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We built the union of these four sets, removing duplicate interactions.
After removing duplicate interactions, we obtained a final data set of 13,030 interactions.
However, duplicate interactions identified via different experimental methods or by different research groups were kept.
After removing duplicate interactions, we retained 11,179 interactions in our dataset (14,283 in the raw data).
When combining interactions data sets, duplicate interactions were removed.
Self-interactions and duplicate interactions were removed previously.
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Two genes, WR1 and WR2 showing duplicate interaction governs the development of aleurone layer colour (wine red / dark wine red/light) with NaOH and KOH in rice plants.
In the following, we will mainly use the duplication subgraph framework, as it gives a simple view of correlations between adjacent duplicated interactions, useful for modeling the process.
For the sampling simulations, we began with a list of all non-duplicate interactions from the combined data set.
The TarBase validated interactions were then added to the filtered list and duplicated interactions were eliminated.
Pairs of UniProt IDs were compared and duplicated interactions were also removed.
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