Correspondence of interval and marker pairs with complexes and functions.

†Node definition: For Storey et al. and Full 2D ANOVA, nodes represent genomic intervals. For the synthetic network, nodes represent genes.
‡All cases report the number of distinct interactions in the network, removing redundancies due to marker pairs that associate with multiple traits (Storey et al., Full 2D ANOVA) or gene pairs scoring positive in multiple data sets (Synthetic Genetic Analysis).
*These bi-clustered interval pairs were used to define the “Natural Network” explored in this work.
**We also considered an exhaustive scan of all marker pairs using two-way analysis of variance (ANOVA). The most significant 4,687 marker-marker interactions (Table S7) were taken to match the number of interactions from Storey et al. (Text S1). Both the raw marker-pairs and the bi-clustered interval network identified substantially fewer enrichments than the Storey et al. method.