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The genes that were not included in these datasets were removed from the gene set for the given pathway.
Additionally, redundant probe sets representing genes found to overlap between datasets were removed from the Se toxicity set.
Furthermore, redundant patients present in KJX64/KJ125 and Uppsala datasets were removed from the validation tests so they were only considered once.
Redundant patients (74 samples) present in KJX64/KJ125 and Uppsala datasets were removed from the validation tests so they were only considered once.
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This has resulted in a significant policy change, with some existing datasets being removed from the internet.
To remove any bias during benchmarking, the ligands found in the Vernalis dataset were removed from the PDB ligand library.
Proteins presented in the training dataset were removed from this testing dataset.
Genes whose function was predicted only [R] or unknown [S], representing about 19% of the all dataset were removed from further analyses.
This and the previously described dataset were made non-redundant as genes included in Group 1 dataset were removed from this dataset (Group 4 = Vogel et al dataset - Group 1, n = 503).
Further, the elements (attributes) that do not appear in the cleaned dataset are removed from the input attribute set.
The gene, UBC, which has >5000 interactions in this dataset was removed from the analysis.
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