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The sodium cations in the binding site were validated with the CheckMyMetal: Metal Binding Site Validation Server.
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Paupar occupancy at nine candidate binding sites was validated using CHART-qPCR in two further independent experiments (Supplementary Fig S4).
The protein binding activity at this site was validated but was not dependent on nitrate in the media [ 64].
The binding of SOX9 at this site was validated by EMSA and ChIP-qPCR.
Also shown are the number and percentage of binding sites that were validated in an independent ChIP experiment.
Such binding sites were subsequently validated in detailed docking studies with known DAT ligands (56).
The putative binding sites were then further validated using JASPAR and ChampionChIP databases [22], and carefully selected for ChIP-qPCR analyses.
As none of these binding sites was experimentally validated, some of them might be false positive.
These binding sites are experimentally validated and documented in the RegulonDB database [ 20].
COX-2 3´UTR luciferase reporters containing two putative miR-199a binding sites were constructed to validate the direct binding between COX-2 mRNA 3´UTR and miR-199a.
Interestingly, several up-regulated target genes (PTHLH, DKK1 and CFLAR), predicted to have a P53 binding site, have been validated experimentally by others, indicating that our prediction approach is correct for these three genes [ 27- 29].
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