Cluster 0 is enriched for supercoiling-dependent gene regulation. (A) Scoring function for supercoiling-dependent transcription. A total of five tests with two replicates were incorporated into our scoring function. Because genes could be up-regulated or down-regulated in response to supercoiling, we took the better score assuming either of these two cases. Thus, scores could range from 5–10. (B) The 175 genes in the putative osmotic stress response were assayed for their consistency with a supercoiling-dependent profile using the scoring function described in A. The minimum score denotes the lowest score or better that is included in the set of supercoiling-regulated genes. (C) For each minimum score, a hypergeometric test was used to gauge statistical enrichment over all clusters. Only cluster 0 shows statistically significant enrichment.