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The larger the Z-score value between the two genes in the TGN, the more reliable interaction (more similar expression profile) between them.
Alternatively, computational approaches integrate several databases to obtain more reliable interaction data, for example, HitPredict [ 53] integrated the databases of IntAct, BIOGRID and HPRD, collecting 168,458 highly reliable interactions across nine species.
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Frequently, the overlap among different datasets contains more reliable interactions, and this overlap will be obvious to users.
To establish more reliable interactions, we applied a previously proposed referencing strategy in which PPIs are filtered with dynamic gene expression patterns [ 45, 46].
More interestingly, we find that for a data set which had previously [ 28] been classified as consisting of more reliable interactions, the degree distribution appears to be reasonably similar to the degree distribution of the overall network (this can be also quantified statistically [ 5]), especially when compared with the randomly generated subnetwork ensemble.
Note that the higher the weight of an interaction, the more reliable the interaction.
The bigger the score, the more reliable the interaction.
Identifying enriched interactions between any two GO terms based on molecular interactions between genes assigned to these two GO terms are more statistically reliable: interactions reflect statistically enriched temporal connections between multiple genes of one GO term and multiple genes of another.
In addition, automatic initialization is more reliable, avoiding human interaction in the whole process.
For this reason, all interaction data that originated from spoke-expanded cocomplexes and with an IntAct MI-score lower than 0.6 were filtered out (Table S3) in order to produce more reliable protein-protein interaction datasets [ 36].
In this paper, we combined 37 features representing 10 distinct groups of biological data sources based on former studies [ 24, 36, 37], including gene expression, physical interactions, domain interactions, HMS_PCI mass, TAP mass, yeast two-hybrid, genetic interactions, gene ontology (GO) annotations, and gene context analysis, to predict the more reliable protein-protein interactions.
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