We clustered microarray data contained in the TB database [75] and searched for upstream regulatory motifs shared in the upstream regions of the resulting clusters using AlignACE (Methods). Because of significant noise in the results, we used a set of stringent filters, including a requirement that candidate motifs be highly conserved. 37 motif instances passed our stringent filters ( Table 7 , Methods). 14 of the top 37 (38%) motif instances correspond to cases of known Mtb motifs (several known Mtb motifs were found more than once, in different clusters, or in clusters with different size parameters). In contrast, none of the top motifs showed similarity only to known E. coli or Corynebacteria motifs. Within these top motifs, we were able to identify four of the nine known Mtb motifs (DosR, IdeR, KstR, and ZurB).