We used GeneNetwork's database of phenotypes to identify associations between paracliques and physiological or behavioral traits previously assayed with the BXD population. This analysis was conducted by calculating correlations between GeneNetwork phenotypes and ‘synthetic traits’ used to represent the expression variation of paraclique trans-bands. These synthetic traits were generated by principal component analysis of centered and scaled probe-set expression values. The principal component (PC) trait accounting for the largest proportion of expression variance was used as a single synthetic PC-trait representing the corresponding paraclique trans-band. For each PC-trait, sample order was permuted 1,000 times and correlated with the BXD phenotype database. The permuted correlation distributions were then used to adjust each observed phenotype/PC-trait correlation's p-value.
