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We were unable to detect any other strongly over-represented binding motifs in the Otx2-bound regions that lacked Oct4 binding, suggesting that this is the most common combinatorial binding mode used by Otx2.
Motif search using Scansite software revealed the presence 14-3-3 14-3-3 14-3-3, Mode 1 in NFκbindingtenin and Bcl-2 proteins.
Then we use empirical P -value to evaluate the statistical significance of enrichment/depletion of each kind of evolutionary motif mode in the real network [ 68, 69].
Noteworthy too is that the motif count for each motif mode can vary considerably among a million motif modes.
Here a "motif mode" is defined as a special combination of GO terms in a motif.
Equally important, for all motif modes, we have found a power-law distribution of the motif counts on each motif mode.
The second is the distribution that characterizes the dependence of the number of motif modes on the conservation ratio of that motif mode.
The "conservation ratio" of a motif topology or a motif mode is the ratio of the conservation fraction over the "random conservation fraction" of topology or mode, respectively.
We calculated the distribution of the motif count for each motif mode based on the logarithmic binning.
