Extraction of differentially expressed genes.

<p>Filtering on a volcano plot of the microarray data analysis of the Experiment 1 (top) and Experiment 2 (bottom). In Experiment 1, we selected the gonadal adipose tissue from male mice from congenic strain 4 with the donor region captured QTL1, QTL2, and QTL3 (42.6 to 58.3 Mb). Half of the mice were heterozygous for the donor region (129/B6; N = 7), and half were littermates homozygous for the donor region (B6/B6; N = 7). Experiment 2 replicated Experiment 1 except with N = 6 mice in each genotype group, for a total of 12 mice. The customized volcano plots depict the estimated log₂-fold change (x-axis) and statistical significance (−log₁₀ p-value; y-axis). Each dot represents one gene. The green dots show genes with absolute log₂-fold change > 0.58 (i.e., 1.5-fold change) and false discovery rate < 0.05; the red dots show genes with false discovery rate < 0.05; the yellow dots show genes with absolute log₂-fold change > 0.58; the black dots show genes that did not reach these statistical thresholds. We label genes that passed any filters by name. Twenty differentially expressed genes are reproducible between Experiment 1 and 2, labeled with blue text and square boxes. Red stars show two genes that passed the filters in one but not both experiments yet are noteworthy because their human orthologues are associated with adiposity or body mass index in genome-wide association studies (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0188972#pone.0188972.t002" target="_blank">Table 2</a>). We summarize the additional experimental details in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0188972#pone.0188972.s012" target="_blank">S12 Table</a>.