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In the third filtering step the FDR cutoff was set as a threshold of 0.001.
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In the third filter, the 229 candidate HGT genes in B. mori were submitted to a BLASTp search against nr database, producing two categories of results.
Since alignments can be ranked, correct assignments will be saved as unique alignments in the first filtering step (Figure S1).
In the first filtering step, probes with low expression were considered to be background probes and thus filtered out.
In detail, in the first filtering step for every probe set of 9 microarrays at each ANOVA at least 3 microarrays called the probe set as "present".
The standard DEG method was used to select candidates that explains the phenotypic differences between KO and WT in the first filtering step.
In the first filtering step, we conducted an epigenome-wide association study (EWAS) to identify CpGs differentially methylated by EOC case/control status.
These are functionally highly conserved elements shared by all tRNA sequences and most of these were used in the first filtering step.
Third, the fact that we selected individuals with the E200K mutation in the first filtering strategy might influence the analysis with respect to prion disease onset or incubation period.
By pruning the search space with constraints, it is more likely that correct models will be retained in the first filtering stage without requiring a very large set of candidate models.
In the second filtering step for every probe set at each comparison, i.e. #25 vs. #26, #25 vs. #27, and #26 vs. #27, the fold change is at least 1.5 fold.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com