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For any two proteins in sweet orange, if their orthologs in the six reference genomes had at least one experimentally verified interaction, the two proteins were predicted to interact.
For some miRNA mRNA pairs, there is more than one verified interaction site.
For this benchmark we do not consider suboptimal duplexes initially, but only whether the first reported hit corresponds to the experimentally verified interaction site.
For any two proteins in M. grisea, an interaction was predicted if their orthologs in five different model organisms have at least one experimentally verified interaction.
A recent report has developed a confidence score for each experimentally verified interaction (Braun et al. 2009), the use of which could potentially mitigate some of these biases.
STRING is a functional association network that contains associations inferred from various data sources (experimentally verified interaction, co-occurences in the literature, coexpression, and similar genomic context).
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The human interactome network was built by combining three previously published datasets consisting mainly of experimentally verified interactions [41].
Here, we pooled experimentally verified interactions between HIV-1 and human proteins, along with a set of HIV-dependency factor proteins (HDF), to investigate the topology of interactions between viral and host proteins on a large scale.
A compilation of experimentally verified interactions between HIV-1 and human proteins and a set of HIV-dependency factors (HDF) allowed insights into the topology and intricate interplay between viral and host proteins on a large scale.
We face a lack of experimentally verified interactions.
Distinction of predicted and experimentally verified interactions is also important.
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