Pleiotropy matrices for eGenes and eQTLs

The Phenotype eQTL overlap sheet has names of phenotypes in columns TraitX and TraitY. The number of eQTLs identified for TraitX and TraitY are given in eQTLsX and eQTLsY. The column, Common, is the number of eQTLsY that are in eQTLsX. Ratio is Common divided by eQTLsX.<br>The Phenotype eGene overlap sheet has names of phenotypes in columns TraitX and TraitY. The number of eQTLs identified for TraitX and TraitY are given in eGenesX and eGenesY. The column, Common, is the number of eGenesY that are in eGenesX. Ratio is Common divided by eGenesX.<br>In the Control eGene overlap sheet, all 7,917 eGenes were pooled together and randomly assigned to phenotypes so that each phenotype in the control matrix had the same number of eGenes as its corresponding phenotype in the eGene matrix. The pairwise ratios of common eGenes among the phenotypes were calculated as done in the eGene matrix. 1000 different null datasets were constructed in this manner and the mean matrix was calculated. The Ratio column is the mean of 1000 null sets between phenotypes in columns TraitX and TraitY.