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The output of our method is a set of spatiotemporal localization tubes with an assigned interaction label.
The latter, however, are special in that around 80% of their predicted encoded proteins have at least one assigned interaction (this percentage can be seen as an approximation of the 'coverage' of the network), which is the highest value among all datasets studied; this may explain differences between these two networks and other Y2H datasets.
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In our confirmatory HTS BioAssay datasets extracted from the PubChem BioAssay Database [38], we have positive and negative assigned interactions.
Finally, because incentives for academic performance were not randomly assigned, interactions with trial arms should be interpreted cautiously.
One of the major problems addressed in this work is to assign interaction partners also to these orphan proteins.
HitPredict uses HUPO PSI-MI defined controlled vocabulary to assign interaction type and experimental method descriptions (14).
Gene expression analysis represents the only current technique that takes into account dynamic behavior to assign interaction and function.
Given the high degree of conservation in this protein sub-family, the data suggests that tissue-specificity may be relevant to assign interaction with membrane targets and not to determine rates of vesicle fusion.
For example, the Babelomics suite, of which Blast2GO is part, contains tools for assigning interactions, pathways or even regulatory annotations to analysed sequences.
Quite simply, if two and only two genes are described in a single article indexed in PubMed [ 22], then one assumes an interaction; weights are assigned to interactions based on the relative number of articles mentioning those genes together.
Therefore, we consider functional annotations of interactions, rather than genes, where the set of functional terms assigned to interaction ij is defined as (5) F ij = F i ∩ F j or the set of common terms of its interacting genes.
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