Effects of the number of aligned mammalian species on the TFBS detection accuracy

<p><b>Copyright information:</b></p><p>Taken from "Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools"</p><p>http://genomebiology.com/2007/8/10/R225</p><p>Genome Biology 2007;8(10):R225-R225.</p><p>Published online 24 Oct 2007</p><p>PMCID:PMC2246299.</p><p></p> Each panel shows the performance of a tool in aligning a different number of species. Human and baboon were used for the two species alignment, mouse was added for the three species alignment, and all five species but cow were used for four species alignment. While all tools have almost the same performance for aligning the two closely related species human and baboon, MUSCLE and DIALIGN performed better than other tools in maintaining or improving performance when adding more species to the alignment

Detection accuracy of individual TFBSs on five-way mammalian alignments

<p><b>Copyright information:</b></p><p>Taken from "Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools"</p><p>http://genomebiology.com/2007/8/10/R225</p><p>Genome Biology 2007;8(10):R225-R225.</p><p>Published online 24 Oct 2007</p><p>PMCID:PMC2246299.</p><p></p> All five tools perform better at detecting YY1E2F and Pax6, which have low RTRs and short restricted distance for translocation, than IRF2 and ROAZ, which have high RTR and long restricted distance for translocation. MUSCLE shows an overall better performance than the other four tools. MLAGAN performs better than DIALIGN on YY1E2F, PAX6, PPARG and ROZA, while DIALIGN shows a better performance than MLAGAN on TP53 and PPARG, which have a long restricted distance for translocation but a relatively low RTR

The average TFBS sensitivity of five tools in aligning TFBS in five mammalian species

<p><b>Copyright information:</b></p><p>Taken from "Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools"</p><p>http://genomebiology.com/2007/8/10/R225</p><p>Genome Biology 2007;8(10):R225-R225.</p><p>Published online 24 Oct 2007</p><p>PMCID:PMC2246299.</p><p></p> The average TFBS sensitivity of all functional TFBSs. The average TFBS sensitivity with the subset of non-turnover sites among all TFBSs. The relative order of TFBS sensitivity for the five tools is almost the same as the order of their TFBS detection accuracy (Figure 10d)

An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer-0

<p><b>Copyright information:</b></p><p>Taken from "An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer"</p><p>http://www.biomedcentral.com/1471-2164/9/S1/S12</p><p>BMC Genomics 2008;9(Suppl 1):S12-S12.</p><p>Published online 20 Mar 2008</p><p>PMCID:PMC2386054.</p><p></p