Seventy-one percent met math targets, compared with 65percentt citywide.
The impact of slower binding kinetics (reduced rates of association and disassociation) at the membrane-bound target compared with that at the soluble target could also be simulated using the model.
And comparing the 46 common TFs between our results and the results of the ECS method, our results still outperformed the results of the ECS method (43 functionally enriched TF functional binding target gene sets compared with 37 functionally enriched TF functional binding target gene sets, i.e. 93.5% compared with 80.4%).
As for the 18 common TFs between our results and the results of the MA algorithm, our results showed better functional enrichment (18 functionally enriched TF functional binding target gene sets compared with 17 functionally enriched TF functional binding target gene sets, i.e. 100% compared with 95.6%).
Even with the low-quality ChIP-chip data, our method obtained 126 common targets for RAP1 between the binding targets and effectual ones, compared with 144 shared between the binding targets from high-quality ChIP-chip and effectual ones.
However, chromatin immunoprecipitation PCR analyses of Aiolos binding near the transcriptional start site of c-Myc or IRF4 resulted in very few binding events (<4) compared with other target promoters (data not shown).
Specifically, the target genes had different consensus binding sequences, different relative binding site positions compared with the RefSeq region and different associated GO terms.
This is an entirely new binding mode compared with the canonical binding modes found in some transcriptional activators or repressors, in which an intrinsically disordered region (Dyson and Wright, 2002) of each activation or repression domain binds to a target protein with part of the flexible region forming an ordered structure upon binding to the target.
This allowed us to identify a c-Myb binding site (CAGTTA) [ 28] as a signature motif of many newly identified v-ErbA repressed target genes compared with v-ErbA activated target genes.
The total free energy of binding of a microRNA-target pair was compared with the total free energy of binding of that microRNA with randomly shuffled versions of the mRNA 3'UTR sequence.
