Figure 1.

DNA topological stress-responsive genes are clustered non-randomly. (A) Schematic representation of cluster definition. Contiguous genes with similar (positive or negative) GRO values were joined in gene clusters, which were defined as the genomic region spanning the chromosomal space from the farthest upstream to the farthest downstream gene boundary. (B) Location of genes and clusters with GRO values in part of chromosome IV. (C) Distribution of number of genes in clusters. Real clusters show a skewed distribution toward larger sizes as compared to the mean of 10 000 random permutation of GRO values. Differences are significant for gene numbers ≥ 6. (D) Mean adjusted correlation scores (ACS) for up- and downregulated gene clusters are significantly higher than the genomic average (randomly selected clusters of equal size and number), indicating increased co-regulation within the confines of the defined clusters.