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For some examples of the topics that are covered by our method, see Stijepic (2016).
The cooperativity between Mbp1 and Swi4 is successfully captured by our method (see Figure 7).
The cooperativity between Stb1 and Swi6 (a member of MBF) is successfully identified by our method (see Figure 7).
Out of these, only RAIDD is not present in the genes selected by our method (see Fig. 7 and Supplementary Material for the list of genes).
There are 13 modules that significantly overlap with the cluster method, while the others represent distinct discoveries by our method (see Supplementary Table S4).
As a result, there were 72 TFs suitable for our analysis and a total of 7259 functional TF-gene binding pairs were established by our method (See Additional File 2).
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We found that BAUs can be found in CCDs as extracted by our octahedron method (See Lots et al. 2013, for a further analysis of this method).
When we examined the profile of the centroid of a cluster identified by our method, we saw a lower amplitude deletion on the p arm as well.
For each PFM the binding affinity, 〈 N〉, between the corresponding TF and a given DNA sequence is computed by our previously published TRAP method (see Supplementary Material for details).
Analysed by appropriate method (see Methods) and adjusted for age and education.
We introduced RSF1010 and RSFmob to P. ananatis SC17 strain by electroporation method (see Methods).
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