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Among all bound regions at 1% FDR level, only 45% (Bcd) and 34% (Kr) were predicted to have conserved affinities in Pse (Table 2), and the fraction of conservation for bound sequences at 25% FDR was even lower.
The fraction of conservation of tiny introns between these ciliates therefore appears to be about 1/3.
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Because we trained our SVM to discriminate between regions with a fairly large fraction of conserved sites according to phastCons (>25%) and regions with zero conservation according to phastCons, regions with lower levels of conservation may not be properly classified.
All seed types have a higher fraction of conserved sites than one would expect by chance, given the conservation of their 3′UTRs (Supplementary Table S5).
In contrast, the presence of TF binding sites can explain a modest fraction of the conservation of enhancer activity.
We extracted the 3391 hexamers occurring in these human exons and computed the fraction of exact conservation for these hexamers in the alignments.
The background conservation of a seed type was computed by calculating the fraction of conserved nucleotides of a non-redundant set of UTRs holding a specific seed type.
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.
The conservation rate C is defined as the conservation fraction of each species relative to that for all human phosphosites that were grouped as a motif.
When we employed the GO terms at depths five and six, the conservation fraction of nearly 93%and94%4% of all motif modes respectively was less than 0.1.
This is due to the fact that the majority of motif counts occur for #4 0 and #4 1, with the average conservation fraction of ~0.05.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com