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To select a conservative set of candidate loci based on this phenomenon, we chose to impose a stringent intersection rule, requiring a threshold of the top 1% of the delta-Rg distribution in both cohorts, in addition to evidence of a strong cis- acting eQTL (genotype effect p < 5 × 10-8) in both cohorts.
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Considering that filtering the gene lists on both statistical significance and reliable signal might be too stringent for all the intersections, we decided to use only the reliable signal as the filter for the intersected gene lists.
There were several statistically significant violations of the more stringent double monotone homogeneity (non-intersection) assumptions, but strong evidence of violation was only seen for a minority of symptoms in certain sites.
It is extraordinarily difficult to sign off on anything other than the most stringent option when presented with the intersection of clear threat and vulnerability.
To achieve stringent filtering, at this stage, the intersection of the results of the 2 metrics (SD and IQR) was preserved, overall reducing the candidate loci list from ~450,000 (485,577) to 76,074.
Clearly, the intersection of a much larger number of cell lines would be too stringent a criterion but we found it appropriate with 7 cell lines.
To investigate robustness of our findings with respect to a less stringent definition of the central proteome, we checked the exon count and network statistics biases either using the intersection of any six cell lines or taking proteins found in 6 out of 7 cell lines.
Only 10 were in the intersection of the binding targets set from low-quality ChIP-chip data and effectual targets set with stringent P-value cutoffs.
In more detail, whereas the insertion did not erase a putative transcription factor binding site according to the analysis tools JASPAR, MatInspector and UniPROBE applied under stringent settings, it created one, three or four novel putative transcription factor binding sites according to the pairwise intersections of the three prediction programs (Fig. 2).
Rationing must be stringent.
Poof! Goodbye, intersection.
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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