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Vesicle formation related functionalities displayed the highest enrichment coefficients among all consistency tiers and were accompanied by the lowest p-values and FDRs.
In that, we implemented sorting out the gene lists into the Consistency Tiers, thus, gaining control of the extent of information loss in the non-overlapping sub-sets.
The statements like [(disease or disorder or pathology)] crossed with the corresponding Boolean representations of the consistency tiers would locate the literature publications associating the genes of interest with any disease, non-specific to the study.
The query statements like [cancer] crossed with the corresponding Boolean representations of the consistency tiers would locate the literature publications associating the genes of interest with cancer as another proxy for a non-specific multiple roles played by many signaling molecules.
In all Consistency Tiers, the fold differences of differential expression effects were relatively small, rarely exceeding 3-fold.
To rule this scenario out, variations were measured among all Consistency Tiers and were compared to variations observed in Random Control genes both globally and in the subsets selected by matching of their expression intensities.
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Variation in the datasets was taken into account by dividing each consistency tier list into subsets and repeating the procedure independently for each subset, pooling the variation and distributing it equally per each subset (within each consistency tier).
Low literature tag enrichment in consistency Tier 3 and in all tiers below Tier 3 questions the meaningfulness of the data not pre-cleaned by triple filtration of CDM or similar knowledge-based techniques.
In some form, the down-regulation bias was traced among ~200 members of the Tiers 0 2 and ~1300 members of consistency Tier 3 and PCS groups.
The input candidate gene lists were processed into different tiers of evidence consistency established by enrichment analysis across subsets of the same experiments and across different experiments and platforms.
The tiers in FSSIM consist of presentation tiers, a data tier, an application tier and domain tier.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com