LEU2</i> and causal for genes with Leu3p binding sites (red nodes); (D) a zoomed-in view of the subnetwork highlighted in (C) (around 2-isopropylmalate). Hexagon-shaped nodes represent metabolites, circular nodes represent genes, and diamond-shaped nodes represent genes with cis-eQTLs.</p

Genes and metabolites linked to eQTL hot spot 3 on Chromosome XIII.

<p>(A) Variations of the metabolites isoleucine and threonine are linked to this locus. (B) These two subnetworks comprise genes and metabolites enriched for linking to the Chromosome XIII locus. The larger network consists of both gene expression and metabolite nodes enriched for the GO biological process nitrogen compound metabolism. The smaller network is enriched for the GO biological process de novo IMP biosynthetic process. Red nodes are genes with eQTLs linked to the Chromosome 13 locus. (C) Expression levels of eight genes (in red) are different between <i>VPS9</i> knockout and the wild-type strains. The shapes of the nodes follow the convention described in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001301#pbio-1001301-g003" target="_blank">Figure 3</a>.</p

Distributions of metabolite concentrations between parental strains and among 120 segregants of a cross between laboratory (BY) and wild (RM) strains of <i>S. cerevisiae</i>[11].

<p>The <i>y</i>-axis is metabolite concentrations (nanomoles per yeast cell). The genotypes for segregants are reported at the loci to which the metabolite concentrations were linked. Represented are the metabolites (A) 2-isopropylmalate; (B) orotic acid; (C) SAH; and (D) threonine.</p

Relationship between metabolites and genes linked to eQTL hot spot 2 on Chromosome V.

<p>(A) De novo biosynthesis of pyrimidine pathway; (B) orotic acid and dihydroorotic acid concentrations are linked to the <i>URA3</i> locus; (C) <i>URA3</i> is predicted as the causal regulator for genes and metabolites linked to the eQTL hot spot. Red nodes are genes or metabolites whose variations are linked the Chromosome V locus. The shapes of the nodes follow the convention described in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001301#pbio-1001301-g003" target="_blank">Figure 3</a>.</p

Overview of the experimental design.

<p>A cross between laboratory (BY) and wild (RM) strains of <i>S. cerevisiae </i><a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001301#pbio.1001301-Brem1" target="_blank">[11]</a> was gene expression profiled. Metabolites were profiled under the same conditions. These data were then integrated with genotype data along with information from public databases to derive a BN. The derived network was used to analyze how cells are regulated.</p

Genes and metabolites linked to eQTL hot spot 4 on Chromosome XV.

<p>(A) Variations in the metabolites glycerol and (B) trehalose are linked to this eQTL hot spot. (C) The part of the subnetwork associated with this eQTL hot spot consists of the causal regulator <i>PHM7</i> at the top, key TFs MSN4 and MSN2 (represented by <i>CTT1</i>), and the genes that encode for the trehalose synthesase complex. Red nodes are genes or metabolites with QTL linked to the Chromosome XV locus.</p

Metabolite concentrations that are under significant genetic control in the BXR cross (LOD score>3.9 corresponds to FDR 0.05), where the metabolite QTL are coincident with eQTL hot spots.

a<p>Of the metabolites listed, 11 are significantly different between the BXR parental strains as well.</p

The <i>PHM7</i> knockout metabolite signature suggests interconnectivity of multiple eQTL hot spots.

<p>(A) The metabolite subnetwork is the same as the subnetwork depicted in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001301#pbio-1001301-g006" target="_blank">Figure 6A</a>. 27 metabolites (in red) whose concentrations differ between the <i>PHM7</i> knockout and the wild-type strains are in this subnetwork. In addition to trehalose, which is linked to the eQTL hot spot 4, the <i>PHM7</i> knockout metabolite signature includes metabolites whose concentrations are linked to eQTL hot spots 1 and 3 (on Chromosomes III and XIII, respectively), suggesting interactions among eQTL hot spots 1, 3 and 4, as we have previously predicted <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001301#pbio.1001301-Zhang2" target="_blank">[44]</a>. (B) The subnetworks for eQTL hot spot 4 (extracted using genes linked to eQTL hot spot 4) suggests that part of this network is regulated by both eQTL hot spots 2 and 4. Red nodes are genes whose expression values are linked to eQTL hot spot 2. (C) A zoomed-in view of the part of the network regulated by eQTL hot spots 2 and 4. The gene that links this part of the network to the rest of the subnetwork associated with eQTL hot spot 4 is <i>GCN4</i>, a master TF regulating amino acid biosynthesis.</p

Metabolite subnetwork.

<p>(A) Variations in valine concentrations are linked to two eQTL hot spots; Chromosome III:100,000 and Chromosome XIII:70,000. (B) Most metabolites are connected. Valine connects to metabolites linked to eQTL hot spots at Chromosome III:100,000 (nodes in blue) and Chromosome XIII:70,000 (nodes in green). (C) 25 metabolites (in red) whose concentrations are different between <i>VPS9</i> knockout and the wild-type strains are in this subnetwork. This structure suggests that <i>VPS9</i> is causal for the variations of these metabolites. The shapes of the nodes follow the convention described in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001301#pbio-1001301-g003" target="_blank">Figure 3</a>.</p