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In fact many gene interactions from these two profiles are significant for these pathways.
For example, the complex of cytoplasmic ribosomal large subunit have three connected subnetworks derived from the reliable GIN, demonstrating that many gene interactions in the reliable GIN are consistent with domain knowledge from protein complexes.
This observation suggests that, while a significant number of dysregulated interactions stem from physical interactions, the nature of many gene interactions may be indirect and mediated by other genes, or their interactions are not discovered by current experiments due to the overall low coverage of the interactome in HPRD.
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Even though the percentile cutoffs result in an equal number of positive and negative interactions being considered, we noticed that many genes interact predominantly through negative interactions or predominantly through positive interactions (Additional File 3).
What is most interesting is that the time-evolving networks provide timelines for many other gene interactions that have not yet been verified experimentally.
Finally, one group has shown that main effects at variants involved in an epistatic interaction are highly dependent on the allele frequency in different populations at each locus, which may explain the lack of replication of many gene-gene interaction studies which rely on main effects [ 87].
In expression data, many gene groups interact closely and gene interactions are important biologically and may contribute to class distinctions.
Corrected Page 3 and 4 – in the "Types of interactions" section, all sub-sections should include the number of interactions e.g. how many gene-tissue interactions are there?
Page 3 and 4 – in the "Types of interactions" section, all sub-sections should include the number of interactions e.g. how many gene-tissue interactions are there?
Functional validation and establishment of real causation is still the bottleneck of many gene-microbe interactions.
However, some think that this requirement may be too stringent, because many genes and interactions are expected to play a role in a complex disorder such as alcoholism.
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