DNA fragment sequences of bands from the gel display of 3′-end restriction fragments were clustered by using Locuslink, Unigene, and similarity as described in “Materials and methods.” DNA fragments represent the number of bands on differential display gels from which DNA sequencing was performed.

From 350 genes, we grouped 224 genes whose expression patterns were reproducibly and prominently modified by bacteria (E coli  K12 or Y pestis substrains KIM5 or KIM6) in 2 hours as described in Tables 4, 5, and 6.