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Using the reference set G T 1, the performance achieved with ComplOverlap was similar to that observed using the graphic oracle, which used the three extractors.
We annotated all the modules using the reference set named PlantGSEA (23).
We also plot receiver operator characteristic (ROC) and precision-recall curves using the reference set to determine true and false instances.
We labeled drug event associations as negative if there was lack of evidence, which in itself is something that may rapidly change over time; checking of the absence of evidence should always be carried out prior to using the reference set.
Therefore, we first evaluated the distribution of multispecies conservation scores (PhastCons score) [41] and regulatory potentials (RegPotential score) [42] for positions in the functional and non-functional STAT3 TFBSs detected by STAT-Scanner using the reference set of 22 genes (Table S1).
As the choice of threshold for these bootstrap values has a significant influence on the outcomes of subsequent analysis, we compared two previously implemented confidence value thresholds of 50% [30] and 80% [40] using the reference set of 7,208 near full-length 16S rRNA genes from human fecal microbiota sequenced by Dethlefsen and colleagues [14].
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I used the reference set in the Ehum.cut file that is distributed with EMBOSS [33].
In order to use the reference set, the events need to be translated into codes.
Similar results were obtained when we used the reference set from MitoP2 [ 57] as a source of mitochondrial proteins.
Specifically, we used LOCOCV, where one cluster at time was used as the target set while the remaining clusters were used at the reference set.
The remaining reference ligands were used as the reference set.
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