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For instance, all the known SL pairs present in the GIM data matrix could be detected already at 50% FPR, when adjusting the QMA-parameters to the shared properties of the three negative interactions categories (Figure S2).
In our target list we kept high-confidence miRNA-target gene interactions (categories 0, 1, 2) and only category 3 targets as low confidence miRNA-target pairs.
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The results showed that part-time farmers had better "animal social interactions" category scores than full-time farmers, which may be due to better weaning and calving scores.
The combined average recall for all methods was more than one-third lower in the protein protein interactions category than in the sequence cluster category (the respective recalls were 0.29 and 0.75).
The relatively large family of eukaryotic-like serine/threonine kinase genes (predominant in the "regulatory functions-protein interactions" category), were not significantly represented (23/106, p = 0.9) in the regulated genes (Additional file 2).
Signal responsive "one component" transcriptional regulators [ 65], mainly lying in the "regulatory functions-DNA interactions" category, were significantly under-represented in the regulated genes (14/160; p = 4 × 10-5) (Additional file 2).
Interaction categories were defined by established criteria.
Interaction categories varied greatly among aztreonam with β-lactam combinations.
It became soon evident that any single scoring function could not provide optimal scoring capability for all the interaction datasets and interaction categories considered.
As the ground truth for the genetic interaction pairs, we used the four different genetic interaction categories as available from the BioGRID database, version 2.0.51 [54].
Similar to the SGA dataset, data preprocessing did not improve the detection accuracy of any of the interaction categories in the GIM dataset.
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