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Incomplete cases in the remaining dataset were removed.
To remove any bias during benchmarking, the ligands found in the Vernalis dataset were removed from the PDB ligand library.
To construct a phylogenetic tree in MEGA4 [26], nifH sequences were first clustered at 92% similarity (complete linkage clustering) and clusters with <10 sequences (together representing 0.9% of the dataset) were removed for clarity.
Genes with missing value in >30% of the samples in a dataset were removed.
ii) Genera-excluded database, in which sequences with the same genus as query dataset were removed.
Gene expressions for non-protein coding genes in the immunome protein dataset were removed.
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E.g., some of the originally 15,000 decoys for each MUV dataset are removed.
Once this series of dedicated correction are made, the lithospheric field model from SH degree 16 to 45 that was first subtracted is added back and the measurements temporarily selected above magnetic latitude |±52°| in the mid-latitude dataset and below magnetic latitude |±52°| in the polar dataset are removed.
If the apparent outlier in the 2002 evenness contrast dataset is removed, the relationship between 2002 evenness and disease becomes stronger, more negative, and more similar to the 1998 analysis (r61 = −0.268, P = 0.035).
The gene, UBC, which has >5000 interactions in this dataset was removed from the analysis.
Redundancy of unique parent ions in the entire dataset was removed and the number of the unique parent ions per protein was counted.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com