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Here we test for the robustness of the baseline results when reducing or increasing the occurrence of reform shocks, i.e. by raising the stringency criterion used to identify them to 2.5 standard deviations or reducing it to 1.5 standard deviations.
Another stringency criterion was that each read had to map with no mismatches.
Although HIC1 and ZNF189 did not fully satisfy our stringency criterion for replication, they were strongly associated with iCP in TRIMM analyses of the Norwegian triads.
Unlike FLNB, HIC1 and ZNF189 did not fully meet our stringency criterion for replication, despite being the top two genes associated with iCP in TRIMM analyses of the Norwegian triads.
The genes for hypermethylated in cancer 1 (HIC1) and zinc finger protein 189 (ZNF189) did not fully meet our stringency criterion for replication (both methods detecting associations in both populations).
LOF of two genes, MNNK1 and HIPK2, only replicated when a more-relaxed stringency (criterion 2) was used.
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We stress that respecting at least three stringency criteria will help to ensure the scientific quality of data interpretation of comparative studies: similar soil fertility status at start, comparable type of crop production, and quantification of off-farm organic and nutrient input.
When gene expression is compared in Xu and Picciotto P4 LGN, 15 genes display significantly altered expression by the chosen stringency criteria (Figure 1A).
Exclusive of the Chrnb2 index gene, 32 transcripts are downregulated in mutant P4 LGNs using the selected stringency criteria (Figure 3A Table S2).
The reason for the low number of SCNA affected genes and corresponding pathways in the latter case may be the high stringency criteria employed in their analysis [13].
Moreover, precise inference is more difficult due to incomplete annotation, along with different stringency criteria, customary thresholds to classify true and erroneous AS events, and various gene models used in different species.
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CEO of Professional Science Editing for Scientists @ prosciediting.com