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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).
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The gene, UBC, which has >5000 interactions in this dataset was removed from the analysis.
We avoid duplicate counting of evidences across the datasets by using their publication IDs (in particular, PPIs from the Consolidated dataset are removed from the BioGRID, IntAct, and MINT datasets).
All but two of the overrepresented biological process terms (skeletal muscle adaptation (GO 0043501) and maintenance of fidelity involved in DNA-dependent DNA replication (GO 0045005)) remained significant when titin (the largest gene in the dataset) was removed from the analysis.
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.
Redundant patients (74 samples) present in KJX64/KJ125 and Uppsala datasets were removed from the validation tests so they were only considered once.
Furthermore, redundant patients present in KJX64/KJ125 and Uppsala datasets were removed from the validation tests so they were only considered once.
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CEO of Professional Science Editing for Scientists @ prosciediting.com