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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 degrees of enrichment against all non-specific disease-related controls were similar in each Consistency Tier and remained within a margin of experiment error.
The highest ranking probes in GSE5281 and GSE15222 were assigned to a Consistency Tier 3, if the functionally related molecules (members of the same pathway) were also displaying high PCS.
The molecules populating Consistency Tier 1 that was optimal in terms of balance between functional enrichment and recall rate of the most relevant mechanistic participant entries were analyzed using Ingenuity Pathway Assistant (IPA) tool.
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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.
Vesicle formation related functionalities displayed the highest enrichment coefficients among all consistency tiers and were accompanied by the lowest p-values and FDRs.
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.
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.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com