These stringency criteria for parsing BLAST output are default parameters, but users have the option to specify alternative criteria.
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.
By lowering the stringency criteria to 1.5-fold change in two or more consecutive time-points, we detected some potentially differentially expressed genes in either endoneurium or DRG of diabetic mice.
We have attempted to alleviate this risk by using high stringency criteria for identification of candidate miRNAs from our aCGH data and subsequently using published NSCLC cohorts with copy number and miRNA expression data to independently validate these candidates.
The complete set of confirmed, high confidence, and potential novel miRNA candidates, as well as the rest of the candidates out of the original list of 132 putative novel miRNAs that failed our additional stringency criteria, are provided as Supporting Data File S1.
We demonstrated how various stringency criteria could be deployed to check data robustness.
