To make sure that crosshybridization from overlapping transcripts does not account for the increased correlation we observed between adjacent pairs of genes, most of the experiments in the paper were repeated excluding the most closely packed adjacent pairs (the ones most likely to have overlapping transcripts). We excluded divergent pairs with intergenic regions smaller than 50 bp, and tandem and convergent pairs separated by less than 200 bp. These cutoffs were picked based on the distribution of 3’ UTR lengths derived from Expressed Sequence Tags (ESTs) from yeast. Approximately 84% of 3’ UTRs should be less than 200 bp long. The results from the figures in the paper are compared with and without these cutoffs.
