Similar softwares
whole genome data
- Procedure:
Identification of motifs for global transcription factors at genome scale: We also tested the prediction performance of the six programs on their prediction of cis motifs of the global transcription factors in E. coli K12. Among all known E. coli K12 regulons in RegulonDB, we consider those containing more than 25 operons as the global regulons (comparing with local regulons), totaling 10 such regulons, namely CRP, Fur, FNR, IHF, Fis, Lrp, CpxR, ArcA, NarL and H-NS. To carry out this prediction, we first extracted 2,390 promoter sequences of E. coli K12 based on the predicted operons. We run BOBRO on these sequences to find significant motif groups, and compared the overlaps between our prediction and the known regulons. The results shows that BOBRO found motif groups for 8 out of 10 global regulons and did not find the motifs of NarL and H-NS. Figure 3 summarizes the key results in terms of the level of overlap between our predicted motifs and known motifs of these 8 regulons. - Results: (Figure 3)
Figure 3: Comparisons between documented and predicted cis motifs for the 8 TFs. Each blue bar represents the total number of documented motifs of the corresponding regulon, and the red bar represents the correctly predicted motifs for the corresponding regulon.
Page last updated: Apr. 29, 2010